From b18212163e0fd9ff56da13ef258005b7d0decced Mon Sep 17 00:00:00 2001 From: jlerbsc Date: Thu, 18 Apr 2024 09:26:14 +0200 Subject: [PATCH] Fix sonar issue S2293 Replace the type specification in this constructor call with the diamond operator ('<>') --- .../nbio/aaproperties/CommandPrompt.java | 12 ++-- .../nbio/aaproperties/Constraints.java | 14 ++-- .../nbio/aaproperties/PeptideProperties.java | 4 +- .../aaproperties/PeptidePropertiesImpl.java | 6 +- .../org/biojava/nbio/aaproperties/Utils.java | 2 +- .../profeat/ProfeatPropertiesImpl.java | 14 ++-- .../xml/AminoAcidCompositionTable.java | 2 +- .../xml/CaseFreeAminoAcidCompoundSet.java | 16 ++--- .../nbio/aaproperties/xml/Element.java | 2 +- .../nbio/aaproperties/xml/ElementTable.java | 4 +- .../xml/ModifiedAminoAcidCompoundSet.java | 4 +- .../src/main/java/demo/CookbookMSA.java | 2 +- .../src/main/java/demo/DemoDistanceTree.java | 4 +- .../biojava/nbio/alignment/Alignments.java | 36 +++++----- .../org/biojava/nbio/alignment/GuideTree.java | 6 +- .../SimpleProfileProfileAligner.java | 2 +- .../biojava/nbio/alignment/SmithWaterman.java | 2 +- .../alignment/io/StockholmFileAnnotation.java | 8 +-- .../alignment/io/StockholmFileParser.java | 2 +- .../io/StockholmSequenceAnnotation.java | 2 +- .../nbio/alignment/io/StockholmStructure.java | 8 +-- .../alignment/routines/AlignerHelper.java | 2 +- .../AnchoredPairwiseSequenceAligner.java | 4 +- .../template/AbstractMatrixAligner.java | 4 +- .../biojava/nbio/phylo/ForesterWrapper.java | 2 +- .../java/demo/DemoSixFrameTranslation.java | 2 +- .../main/java/demo/ParseFastaFileDemo.java | 2 +- .../core/alignment/SimpleAlignedSequence.java | 4 +- .../nbio/core/alignment/SimpleProfile.java | 28 ++++---- .../alignment/matrices/AAIndexFileParser.java | 6 +- .../matrices/ScaledSubstitutionMatrix.java | 4 +- .../matrices/SimpleSubstitutionMatrix.java | 12 ++-- .../matrices/SubstitutionMatrixHelper.java | 4 +- .../org/biojava/nbio/core/search/io/Hsp.java | 4 +- .../biojava/nbio/core/search/io/SearchIO.java | 2 +- .../search/io/blast/BlastTabularParser.java | 10 +-- .../core/search/io/blast/BlastXMLParser.java | 12 ++-- .../core/sequence/ChromosomeSequence.java | 2 +- .../nbio/core/sequence/DNASequence.java | 4 +- .../nbio/core/sequence/GeneSequence.java | 10 +-- .../sequence/MultipleSequenceAlignment.java | 4 +- .../nbio/core/sequence/ProteinSequence.java | 2 +- .../core/sequence/TranscriptSequence.java | 6 +- .../compound/AminoAcidCompoundSet.java | 16 ++--- .../nbio/core/sequence/edits/Edit.java | 8 +-- .../sequence/features/AbstractFeature.java | 6 +- .../sequence/features/DBReferenceInfo.java | 2 +- .../features/FeatureDbReferenceInfo.java | 8 +-- .../sequence/features/QualityFeature.java | 2 +- .../sequence/features/QuantityFeature.java | 2 +- .../CasePreservingProteinSequenceCreator.java | 4 +- .../core/sequence/io/DNASequenceCreator.java | 2 +- .../nbio/core/sequence/io/FastaReader.java | 2 +- .../core/sequence/io/FastaReaderHelper.java | 10 +-- .../core/sequence/io/FastaWriterHelper.java | 8 +-- .../io/FileProxyDNASequenceCreator.java | 2 +- .../io/FileProxyProteinSequenceCreator.java | 2 +- .../io/FileProxyRNASequenceCreator.java | 2 +- .../core/sequence/io/GenbankReaderHelper.java | 12 ++-- .../core/sequence/io/GenbankWriterHelper.java | 14 ++-- .../sequence/io/GenericFastaHeaderParser.java | 2 +- .../sequence/io/GenericInsdcHeaderFormat.java | 12 ++-- .../nbio/core/sequence/io/IUPACParser.java | 12 ++-- .../sequence/io/ProteinSequenceCreator.java | 2 +- .../core/sequence/io/RNASequenceCreator.java | 2 +- .../nbio/core/sequence/io/util/IOUtils.java | 2 +- .../loader/GenbankProxySequenceReader.java | 2 +- .../loader/SequenceFileProxyLoader.java | 6 +- .../loader/StringProxySequenceReader.java | 6 +- .../loader/UniprotProxySequenceReader.java | 22 +++---- .../core/sequence/location/InsdcParser.java | 4 +- .../sequence/location/LocationHelper.java | 4 +- .../location/template/AbstractLocation.java | 16 ++--- .../sequence/location/template/Location.java | 2 +- .../storage/ArrayListSequenceReader.java | 6 +- .../storage/FourBitSequenceReader.java | 10 +-- .../storage/JoiningSequenceReader.java | 2 +- .../storage/SingleCompoundSequenceReader.java | 4 +- .../storage/TwoBitSequenceReader.java | 2 +- .../template/AbstractCompoundSet.java | 10 +-- .../template/AbstractCompoundTranslator.java | 12 ++-- .../AbstractNucleotideCompoundSet.java | 8 +-- .../sequence/template/AbstractSequence.java | 22 +++---- .../core/sequence/template/SequenceMixin.java | 22 +++---- .../sequence/template/SequenceProxyView.java | 4 +- .../transcription/DNAToRNATranslator.java | 2 +- .../core/sequence/transcription/Frame.java | 2 +- .../RNAToAminoAcidTranslator.java | 8 +-- .../transcription/TranscriptionEngine.java | 2 +- .../core/sequence/views/RnaSequenceView.java | 4 +- .../biojava/nbio/core/util/FlatFileCache.java | 2 +- .../nbio/core/util/PrettyXMLWriter.java | 8 +-- .../core/util/SingleLinkageClusterer.java | 10 +-- .../biojava/nbio/core/util/SoftHashMap.java | 6 +- .../org/biojava/nbio/core/util/XMLHelper.java | 2 +- .../nbio/genome/GeneFeatureHelper.java | 10 +-- .../genome/homology/BlastHomologyHits.java | 2 +- .../homology/GFF3FromUniprotBlastHits.java | 4 +- .../nbio/genome/io/fastq/FastqTools.java | 4 +- .../nbio/genome/io/fastq/FastqVariant.java | 2 +- .../parsers/cytoband/CytobandParser.java | 4 +- .../parsers/geneid/GeneIDXMLReader.java | 4 +- .../GeneChromosomePositionParser.java | 4 +- .../parsers/genename/GeneNamesParser.java | 2 +- .../nbio/genome/parsers/gff/Feature.java | 6 +- .../genome/parsers/gff/FeatureHelper.java | 2 +- .../nbio/genome/parsers/gff/FeatureList.java | 12 ++-- .../nbio/genome/parsers/gff/GFF3Writer.java | 2 +- .../genome/parsers/twobit/TwoBitParser.java | 2 +- .../nbio/genome/query/BlastXMLQuery.java | 4 +- .../nbio/genome/uniprot/UniprotToFasta.java | 6 +- .../biojava/nbio/genome/util/SplitFasta.java | 2 +- .../org/biojava/nbio/protmod/Component.java | 8 +-- .../nbio/protmod/ModificationCategory.java | 2 +- .../protmod/ModificationConditionImpl.java | 2 +- .../protmod/ModificationOccurrenceType.java | 2 +- .../nbio/protmod/ProteinModificationImpl.java | 6 +- .../protmod/ProteinModificationRegistry.java | 30 ++++----- .../protmod/io/ComponentXMLConverter.java | 2 +- .../io/ModifiedCompoundXMLConverter.java | 2 +- .../io/ProteinModificationXmlReader.java | 12 ++-- .../structure/ModifiedCompoundImpl.java | 16 ++--- .../ProteinModificationIdentifier.java | 46 ++++++------- .../nbio/protmod/structure/StructureUtil.java | 4 +- .../org/biojava/nbio/ontology/Ontology.java | 20 +++--- .../java/org/biojava/nbio/ontology/Term.java | 2 +- .../org/biojava/nbio/ontology/Triple.java | 2 +- .../biojava/nbio/ontology/io/GOParser.java | 4 +- .../nbio/ontology/obo/OboFileHandler.java | 2 +- .../nbio/ontology/obo/OboFileParser.java | 10 +-- .../src/main/java/demo/PredictDisorder.java | 2 +- .../nbio/data/sequence/SequenceUtil.java | 2 +- .../java/org/biojava/nbio/ronn/Jronn.java | 6 +- .../org/biojava/nbio/ronn/ModelLoader.java | 2 +- .../java/demo/DemoAlignmentFromFasta.java | 2 +- .../src/main/java/demo/DemoMultipleMC.java | 4 +- .../java/demo/DemoStructureFromFasta.java | 2 +- .../nbio/structure/align/gui/DisplayAFP.java | 10 +-- .../structure/align/gui/DotPlotPanel.java | 2 +- .../align/gui/MultipleAlignmentCalc.java | 2 +- .../gui/MultipleAlignmentJmolDisplay.java | 2 +- .../structure/align/gui/ParameterGUI.java | 2 +- .../AligPanelMouseMotionListener.java | 2 +- .../gui/aligpanel/MultipleAligPanel.java | 6 +- .../MultipleAligPanelMouseMotionListener.java | 2 +- .../DefaultAutoSuggestProvider.java | 2 +- .../align/gui/autosuggest/JAutoSuggest.java | 2 +- .../autosuggest/SCOPAutoSuggestProvider.java | 6 +- .../align/gui/jmol/MultipleAlignmentJmol.java | 6 +- .../align/gui/jmol/RasmolCommandListener.java | 2 +- .../gui/jmol/StructureAlignmentJmol.java | 6 +- .../structure/gui/ScaleableMatrixPanel.java | 2 +- .../nbio/structure/gui/SequenceDisplay.java | 2 +- .../structure/gui/util/PDBUploadPanel.java | 2 +- .../gui/util/SelectMultiplePanel.java | 4 +- .../gui/util/SequenceMouseListener.java | 2 +- .../gui/util/SequenceScalePanel.java | 2 +- .../gui/util/color/GradientMapper.java | 2 +- .../symmetry/gui/SymmetryDisplay.java | 2 +- .../JmolSymmetryScriptGeneratorH.java | 6 +- ...JmolSymmetryScriptGeneratorPointGroup.java | 12 ++-- .../src/main/java/demo/DemoMultipleMC.java | 4 +- .../nbio/structure/AtomPositionMap.java | 6 +- .../org/biojava/nbio/structure/BondImpl.java | 2 +- .../org/biojava/nbio/structure/Element.java | 2 +- .../biojava/nbio/structure/EntityInfo.java | 6 +- .../nbio/structure/ExperimentalTechnique.java | 2 +- .../org/biojava/nbio/structure/GroupType.java | 4 +- .../nbio/structure/JournalArticle.java | 4 +- .../org/biojava/nbio/structure/Mutator.java | 2 +- .../org/biojava/nbio/structure/PDBHeader.java | 2 +- .../biojava/nbio/structure/ResidueRange.java | 6 +- .../nbio/structure/ResidueRangeAndLength.java | 4 +- .../java/org/biojava/nbio/structure/Site.java | 2 +- .../nbio/structure/StandardAminoAcid.java | 2 +- .../biojava/nbio/structure/StructureImpl.java | 2 +- .../nbio/structure/StructureTools.java | 22 +++---- .../structure/SubstructureIdentifier.java | 2 +- .../nbio/structure/align/AFPTwister.java | 2 +- .../align/StructureAlignmentFactory.java | 2 +- .../ce/AbstractUserArgumentProcessor.java | 2 +- .../nbio/structure/align/ce/CECalculator.java | 6 +- .../nbio/structure/align/ce/CeCPMain.java | 6 +- .../align/ce/CeCalculatorEnhanced.java | 6 +- .../nbio/structure/align/ce/CeParameters.java | 8 +-- .../structure/align/ce/OptimalCECPMain.java | 8 +-- .../structure/align/client/StructureName.java | 4 +- .../align/fatcat/calc/AFPCalculator.java | 2 +- .../align/fatcat/calc/FatCatParameters.java | 8 +-- .../align/helper/JointFragments.java | 2 +- .../nbio/structure/align/model/AFPChain.java | 4 +- .../align/multiple/AbstractScoresCache.java | 2 +- .../structure/align/multiple/BlockImpl.java | 4 +- .../align/multiple/BlockSetImpl.java | 6 +- .../MultipleAlignmentEnsembleImpl.java | 16 ++--- .../align/multiple/MultipleAlignmentImpl.java | 12 ++-- .../align/multiple/mc/MultipleMcMain.java | 12 ++-- .../multiple/mc/MultipleMcOptimizer.java | 26 ++++---- .../multiple/mc/MultipleMcParameters.java | 8 +-- .../align/multiple/util/CoreSuperimposer.java | 4 +- .../util/MultipleAlignmentDisplay.java | 2 +- .../util/MultipleAlignmentScorer.java | 6 +- .../multiple/util/MultipleAlignmentTools.java | 24 +++---- .../util/MultipleAlignmentWriter.java | 2 +- .../multiple/util/ReferenceSuperimposer.java | 4 +- .../align/pairwise/FragmentJoiner.java | 8 +-- .../nbio/structure/align/pairwise/Gotoh.java | 2 +- .../structure/align/quaternary/QsAlign.java | 22 +++---- .../align/seq/SmithWaterman3DParameters.java | 8 +-- .../align/util/AFPAlignmentDisplay.java | 18 ++--- .../structure/align/util/AlignmentTools.java | 44 ++++++------- .../nbio/structure/align/util/CliTools.java | 8 +-- .../align/xml/AFPChainXMLParser.java | 4 +- .../align/xml/MultipleAlignmentXMLParser.java | 6 +- .../align/xml/PdbPairXMLConverter.java | 2 +- .../structure/align/xml/PdbPairsMessage.java | 2 +- .../biojava/nbio/structure/asa/GroupAsa.java | 6 +- .../nbio/structure/cath/CathDomain.java | 4 +- .../nbio/structure/cath/CathFactory.java | 2 +- .../nbio/structure/cath/CathInstallation.java | 32 ++++----- .../structure/cluster/SubunitCluster.java | 6 +- .../structure/cluster/SubunitExtractor.java | 4 +- .../structure/contact/AtomContactSet.java | 6 +- .../nbio/structure/contact/Contact.java | 2 +- .../nbio/structure/contact/GridCell.java | 8 +-- .../nbio/structure/contact/GroupContact.java | 4 +- .../structure/contact/GroupContactSet.java | 10 +-- .../structure/contact/StructureInterface.java | 8 +-- .../contact/StructureInterfaceCluster.java | 2 +- .../structure/domain/SerializableCache.java | 2 +- .../structure/domain/pdp/ClusterDomains.java | 2 +- .../nbio/structure/domain/pdp/CutDomain.java | 2 +- .../nbio/structure/domain/pdp/Domain.java | 2 +- .../nbio/structure/ecod/EcodDomain.java | 2 +- .../nbio/structure/ecod/EcodInstallation.java | 12 ++-- .../structure/geometry/MomentsOfInertia.java | 2 +- .../nbio/structure/io/CAConverter.java | 2 +- .../structure/io/FastaAFPChainConverter.java | 20 +++--- .../biojava/nbio/structure/io/GroupToSDF.java | 2 +- .../nbio/structure/io/LocalPDBDirectory.java | 4 +- .../structure/io/PDBBioAssemblyParser.java | 6 +- .../nbio/structure/io/PDBFileParser.java | 66 +++++++++---------- .../nbio/structure/io/SeqRes2AtomAligner.java | 8 +-- .../io/StructureSequenceMatcher.java | 8 +-- .../io/cif/CifStructureConsumerImpl.java | 2 +- .../nbio/structure/io/mmtf/MmtfUtils.java | 4 +- .../io/sifts/SiftsChainToUniprotMapping.java | 4 +- .../nbio/structure/io/sifts/SiftsEntity.java | 2 +- .../nbio/structure/io/sifts/SiftsSegment.java | 2 +- .../structure/io/sifts/SiftsXMLParser.java | 6 +- .../nbio/structure/math/SparseVector.java | 2 +- .../nbio/structure/math/SymbolTable.java | 2 +- .../quaternary/BioAssemblyTools.java | 6 +- .../quaternary/BiologicalAssemblyBuilder.java | 2 +- .../BiologicalAssemblyTransformation.java | 2 +- .../quaternary/CartesianProduct.java | 2 +- .../biojava/nbio/structure/scop/Astral.java | 6 +- .../scop/BerkeleyScopInstallation.java | 2 +- .../nbio/structure/scop/ScopDomain.java | 2 +- .../nbio/structure/scop/ScopInstallation.java | 32 ++++----- .../nbio/structure/secstruc/DSSPParser.java | 2 +- .../nbio/structure/secstruc/SecStrucCalc.java | 16 ++--- .../structure/secstruc/SecStrucTools.java | 2 +- .../symmetry/axis/HelixAxisAligner.java | 4 +- .../symmetry/axis/RotationAxisAligner.java | 10 +-- .../symmetry/core/HelicalRepeatUnit.java | 22 +++---- .../nbio/structure/symmetry/core/Helix.java | 4 +- .../symmetry/core/HelixExtender.java | 2 +- .../structure/symmetry/core/HelixLayers.java | 2 +- .../structure/symmetry/core/HelixSolver.java | 6 +- .../symmetry/core/PermutationGroup.java | 14 ++-- .../symmetry/core/QuatSymmetryResults.java | 4 +- .../symmetry/core/QuatSymmetrySubunits.java | 4 +- .../symmetry/core/RotationGroup.java | 4 +- .../symmetry/core/RotationSolver.java | 8 +-- .../symmetry/core/SystematicSolver.java | 4 +- .../symmetry/geometry/DistanceBox.java | 14 ++-- .../structure/symmetry/geometry/Prism.java | 2 +- .../structure/symmetry/internal/CeSymm.java | 2 +- .../symmetry/internal/CeSymmIterative.java | 4 +- .../symmetry/internal/CeSymmResult.java | 2 +- .../internal/GraphComponentOrderDetector.java | 2 +- .../internal/GraphComponentRefiner.java | 6 +- .../symmetry/internal/ResidueGroup.java | 2 +- .../internal/SequenceFunctionRefiner.java | 16 ++--- .../symmetry/internal/SymmOptimizer.java | 34 +++++----- .../symmetry/internal/SymmetryAxes.java | 2 +- .../misc/ProteinComplexSignature.java | 8 +-- .../symmetry/utils/BlastClustReader.java | 6 +- .../structure/symmetry/utils/PowerSet.java | 8 +-- .../symmetry/utils/SymmetryTools.java | 18 ++--- .../nbio/structure/xtal/BravaisLattice.java | 2 +- .../nbio/structure/xtal/CrystalCell.java | 2 +- .../nbio/structure/xtal/SpaceGroup.java | 4 +- .../nbio/structure/xtal/SymoplibParser.java | 8 +-- .../xtal/io/SpaceGroupMapAdapter.java | 2 +- .../structure/xtal/io/SpaceGroupMapRoot.java | 2 +- .../xtal/io/TransfAlgebraicAdapter.java | 2 +- .../xtal/io/TreeMapSpaceGroupWrapper.java | 2 +- .../org/biojava/nbio/survival/cox/CoxCC.java | 12 ++-- .../biojava/nbio/survival/cox/CoxHelper.java | 4 +- .../biojava/nbio/survival/cox/CoxInfo.java | 12 ++-- .../org/biojava/nbio/survival/cox/CoxR.java | 8 +-- .../biojava/nbio/survival/cox/CoxScore.java | 2 +- .../nbio/survival/cox/CoxVariables.java | 2 +- .../nbio/survival/cox/ResidualsCoxph.java | 4 +- .../biojava/nbio/survival/cox/StrataInfo.java | 26 ++++---- .../nbio/survival/cox/SurvFitInfo.java | 4 +- .../nbio/survival/cox/SurvivalInfo.java | 12 ++-- .../nbio/survival/cox/SurvivalInfoHelper.java | 12 ++-- .../nbio/survival/cox/stats/AgScore.java | 2 +- .../biojava/nbio/survival/data/WorkSheet.java | 66 +++++++++---------- .../kaplanmeier/figure/ExpressionFigure.java | 14 ++-- .../kaplanmeier/figure/KMFigureInfo.java | 2 +- .../kaplanmeier/figure/KaplanMeierFigure.java | 32 ++++----- .../figure/NumbersAtRiskPanel.java | 4 +- .../kaplanmeier/figure/SurvFitKM.java | 26 ++++---- .../metadata/ClinicalMetaDataOutcome.java | 4 +- .../kaplanmeier/metadata/MetaDataInfo.java | 2 +- biojava-ws/src/main/java/demo/HmmerDemo.java | 2 +- .../qblast/NCBIQBlastAlignmentProperties.java | 4 +- .../qblast/NCBIQBlastOutputProperties.java | 4 +- .../alignment/qblast/NCBIQBlastService.java | 6 +- .../nbio/ws/hmmer/RemoteHmmerScan.java | 4 +- 324 files changed, 1102 insertions(+), 1102 deletions(-) diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java index aa3c5cdd5b..727c83b388 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java @@ -95,8 +95,8 @@ public static void run(String[] args) throws Exception{ /* * Parse input arguments */ - List propertyList = new ArrayList(); - List specificList = new ArrayList(); + List propertyList = new ArrayList<>(); + List specificList = new ArrayList<>(); String inputLocation = null; String outputLocation = null; String aminoAcidCompositionLocation = null; @@ -179,14 +179,14 @@ private static LinkedHashMap readInputFile(String input } LinkedHashMap ret; if ( inputLocation.toLowerCase().contains(".gb")) { - GenbankReader genbankReader = new GenbankReader( + GenbankReader genbankReader = new GenbankReader<>( inStream, new GenericGenbankHeaderParser(), new ProteinSequenceCreator(set)); ret = genbankReader.process(); } else { - FastaReader fastaReader = new FastaReader( + FastaReader fastaReader = new FastaReader<>( inStream, new GenericFastaHeaderParser(), new ProteinSequenceCreator(set)); ret = fastaReader.process(); @@ -214,7 +214,7 @@ private static void printHeader(PrintStream output, List propertyList * 9 Composition of the 20 standard amino acid * 0 Composition of the specific amino acid */ - List sList = new ArrayList(); + List sList = new ArrayList<>(); sList.add("SequenceName"); for(Character c:propertyList){ switch(c){ @@ -277,7 +277,7 @@ private static void compute(PrintStream output, String header, String sequence, IPeptideProperties pp = new PeptidePropertiesImpl(); int specificCount = 0; - List dList = new ArrayList(); + List dList = new ArrayList<>(); for(Character c:propertyList){ switch(c){ case '1': diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java index f223eaca23..d525c6bfe8 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java @@ -64,14 +64,14 @@ public class Constraints { public static AminoAcidCompound Y = aaSet.getCompoundForString("Y"); public static AminoAcidCompound V = aaSet.getCompoundForString("V"); - public static Map aa2ExtinctionCoefficient = new HashMap(); - public static Map aa2MolecularWeight = new HashMap(); - public static Map aa2Hydrophathicity = new HashMap(); - public static Map aa2PKa = new HashMap(); - public static Map diAA2Instability = new HashMap(); + public static Map aa2ExtinctionCoefficient = new HashMap<>(); + public static Map aa2MolecularWeight = new HashMap<>(); + public static Map aa2Hydrophathicity = new HashMap<>(); + public static Map aa2PKa = new HashMap<>(); + public static Map diAA2Instability = new HashMap<>(); - public static Map aa2NTerminalPka = new HashMap(); - public static Map aa2CTerminalPka = new HashMap(); + public static Map aa2NTerminalPka = new HashMap<>(); + public static Map aa2CTerminalPka = new HashMap<>(); static{ initMolecularWeight(); diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java index da0cef9997..d14a4d906b 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java @@ -532,7 +532,7 @@ public static final Map getAAComposition(String seque */ public static final Map getAACompositionString(String sequence){ Map aa2Composition = getAAComposition(sequence); - Map aaString2Composition = new HashMap(); + Map aaString2Composition = new HashMap<>(); aaString2Composition = aa2Composition.keySet().stream() .collect(Collectors.toMap(aaCompound -> aaCompound.getShortName(),aaCompound ->aa2Composition.get(aaCompound))); return aaString2Composition; } @@ -550,7 +550,7 @@ public static final Map getAACompositionString(String sequence){ */ public static final Map getAACompositionChar(String sequence){ Map aa2Composition = getAAComposition(sequence); - Map aaChar2Composition = new HashMap(); + Map aaChar2Composition = new HashMap<>(); for(AminoAcidCompound aaCompound:aa2Composition.keySet()){ aaChar2Composition.put(aaCompound.getShortName().charAt(0), aa2Composition.get(aaCompound)); } diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java index fc31b9510b..ceb0b234ed 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java @@ -210,7 +210,7 @@ private Map getExtinctAACount(ProteinSequence sequen } } AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet(); - Map extinctAA2Count = new HashMap(); + Map extinctAA2Count = new HashMap<>(); //Ignore Case is always true extinctAA2Count.put(aaSet.getCompoundForString("W"), numW + smallW); extinctAA2Count.put(aaSet.getCompoundForString("C"), (int) (numC + smallC)); @@ -532,7 +532,7 @@ private Map getChargedAACount(ProteinSequence sequen } } AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet(); - Map chargedAA2Count = new HashMap(); + Map chargedAA2Count = new HashMap<>(); chargedAA2Count.put(aaSet.getCompoundForString("K"), numK); chargedAA2Count.put(aaSet.getCompoundForString("R"), numR); chargedAA2Count.put(aaSet.getCompoundForString("H"), numH); @@ -558,7 +558,7 @@ public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAci @Override public Map getAAComposition(ProteinSequence sequence) { int validLength = 0; - Map aa2Composition = new HashMap(); + Map aa2Composition = new HashMap<>(); AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet(); for(AminoAcidCompound aa:aaSet.getAllCompounds()){ aa2Composition.put(aa, 0.0); diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java index b66e879d7a..298ad61330 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java @@ -106,7 +106,7 @@ public final static int getNumberOfInvalidChar(String sequence, Set * a new sequence with all invalid characters being replaced by '-'. */ public final static String cleanSequence(String sequence, Set cSet){ - Set invalidCharSet = new HashSet(); + Set invalidCharSet = new HashSet<>(); StringBuilder cleanSeq = new StringBuilder(); if(cSet == null) cSet = PeptideProperties.standardAASet; for(char c:sequence.toCharArray()){ diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java index 75b0ff3064..18b63a468b 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java @@ -125,35 +125,35 @@ private Convertor getConvertor(ATTRIBUTE attribute) throws Exception{ @Override public Map getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception { - Map grouping2Composition = new HashMap(); + Map grouping2Composition = new HashMap<>(); for(GROUPING group:GROUPING.values()) grouping2Composition.put(group, getComposition(sequence, attribute, group)); return grouping2Composition; } @Override public Map> getComposition(ProteinSequence sequence) throws Exception { - Map> attribute2Grouping2Composition = new HashMap>(); + Map> attribute2Grouping2Composition = new HashMap<>(); for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Grouping2Composition.put(attribute, getComposition(sequence, attribute)); return attribute2Grouping2Composition; } @Override public Map getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception { - Map transition2Double = new HashMap(); + Map transition2Double = new HashMap<>(); for(TRANSITION transition:TRANSITION.values()) transition2Double.put(transition, getTransition(sequence, attribute, transition)); return transition2Double; } @Override public Map> getTransition(ProteinSequence sequence) throws Exception { - Map> attribute2Transition2Double = new HashMap>(); + Map> attribute2Transition2Double = new HashMap<>(); for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Transition2Double.put(attribute, getTransition(sequence, attribute)); return attribute2Transition2Double; } @Override public Map getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception { - Map distribution2Double = new HashMap(); + Map distribution2Double = new HashMap<>(); for(DISTRIBUTION distribution:DISTRIBUTION.values()) distribution2Double.put(distribution, getDistributionPosition(sequence, attribute, group, distribution)); return distribution2Double; @@ -161,7 +161,7 @@ public Map getDistributionPosition(ProteinSequence sequenc @Override public Map> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception { - Map> grouping2Distribution2Double = new HashMap>(); + Map> grouping2Distribution2Double = new HashMap<>(); for(GROUPING group:GROUPING.values()) grouping2Distribution2Double.put(group, getDistributionPosition(sequence, attribute, group)); return grouping2Distribution2Double; @@ -170,7 +170,7 @@ public Map> getDistributionPosition(ProteinS @Override public Map>> getDistributionPosition(ProteinSequence sequence) throws Exception { Map>> attribute2Grouping2Distribution2Double = - new HashMap>>(); + new HashMap<>(); for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Grouping2Distribution2Double.put(attribute, getDistributionPosition(sequence, attribute)); return attribute2Grouping2Distribution2Double; diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java index c0b2e1489d..b209859600 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java @@ -83,7 +83,7 @@ private void generatesAminoAcidCompoundSet(){ * Stores the mass of elements and isotopes */ public void computeMolecularWeight(ElementTable eTable){ - this.aaSymbol2MolecularWeight = new HashMap(); + this.aaSymbol2MolecularWeight = new HashMap<>(); for(AminoAcidComposition a:aminoacid){ //Check to ensure that the symbol is of single character if(a.getSymbol().length() != 1){ diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java index 9b211ab305..7a436d32cd 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java @@ -39,9 +39,9 @@ */ public class CaseFreeAminoAcidCompoundSet implements CompoundSet { - private final Map aminoAcidCompoundCache = new HashMap(); + private final Map aminoAcidCompoundCache = new HashMap<>(); private final Map> equivalentsCache = - new HashMap>(); + new HashMap<>(); public CaseFreeAminoAcidCompoundSet() { aminoAcidCompoundCache.put("A", new AminoAcidCompound(null, "A", "Ala", "Alanine", 71.0788f)); @@ -83,7 +83,7 @@ public CaseFreeAminoAcidCompoundSet() { //which then does the actual conversion to Pyl. aminoAcidCompoundCache.put("O", new AminoAcidCompound(null, "O", "Pyl", "Pyrrolysine", 255.3172f)); - Map lowerCaseSet = new HashMap(); + Map lowerCaseSet = new HashMap<>(); for(String s:this.aminoAcidCompoundCache.keySet()){ lowerCaseSet.put(s.toLowerCase(), this.aminoAcidCompoundCache.get(s)); } @@ -144,7 +144,7 @@ public Set getEquivalentCompounds(AminoAcidCompound compound) addAmbiguousEquivalents("I", "L", "J"); // ambiguous gaps AminoAcidCompound gap1, gap2, gap3; - Set gaps = new HashSet(); + Set gaps = new HashSet<>(); gaps.add(gap1 = aminoAcidCompoundCache.get("-")); gaps.add(gap2 = aminoAcidCompoundCache.get(".")); gaps.add(gap3 = aminoAcidCompoundCache.get("_")); @@ -162,18 +162,18 @@ private void addAmbiguousEquivalents(String one, String two, String either) { Set equivalents; AminoAcidCompound cOne, cTwo, cEither; - equivalents = new HashSet(); + equivalents = new HashSet<>(); equivalents.add(cOne = aminoAcidCompoundCache.get(one)); equivalents.add(cTwo = aminoAcidCompoundCache.get(two)); equivalents.add(cEither = aminoAcidCompoundCache.get(either)); equivalentsCache.put(cEither, equivalents); - equivalents = new HashSet(); + equivalents = new HashSet<>(); equivalents.add(cOne); equivalents.add(cEither); equivalentsCache.put(cOne, equivalents); - equivalents = new HashSet(); + equivalents = new HashSet<>(); equivalents.add(cTwo); equivalents.add(cEither); equivalentsCache.put(cTwo, equivalents); @@ -186,7 +186,7 @@ public boolean hasCompound(AminoAcidCompound compound) { @Override public List getAllCompounds() { - return new ArrayList(aminoAcidCompoundCache.values()); + return new ArrayList<>(aminoAcidCompoundCache.values()); } diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java index 4fc5f5ad66..c7b9a425fc 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java @@ -120,7 +120,7 @@ public List getIsotopes() { public void setIsotopes(List isotopes) { this.isotope = isotopes; - this.name2Isotope = new HashMap(); + this.name2Isotope = new HashMap<>(); if(isotopes != null){ for(Isotope i:isotopes){ name2Isotope.put(i.getName(), i); diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java index acdcee25d9..e2b30c6211 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java @@ -58,8 +58,8 @@ public void setElement(List eList){ * Populate the Maps for quick retrieval */ public void populateMaps(){ - this.elementName2Element = new HashMap(); - this.isotopeName2Isotope = new HashMap(); + this.elementName2Element = new HashMap<>(); + this.isotopeName2Isotope = new HashMap<>(); if(this.element != null){ for(Element e:this.element){ this.elementName2Element.put(e.getName(), e); diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java index d9c11c7e66..b1c63e9655 100644 --- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java +++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java @@ -28,7 +28,7 @@ public class ModifiedAminoAcidCompoundSet implements CompoundSet { - private final Map aminoAcidCompoundCache = new HashMap(); + private final Map aminoAcidCompoundCache = new HashMap<>(); public ModifiedAminoAcidCompoundSet(List aaList, Map aaSymbol2MolecularWeight) { this.aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "", "", 0.0f)); @@ -84,7 +84,7 @@ public boolean hasCompound(AminoAcidCompound compound) { @Override public List getAllCompounds() { - return new ArrayList(aminoAcidCompoundCache.values()); + return new ArrayList<>(aminoAcidCompoundCache.values()); } @Override diff --git a/biojava-alignment/src/main/java/demo/CookbookMSA.java b/biojava-alignment/src/main/java/demo/CookbookMSA.java index d2952bbeac..c617745539 100644 --- a/biojava-alignment/src/main/java/demo/CookbookMSA.java +++ b/biojava-alignment/src/main/java/demo/CookbookMSA.java @@ -43,7 +43,7 @@ public static void main(String[] args) throws Exception { } private static void multipleSequenceAlignment(String[] ids) throws Exception { - List lst = new ArrayList(); + List lst = new ArrayList<>(); for (String id : ids) { lst.add(getSequenceForId(id)); } diff --git a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java index c9f82d39f7..e7e0561a9d 100644 --- a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java +++ b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java @@ -58,7 +58,7 @@ public static void main(String[] args) throws Exception { .getResourceAsStream("/PF00104_small.fasta"); FastaReader fastaReader = - new FastaReader( + new FastaReader<>( inStream, new GenericFastaHeaderParser(), new ProteinSequenceCreator(AminoAcidCompoundSet @@ -70,7 +70,7 @@ public static void main(String[] args) throws Exception { inStream.close(); MultipleSequenceAlignment msa = - new MultipleSequenceAlignment(); + new MultipleSequenceAlignment<>(); for (ProteinSequence proteinSequence : proteinSequences.values()) { msa.addAlignedSequence(proteinSequence); diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java index 4ed72d0979..6cc2eb3f35 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java @@ -189,7 +189,7 @@ public static , C extends Compound> Profile getMulti runPairwiseScorers(scorers); // stage 2: hierarchical clustering into a guide tree - GuideTree tree = new GuideTree(sequences, scorers); + GuideTree tree = new GuideTree<>(sequences, scorers); scorers = null; // stage 3: progressive alignment @@ -233,7 +233,7 @@ public static , C extends Compound> SequencePair get static , C extends Compound> List> getAllPairsAligners( List sequences, PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix subMatrix) { - List> allPairs = new ArrayList>(); + List> allPairs = new ArrayList<>(); for (int i = 0; i < sequences.size(); i++) { for (int j = i+1; j < sequences.size(); j++) { allPairs.add(getPairwiseAligner(sequences.get(i), sequences.get(j), type, gapPenalty, subMatrix)); @@ -256,7 +256,7 @@ static , C extends Compound> List, C extends Compound> List> getAllPairsScorers( List sequences, PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix subMatrix) { - List> allPairs = new ArrayList>(); + List> allPairs = new ArrayList<>(); for (int i = 0; i < sequences.size(); i++) { for (int j = i+1; j < sequences.size(); j++) { allPairs.add(getPairwiseScorer(sequences.get(i), sequences.get(j), type, gapPenalty, subMatrix)); @@ -291,7 +291,7 @@ public static , C extends Compound> double[] getAllPairsSc * @return calculated elements */ static List getListFromFutures(List> futures) { - List list = new ArrayList(); + List list = new ArrayList<>(); for (Future f : futures) { // TODO when added to ConcurrencyTools, log completions and exceptions instead of printing stack traces try { @@ -326,9 +326,9 @@ public static , C extends Compound> PairwiseSequenceAligne switch (type) { default: case GLOBAL: - return new NeedlemanWunsch(query, target, gapPenalty, subMatrix); + return new NeedlemanWunsch<>(query, target, gapPenalty, subMatrix); case LOCAL: - return new SmithWaterman(query, target, gapPenalty, subMatrix); + return new SmithWaterman<>(query, target, gapPenalty, subMatrix); case GLOBAL_LINEAR_SPACE: case LOCAL_LINEAR_SPACE: // TODO other alignment options (Myers-Miller, Thompson) @@ -374,18 +374,18 @@ static , C extends Compound> PairwiseSequenceScorer case GLOBAL: return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix); case GLOBAL_IDENTITIES: - return new FractionalIdentityScorer(getPairwiseAligner(query, target, + return new FractionalIdentityScorer<>(getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix)); case GLOBAL_SIMILARITIES: - return new FractionalSimilarityScorer(getPairwiseAligner(query, target, + return new FractionalSimilarityScorer<>(getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix)); case LOCAL: return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix); case LOCAL_IDENTITIES: - return new FractionalIdentityScorer(getPairwiseAligner(query, target, + return new FractionalIdentityScorer<>(getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix)); case LOCAL_SIMILARITIES: - return new FractionalSimilarityScorer(getPairwiseAligner(query, target, + return new FractionalSimilarityScorer<>(getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix)); case KMERS: case WU_MANBER: @@ -413,7 +413,7 @@ static , C extends Compound> ProfileProfileAligner g switch (type) { default: case GLOBAL: - return new SimpleProfileProfileAligner(profile1, profile2, gapPenalty, subMatrix); + return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix); case GLOBAL_LINEAR_SPACE: case GLOBAL_CONSENSUS: case LOCAL: @@ -443,7 +443,7 @@ static , C extends Compound> ProfileProfileAligner g switch (type) { default: case GLOBAL: - return new SimpleProfileProfileAligner(profile1, profile2, gapPenalty, subMatrix); + return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix); case GLOBAL_LINEAR_SPACE: case GLOBAL_CONSENSUS: case LOCAL: @@ -473,7 +473,7 @@ static , C extends Compound> ProfileProfileAligner g switch (type) { default: case GLOBAL: - return new SimpleProfileProfileAligner(profile1, profile2, gapPenalty, subMatrix); + return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix); case GLOBAL_LINEAR_SPACE: case GLOBAL_CONSENSUS: case LOCAL: @@ -503,7 +503,7 @@ static , C extends Compound> ProfileProfileAligner g switch (type) { default: case GLOBAL: - return new SimpleProfileProfileAligner(profile1, profile2, gapPenalty, subMatrix); + return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix); case GLOBAL_LINEAR_SPACE: case GLOBAL_CONSENSUS: case LOCAL: @@ -550,7 +550,7 @@ public static , C extends Compound> Profile getProgr ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix subMatrix) { // find inner nodes in post-order traversal of tree (each leaf node has a single sequence profile) - List> innerNodes = new ArrayList>(); + List> innerNodes = new ArrayList<>(); for (GuideTreeNode n : tree) { if (n.getProfile() == null) { innerNodes.add(n); @@ -599,7 +599,7 @@ public static , C extends Compound> Profile getProgr static , C extends Compound> List> runPairwiseAligners(List> aligners) { int n = 1, all = aligners.size(); - List>> futures = new ArrayList>>(); + List>> futures = new ArrayList<>(); for (PairwiseSequenceAligner aligner : aligners) { futures.add(ConcurrencyTools.submit(new CallablePairwiseSequenceAligner(aligner), String.format("Aligning pair %d of %d", n++, all))); @@ -619,7 +619,7 @@ public static , C extends Compound> Profile getProgr public static , C extends Compound> double[] runPairwiseScorers( List> scorers) { int n = 1, all = scorers.size(); - List> futures = new ArrayList>(); + List> futures = new ArrayList<>(); for (PairwiseSequenceScorer scorer : scorers) { futures.add(ConcurrencyTools.submit(new CallablePairwiseSequenceScorer(scorer), String.format("Scoring pair %d of %d", n++, all))); @@ -644,7 +644,7 @@ public static , C extends Compound> double[] runPairwiseSc static , C extends Compound> List> runProfileAligners(List> aligners) { int n = 1, all = aligners.size(); - List>> futures = new ArrayList>>(); + List>> futures = new ArrayList<>(); for (ProfileProfileAligner aligner : aligners) { futures.add(ConcurrencyTools.submit(new CallableProfileProfileAligner(aligner), String.format("Aligning pair %d of %d", n++, all))); diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java index ecbcf66e79..c67caa8a4f 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java @@ -182,7 +182,7 @@ private Node(PhylogenyNode node, Node parent) { distance = node.getDistanceToParent(); name = node.getName(); if(isLeaf = node.isExternal()) { - profile = new SimpleProfile(sequences.get(distances.getIndex(name))); + profile = new SimpleProfile<>(sequences.get(distances.getIndex(name))); } else { child1 = new Node(node.getChildNode1(), this); child2 = new Node(node.getChildNode2(), this); @@ -237,7 +237,7 @@ public void setProfileFuture(Future> profileFuture) { @Override public Enumeration> children() { - Vector> children = new Vector>(); + Vector> children = new Vector<>(); children.add(getChild1()); children.add(getChild2()); return children.elements(); @@ -305,7 +305,7 @@ private class PostOrderIterator implements Iterator> { private PostOrderIterator() { getRoot().clearVisited(); - nodes = new Stack(); + nodes = new Stack<>(); nodes.push(getRoot()); } diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java index 73579ab8f4..47fb7976e0 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java @@ -110,7 +110,7 @@ public SimpleProfileProfileAligner(Future> query, Profile sx, List sy) { - profile = pair = new SimpleProfilePair(getQuery(), getTarget(), sx, sy); + profile = pair = new SimpleProfilePair<>(getQuery(), getTarget(), sx, sy); } } diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java index 7d7e017694..819d8f5187 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java @@ -69,7 +69,7 @@ public SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatri @Override protected void setProfile(List sx, List sy) { - profile = pair = new SimpleSequencePair(getQuery(), getTarget(), sx, xyStart[0], + profile = pair = new SimpleSequencePair<>(getQuery(), getTarget(), sx, xyStart[0], getQuery().getLength() - xyMax[0], sy, xyStart[1], getTarget().getLength() - xyMax[1]); } diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java index 80389ca000..f0ca2bfa23 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java @@ -125,7 +125,7 @@ public void setRefLocation(String refLocation) { private Set dbReferences; private StringBuffer refComment; /**TODO When implementing toString(), the function should loop on the vector */ - private Vector references = new Vector(); + private Vector references = new Vector<>(); private StringBuffer keywords; private CharSequence comment; private StringBuffer pfamAccession; @@ -137,7 +137,7 @@ public void setRefLocation(String refLocation) { private float falseDiscoveryRate; public StockholmFileAnnotation() { - embTrees = new HashMap>(); + embTrees = new HashMap<>(); } public StringBuffer getDbComment() { @@ -164,7 +164,7 @@ public void setDbReferences(Set dbReferences) { */ public void addDBReference(String dbReferenceRepresentingString) { if (this.dbReferences == null) { - this.dbReferences = new HashSet(); + this.dbReferences = new HashSet<>(); } dbReferences.add(new DatabaseReference(dbReferenceRepresentingString)); } @@ -492,7 +492,7 @@ public void setGFMembership(String membership) { public void addGFNewHampshire(String newHampshire) { List hampshireTree = embTrees.get(TREE_DEFAULT_ID); if (hampshireTree == null) { - hampshireTree = new ArrayList(); + hampshireTree = new ArrayList<>(); } hampshireTree.add(newHampshire); embTrees.put(TREE_DEFAULT_ID, hampshireTree); diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java index 2d19a5e8df..83afc9d5a0 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java @@ -356,7 +356,7 @@ public List parse(InputStream inStream, int max) throws IOEx if (internalScanner == null) { internalScanner = new Scanner(inStream); } - ArrayList structures = new ArrayList(); + ArrayList structures = new ArrayList<>(); while (max != INFINITY && max-- > 0) { StockholmStructure structure = parse(internalScanner); if (structure != null) { diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java index 4b36dc192e..6c203bfc5b 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmSequenceAnnotation.java @@ -74,7 +74,7 @@ public void setDbReferences(Set dbReferences) { */ public void addDBReference(String dbReferenceRepresentingString) { if (this.dbReferences == null) { - this.dbReferences = new HashSet(); + this.dbReferences = new HashSet<>(); } dbReferences.add(new DatabaseReference(dbReferenceRepresentingString)); } diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java index 8e9380ec06..d95a2bfa97 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java @@ -94,9 +94,9 @@ public class StockholmStructure { public StockholmStructure() { fileAnnotation = new StockholmFileAnnotation(); consAnnotation = new StockholmConsensusAnnotation(); - sequences = new HashMap(); - seqsAnnotation = new HashMap(); - resAnnotation = new HashMap(); + sequences = new HashMap<>(); + seqsAnnotation = new HashMap<>(); + resAnnotation = new HashMap<>(); } public StockholmFileAnnotation getFileAnnotation() { @@ -235,7 +235,7 @@ public List> getBioSequences(boolea if (forcedSequenceType != null && !(forcedSequenceType.equals(PFAM) || forcedSequenceType.equals(RFAM))) { throw new IllegalArgumentException("Illegal Argument " + forcedSequenceType); } - List> seqs = new ArrayList>(); + List> seqs = new ArrayList<>(); for (String sequencename : sequences.keySet()) { AbstractSequence seq = null; String sequence = sequences.get(sequencename).toString(); diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java index f00ce2101f..e53fe56c05 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java @@ -268,7 +268,7 @@ public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, */ public static List getSubproblems(List anchors, int querySequenceLength, int targetSequenceLength) { Collections.sort(anchors, new Anchor.QueryIndexComparator()); - List list = new ArrayList(); + List list = new ArrayList<>(); Anchor last = new Anchor(-1, -1); // sentinal anchor boolean isAnchored = false; for (int i = 0; i < anchors.size(); i++) { diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java index 41b9502782..95d5264f1e 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java @@ -111,7 +111,7 @@ public int[] getAnchors() { * @param anchors list of points that are tied to the given indices in the target */ public void setAnchors(int[] anchors) { - super.anchors = new ArrayList(); + super.anchors = new ArrayList<>(); if (anchors != null) { for (int i = 0; i < anchors.length; i++) { if (anchors[i] >= 0) { @@ -133,7 +133,7 @@ public void addAnchor(int queryIndex, int targetIndex) { @Override protected void setProfile(List sx, List sy) { - profile = pair = new SimpleSequencePair(getQuery(), getTarget(), sx, sy); + profile = pair = new SimpleSequencePair<>(getQuery(), getTarget(), sx, sy); } } diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java index b5e6f6188c..19fcc9c98f 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java @@ -55,7 +55,7 @@ public abstract class AbstractMatrixAligner, C extends Com protected GapPenalty gapPenalty; private SubstitutionMatrix subMatrix; private boolean local, storingScoreMatrix; - protected List anchors = new ArrayList(); + protected List anchors = new ArrayList<>(); protected int cutsPerSection; // output fields @@ -312,7 +312,7 @@ protected void align() { } boolean linear = (gapPenalty.getType() == GapPenalty.Type.LINEAR); Last[][][] traceback = new Last[dim[0]][][]; - List sx = new ArrayList(), sy = new ArrayList(); + List sx = new ArrayList<>(), sy = new ArrayList<>(); if (!local) { xyMax = new int[] { dim[0] - 1, dim[1] - 1 }; diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java index 74cdf2e2f4..5ad8b2f2e0 100644 --- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java +++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java @@ -64,7 +64,7 @@ public static , D extends Compound> Msa convert( // Convert the biojava MSA to a FASTA String OutputStream os = new ByteArrayOutputStream(); - FastaWriter fastaW = new FastaWriter(os, + FastaWriter fastaW = new FastaWriter<>(os, msa.getAlignedSequences(), new FastaHeaderFormatInterface() { @Override diff --git a/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java b/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java index 354e0bea26..cf321baee6 100644 --- a/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java +++ b/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java @@ -106,7 +106,7 @@ public static void main(String[] args){ CompoundSet nucleotideCompoundSet = AmbiguityRNACompoundSet.getRNACompoundSet(); FastaReader proxy = - new FastaReader( + new FastaReader<>( stream, new GenericFastaHeaderParser(), new DNASequenceCreator(ambiguityDNACompoundSet)); diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java index 5951ed3ad6..7361de9974 100644 --- a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java +++ b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java @@ -94,7 +94,7 @@ public static void main(String[] args) throws Exception { InputStream inStream = isp.getInputStream(f); - FastaReader fastaReader = new FastaReader( + FastaReader fastaReader = new FastaReader<>( inStream, new GenericFastaHeaderParser(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java index 8980fdad7b..85d0a03c26 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java @@ -285,7 +285,7 @@ public AccessionID getAccession() { @Override public List getAsList() { - List compounds = new ArrayList(); + List compounds = new ArrayList<>(); for (int i = 1; i <= length; i++) { compounds.add(getCompoundAt(i)); } @@ -382,7 +382,7 @@ public String toString() { // helper method to initialize the location private void setLocation(List steps) { - List sublocations = new ArrayList(); + List sublocations = new ArrayList<>(); int start = 0, step = 0, oStep = numBefore+numAfter, oMax = this.original.getLength(), pStep = 0, pMax = (prev == null) ? 0 : prev.getLength(); boolean inGap = true; diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java index 7cd7ef1bf5..4b853fcb37 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java @@ -70,11 +70,11 @@ protected SimpleProfile(AlignedSequence query, AlignedSequence targe if (query.getLength() != target.getLength()) { throw new IllegalArgumentException("Aligned sequences differ in size"); } - list = new ArrayList>(); + list = new ArrayList<>(); list.add(query); list.add(target); list = Collections.unmodifiableList(list); - originals = new ArrayList(); + originals = new ArrayList<>(); originals.add(query.getOriginalSequence()); originals.add(target.getOriginalSequence()); originals = Collections.unmodifiableList(originals); @@ -87,14 +87,14 @@ protected SimpleProfile(AlignedSequence query, AlignedSequence targe * @param sequence sequence to seed profile */ public SimpleProfile(S sequence) { - List s = new ArrayList(); + List s = new ArrayList<>(); for (int i = 0; i < sequence.getLength(); i++) { s.add(Step.COMPOUND); } - list = new ArrayList>(); + list = new ArrayList<>(); list.add(new SimpleAlignedSequence(sequence, s)); list = Collections.unmodifiableList(list); - originals = new ArrayList(); + originals = new ArrayList<>(); originals.add(sequence); originals = Collections.unmodifiableList(originals); length = sequence.getLength(); @@ -117,11 +117,11 @@ protected SimpleProfile(S query, S target, List sx, int xb, int xa, List>(); + list = new ArrayList<>(); list.add(new SimpleAlignedSequence(query, sx, xb, xa)); list.add(new SimpleAlignedSequence(target, sy, yb, ya)); list = Collections.unmodifiableList(list); - originals = new ArrayList(); + originals = new ArrayList<>(); originals.add(query); originals.add(target); originals = Collections.unmodifiableList(originals); @@ -141,7 +141,7 @@ protected SimpleProfile(Profile query, Profile target, List sx if (sx.size() != sy.size()) { throw new IllegalArgumentException("Alignments differ in size"); } - list = new ArrayList>(); + list = new ArrayList<>(); for (AlignedSequence s : query) { list.add(new SimpleAlignedSequence(s, sx)); } @@ -149,7 +149,7 @@ protected SimpleProfile(Profile query, Profile target, List sx list.add(new SimpleAlignedSequence(s, sy)); } list = Collections.unmodifiableList(list); - originals = new ArrayList(); + originals = new ArrayList<>(); originals.addAll(query.getOriginalSequences()); originals.addAll(target.getOriginalSequences()); originals = Collections.unmodifiableList(originals); @@ -163,8 +163,8 @@ protected SimpleProfile(Profile query, Profile target, List sx * collection is empty. */ public SimpleProfile(Collection> alignedSequences) { - list = new ArrayList>(); - originals = new ArrayList(); + list = new ArrayList<>(); + originals = new ArrayList<>(); Iterator> itr = alignedSequences.iterator(); if(!itr.hasNext()) { @@ -213,7 +213,7 @@ public List> getAlignedSequences() { @Override public List> getAlignedSequences(int... listIndices) { - List> tempList = new ArrayList>(); + List> tempList = new ArrayList<>(); for (int i : listIndices) { tempList.add(getAlignedSequence(i)); } @@ -222,7 +222,7 @@ public List> getAlignedSequences(int... listIndices) { @Override public List> getAlignedSequences(S... sequences) { - List> tempList = new ArrayList>(); + List> tempList = new ArrayList<>(); for (S s : sequences) { tempList.add(getAlignedSequence(s)); } @@ -262,7 +262,7 @@ public int[] getCompoundCountsAt(int alignmentIndex, List compounds) { @Override public List getCompoundsAt(int alignmentIndex) { // TODO handle circular alignments - List column = new ArrayList(); + List column = new ArrayList<>(); for (AlignedSequence s : list) { column.add(s.getCompoundAt(alignmentIndex)); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java index 82c8abe914..606b913e59 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java @@ -52,7 +52,7 @@ public class AAIndexFileParser { boolean symmetricMatrix ; public AAIndexFileParser(){ - matrices = new HashMap>(); + matrices = new HashMap<>(); } /** Parse an inputStream that points to an AAINDEX database file @@ -154,8 +154,8 @@ private void initMatrix(String line) { matrix = new short[nrRows][nrCols]; - rows = new ArrayList(); - cols = new ArrayList(); + rows = new ArrayList<>(); + cols = new ArrayList<>(); //System.out.println(">" + currentRows+"<"); AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java index ee26384bfa..9d18d50b36 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java @@ -216,7 +216,7 @@ public SubstitutionMatrix normalizeMatrix(short scale) { @Override public Map getRow(AminoAcidCompound row) { int rowIndex = rows.indexOf(row); - Map map = new HashMap(); + Map map = new HashMap<>(); for (int colIndex = 0; colIndex < matrix[rowIndex].length; colIndex++) { map.put(cols.get(colIndex), matrix[rowIndex][colIndex]); } @@ -226,7 +226,7 @@ public Map getRow(AminoAcidCompound row) { @Override public Map getColumn(AminoAcidCompound column) { int colIndex = cols.indexOf(column); - Map map = new HashMap(); + Map map = new HashMap<>(); for (int i = 0; i < matrix.length; i++) { map.put(rows.get(i), matrix[i][colIndex]); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java index 8eb897219e..9da982dbf1 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java @@ -57,7 +57,7 @@ public class SimpleSubstitutionMatrix implements Substitutio private List rows, cols; public static SubstitutionMatrix getBlosum62() { - return new SimpleSubstitutionMatrix(AminoAcidCompoundSet.getAminoAcidCompoundSet(), new InputStreamReader( + return new SimpleSubstitutionMatrix<>(AminoAcidCompoundSet.getAminoAcidCompoundSet(), new InputStreamReader( SimpleSubstitutionMatrix.class.getResourceAsStream("/matrices/blosum62.txt")), "blosum62"); } @@ -126,10 +126,10 @@ private SimpleSubstitutionMatrix(CompoundSet compoundSet, Scanner input, Stri this.name = name; max = Short.MIN_VALUE; min = Short.MAX_VALUE; - rows = new ArrayList(); - cols = new ArrayList(); + rows = new ArrayList<>(); + cols = new ArrayList<>(); StringBuilder descriptionIn = new StringBuilder(); - List matrixIn = new ArrayList(); + List matrixIn = new ArrayList<>(); while(input.hasNextLine()) { String line = input.nextLine(); if (line.startsWith(comment)) { @@ -288,7 +288,7 @@ public String toString() { @Override public Map getRow(C row) { int rowIndex = rows.indexOf(row); - Map map = new HashMap(); + Map map = new HashMap<>(); for (int colIndex = 0; colIndex < matrix[rowIndex].length; colIndex++) { map.put(cols.get(colIndex), matrix[rowIndex][colIndex]); } @@ -298,7 +298,7 @@ public Map getRow(C row) { @Override public Map getColumn(C column) { int colIndex = cols.indexOf(column); - Map map = new HashMap(); + Map map = new HashMap<>(); for (int i = 0; i < matrix.length; i++) { map.put(rows.get(i), matrix[i][colIndex]); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java index ca93b1818f..3f55a3897a 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java @@ -50,9 +50,9 @@ public class SubstitutionMatrixHelper implements Serializable { private static final long serialVersionUID = 148491724604653225L; private static Map> aminoAcidMatrices = - new HashMap>(); + new HashMap<>(); private static Map> nucleotideMatrices = - new HashMap>(); + new HashMap<>(); // prevents instantiation private SubstitutionMatrixHelper() { } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java index 8245c635c3..7a27828feb 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java @@ -120,7 +120,7 @@ public SequencePair getAlignment(){ alignedQuery = new SimpleAlignedSequence(getSequence(hspQseq), getAlignmentsSteps(hspQseq)); alignedHit = new SimpleAlignedSequence(getSequence(hspHseq), getAlignmentsSteps(hspHseq)); - returnAln = new SimpleSequencePair(alignedQuery, alignedHit); + returnAln = new SimpleSequencePair<>(alignedQuery, alignedHit); return returnAln; } @@ -145,7 +145,7 @@ else if (sequenceString.matches("^[ACUG]+$")) } private List getAlignmentsSteps(String gappedSequenceString){ - List returnList = new ArrayList(); + List returnList = new ArrayList<>(); for (char c: gappedSequenceString.toCharArray()){ if (c=='-') returnList.add(Step.GAP); else returnList.add(Step.COMPOUND); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java index 52654720d9..d10717ee9e 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java @@ -140,7 +140,7 @@ public void writeResults() throws IOException, ParseException { */ private ResultFactory guessFactory(File f){ if (extensionFactoryAssociation == null){ - extensionFactoryAssociation = new HashMap(); + extensionFactoryAssociation = new HashMap<>(); ServiceLoader impl = ServiceLoader.load(ResultFactory.class); for (ResultFactory loadedImpl : impl) { List fileExtensions = loadedImpl.getFileExtensions(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java index b4593e8135..be3d2f81f1 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java @@ -71,7 +71,7 @@ private enum PARSING_CONSISTENCY { // data imported private: int queryIdNumber = 0; - HashMap queryIdMapping = new HashMap(); + HashMap queryIdMapping = new HashMap<>(); String programName=null, queryName = null, databaseFile = null; private String queryId ; private String subjectId ; @@ -89,7 +89,7 @@ private enum PARSING_CONSISTENCY { @Override public List getFileExtensions() { - List l = new ArrayList(); + List l = new ArrayList<>(); l.add("blasttabular"); l.add("blasttxt"); return l; @@ -102,7 +102,7 @@ public void setFile(File f) { @Override public List createObjects(double maxEScore) throws IOException, ParseException { - List results = new ArrayList(); + List results = new ArrayList<>(); log.info("Query for hits"); LineNumberReader lnr = new LineNumberReader(new FileReader(targetFile)); @@ -126,13 +126,13 @@ public List createObjects(double maxEScore) throws IOException, ParseExc .setQueryDef(queryName) .setReference(blastReference); - List hits = new ArrayList(); + List hits = new ArrayList<>(); String currentQueryId = queryId; while (currentQueryId.equals(queryId) && lineNumber < fileLinesCount){ BlastHitBuilder hitBuilder = new BlastHitBuilder(); - List hsps = new ArrayList(); + List hsps = new ArrayList<>(); String currentSubjectId=subjectId; while (currentSubjectId.equals(subjectId) && lineNumber < fileLinesCount){ diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java index 9d93f5b325..7714f44749 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java @@ -105,7 +105,7 @@ public List createObjects(double maxEScore) throws IOException, ParseExc ArrayList IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]"); logger.info(IterationsList.size() + " results"); - resultsCollection = new ArrayList(); + resultsCollection = new ArrayList<>(); for (Element element : IterationsList) { BlastResultBuilder resultBuilder = new BlastResultBuilder(); // will add BlastOutput* key sections in the result object @@ -131,7 +131,7 @@ public List createObjects(double maxEScore) throws IOException, ParseExc Element iterationHitsElement = XMLHelper.selectSingleElement(element, "Iteration_hits"); ArrayList hitList = XMLHelper.selectElements(iterationHitsElement, "Hit"); - hitsCollection = new ArrayList(); + hitsCollection = new ArrayList<>(); for (Element hitElement : hitList) { BlastHitBuilder blastHitBuilder = new BlastHitBuilder(); blastHitBuilder @@ -148,7 +148,7 @@ public List createObjects(double maxEScore) throws IOException, ParseExc Element hithspsElement = XMLHelper.selectSingleElement(hitElement, "Hit_hsps"); ArrayList hspList = XMLHelper.selectElements(hithspsElement, "Hsp"); - hspsCollection = new ArrayList(); + hspsCollection = new ArrayList<>(); for (Element hspElement : hspList) { Double evalue = Double.valueOf(XMLHelper.selectSingleElement(hspElement, "Hsp_evalue").getTextContent()); @@ -195,7 +195,7 @@ public List createObjects(double maxEScore) throws IOException, ParseExc @Override public List getFileExtensions(){ - ArrayList extensions = new ArrayList(1); + ArrayList extensions = new ArrayList<>(1); extensions.add("blastxml"); return extensions; } @@ -215,7 +215,7 @@ public void setDatabaseReferences(List sequences) { */ private void mapIds() { if (queryReferences != null) { - queryReferencesMap = new HashMap(queryReferences.size()); + queryReferencesMap = new HashMap<>(queryReferences.size()); for (int counter=0; counter < queryReferences.size() ; counter ++){ String id = "Query_"+(counter+1); queryReferencesMap.put(id, queryReferences.get(counter)); @@ -223,7 +223,7 @@ private void mapIds() { } if (databaseReferences != null) { - databaseReferencesMap = new HashMap(databaseReferences.size()); + databaseReferencesMap = new HashMap<>(databaseReferences.size()); for (int counter=0; counter < databaseReferences.size() ; counter ++){ // this is strange: while Query_id are 1 based, Hit (database) id are 0 based String id = "gnl|BL_ORD_ID|"+(counter); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java index 8b16c66472..8b11fa0b63 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java @@ -37,7 +37,7 @@ public class ChromosomeSequence extends DNASequence { private int chromosomeNumber; - private LinkedHashMap geneSequenceHashMap = new LinkedHashMap(); + private LinkedHashMap geneSequenceHashMap = new LinkedHashMap<>(); /** * Empty constructor used by tools that need a proper Bean that allows the actual diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java index 215e3c8a26..08352cb009 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DNASequence.java @@ -136,14 +136,14 @@ public int getGCCount() { * Returns a Sequence which runs in the current reverse order */ public SequenceView getReverse() { - return new ReversedSequenceView(this); + return new ReversedSequenceView<>(this); } /** * Returns a Sequence which will complement every base */ public SequenceView getComplement() { - return new ComplementSequenceView(this); + return new ComplementSequenceView<>(this); } /** diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java index 34f1ec3986..ed6f635611 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java @@ -41,11 +41,11 @@ public class GeneSequence extends DNASequence { private final static Logger logger = LoggerFactory.getLogger(GeneSequence.class); - private final LinkedHashMap transcriptSequenceHashMap = new LinkedHashMap(); - private final LinkedHashMap intronSequenceHashMap = new LinkedHashMap(); - private final LinkedHashMap exonSequenceHashMap = new LinkedHashMap(); - private final ArrayList intronSequenceList = new ArrayList(); - private final ArrayList exonSequenceList = new ArrayList(); + private final LinkedHashMap transcriptSequenceHashMap = new LinkedHashMap<>(); + private final LinkedHashMap intronSequenceHashMap = new LinkedHashMap<>(); + private final LinkedHashMap exonSequenceHashMap = new LinkedHashMap<>(); + private final ArrayList intronSequenceList = new ArrayList<>(); + private final ArrayList exonSequenceList = new ArrayList<>(); boolean intronAdded = false; // need to deal with the problem that typically introns are not added when validating the list and adding in introns as the regions not included in exons private Strand strand = Strand.UNDEFINED; private ChromosomeSequence chromosomeSequence; diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java index a0fb3a37bc..47355db090 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java @@ -42,7 +42,7 @@ */ public class MultipleSequenceAlignment, C extends Compound> implements LightweightProfile { - private List sequences = new ArrayList(); + private List sequences = new ArrayList<>(); private Integer length = null; /** @@ -98,7 +98,7 @@ public List getAlignedSequences() { */ @Override public List getCompoundsAt(int alignmentIndex) { - List column = new ArrayList(); + List column = new ArrayList<>(); for (S s : sequences) { column.add(s.getCompoundAt(alignmentIndex)); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java index 2e44cd12c7..4248bc908c 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java @@ -160,7 +160,7 @@ private DNASequence getRawParentSequence(String accessId) throws IOException { InputStream is = url.openConnection().getInputStream(); FastaReader parentReader - = new FastaReader(is, + = new FastaReader<>(is, new PlainFastaHeaderParser(), new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet())); LinkedHashMap seq = parentReader.process(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java index 83e50474bd..460ca6ab45 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java @@ -41,8 +41,8 @@ public class TranscriptSequence extends DNASequence { private final static Logger logger = LoggerFactory.getLogger(TranscriptSequence.class); - private final ArrayList cdsSequenceList = new ArrayList(); - private final LinkedHashMap cdsSequenceHashMap = new LinkedHashMap(); + private final ArrayList cdsSequenceList = new ArrayList<>(); + private final LinkedHashMap cdsSequenceHashMap = new LinkedHashMap<>(); private StartCodonSequence startCodonSequence = null; private StopCodonSequence stopCodonSequence = null; private GeneSequence parentGeneSequence = null; @@ -153,7 +153,7 @@ public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase) * @return */ public ArrayList getProteinCDSSequences() { - ArrayList proteinSequenceList = new ArrayList(); + ArrayList proteinSequenceList = new ArrayList<>(); for (int i = 0; i < cdsSequenceList.size(); i++) { CDSSequence cdsSequence = cdsSequenceList.get(i); String codingSequence = cdsSequence.getCodingSequence(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java index 8252f27198..82546b5a56 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java @@ -44,11 +44,11 @@ public class AminoAcidCompoundSet implements CompoundSet, Ser * */ private static final long serialVersionUID = 4000344194364133456L; - private final Map aminoAcidCompoundCache = new HashMap(); - private final Map aminoAcidCompoundCache3Letter = new HashMap(); + private final Map aminoAcidCompoundCache = new HashMap<>(); + private final Map aminoAcidCompoundCache3Letter = new HashMap<>(); private final Map> equivalentsCache = - new HashMap>(); + new HashMap<>(); public AminoAcidCompoundSet() { aminoAcidCompoundCache.put("A", new AminoAcidCompound(this, "A", "Ala", "Alanine", 71.0788f)); @@ -154,7 +154,7 @@ public Set getEquivalentCompounds(AminoAcidCompound compound) addAmbiguousEquivalents("I", "L", "J"); // ambiguous gaps AminoAcidCompound gap1, gap2, gap3; - Set gaps = new HashSet(); + Set gaps = new HashSet<>(); gaps.add(gap1 = aminoAcidCompoundCache.get("-")); gaps.add(gap2 = aminoAcidCompoundCache.get(".")); gaps.add(gap3 = aminoAcidCompoundCache.get("_")); @@ -172,18 +172,18 @@ private void addAmbiguousEquivalents(String one, String two, String either) { Set equivalents; AminoAcidCompound cOne, cTwo, cEither; - equivalents = new HashSet(); + equivalents = new HashSet<>(); equivalents.add(cOne = aminoAcidCompoundCache.get(one)); equivalents.add(cTwo = aminoAcidCompoundCache.get(two)); equivalents.add(cEither = aminoAcidCompoundCache.get(either)); equivalentsCache.put(cEither, equivalents); - equivalents = new HashSet(); + equivalents = new HashSet<>(); equivalents.add(cOne); equivalents.add(cEither); equivalentsCache.put(cOne, equivalents); - equivalents = new HashSet(); + equivalents = new HashSet<>(); equivalents.add(cTwo); equivalents.add(cEither); equivalentsCache.put(cTwo, equivalents); @@ -206,7 +206,7 @@ public boolean isValidSequence(Sequence sequence) { @Override public List getAllCompounds() { - return new ArrayList(aminoAcidCompoundCache.values()); + return new ArrayList<>(aminoAcidCompoundCache.values()); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java index 19923effed..edf891c4f7 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java @@ -78,13 +78,13 @@ public static abstract class AbstractEdit implements Edit @Override public Sequence edit(Sequence editingSequence) { Sequence targetSequence = getTargetSequence(editingSequence); - List> sequences = new ArrayList>(); + List> sequences = new ArrayList<>(); sequences.add(getFivePrime(editingSequence)); sequences.add(targetSequence); sequences.add(getThreePrime(editingSequence)); - return new JoiningSequenceReader(sequences); + return new JoiningSequenceReader<>(sequences); } private int start = -1; private int end = -1; @@ -119,7 +119,7 @@ protected void setSequence(Sequence sequence) { public Sequence getTargetSequence(Sequence editingSequence) { if (sequence == null && stringSequence != null) { try { - sequence = new BasicSequence( + sequence = new BasicSequence<>( stringSequence, editingSequence.getCompoundSet()); } catch (CompoundNotFoundException e) { // TODO is there a better way to handle this exception? @@ -136,7 +136,7 @@ public Sequence getTargetSequence(Sequence editingSequence) { protected Sequence getEmptySequence(Sequence editingSequence) { Sequence s = null; try { - s = new BasicSequence("", editingSequence.getCompoundSet()); + s = new BasicSequence<>("", editingSequence.getCompoundSet()); } catch (CompoundNotFoundException e) { // should not happen logger.error("Could not construct empty sequence. {}. This is most likely a bug.", e.getMessage()); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java index d601c573b0..16e894697c 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java @@ -40,7 +40,7 @@ */ public abstract class AbstractFeature, C extends Compound> implements FeatureInterface { - List> childrenFeatures = new ArrayList>(); + List> childrenFeatures = new ArrayList<>(); FeatureInterface parentFeature; AbstractLocation sequenceLocation; String type = ""; @@ -48,7 +48,7 @@ public abstract class AbstractFeature, C extends C private String description = ""; private String shortDescription = ""; private Object userObject = null; - private Map> Qualifiers = new HashMap>(); + private Map> Qualifiers = new HashMap<>(); /** * A feature has a type and a source @@ -292,7 +292,7 @@ public void addQualifier(String key, Qualifier qualifier) { vals.add(qualifier); Qualifiers.put(key, vals); } else { - List vals = new ArrayList(); + List vals = new ArrayList<>(); vals.add(qualifier); Qualifiers.put(key, vals); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java index fc9f7fc8f6..0d2ff2de9a 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java @@ -37,7 +37,7 @@ * @author Paolo Pavan */ public class DBReferenceInfo extends Qualifier { - private LinkedHashMap properties = new LinkedHashMap(); + private LinkedHashMap properties = new LinkedHashMap<>(); private String database = ""; private String id = ""; diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java index c270cc74e7..3b49341d22 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java @@ -46,11 +46,11 @@ public class FeatureDbReferenceInfo, C extends Com private AbstractLocation location; private FeatureInterface parentFeature; - private List> childrenFeatures = new ArrayList>(); + private List> childrenFeatures = new ArrayList<>(); private String description = ""; private String shortDescription = ""; private Object userObject; - private Map> qualifiers = new HashMap>(); + private Map> qualifiers = new HashMap<>(); public FeatureDbReferenceInfo(String database, String id) { @@ -150,7 +150,7 @@ public void setQualifiers(Map> qualifiers) { @Override public void addQualifier(String key, Qualifier qualifier) { if (qualifiers == null) { - qualifiers = new HashMap>(); + qualifiers = new HashMap<>(); } // Check for key. Update list of values if (qualifiers.containsKey(key)){ @@ -158,7 +158,7 @@ public void addQualifier(String key, Qualifier qualifier) { vals.add(qualifier); qualifiers.put(key, vals); } else { - List vals = new ArrayList(); + List vals = new ArrayList<>(); vals.add(qualifier); qualifiers.put(key, vals); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java index 7eec33a62a..0e7da9a97b 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QualityFeature.java @@ -37,7 +37,7 @@ */ public class QualityFeature, C extends Compound> extends AbstractFeature { - private List qualities = new ArrayList(); + private List qualities = new ArrayList<>(); /** * @param type diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java index bce00e2729..524bdfdaa3 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java @@ -35,7 +35,7 @@ */ public class QuantityFeature, C extends Compound> extends AbstractFeature { - private List quantities = new ArrayList(); + private List quantities = new ArrayList<>(); /** * diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java index 1a6c20eba1..94b2a6d918 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java @@ -90,7 +90,7 @@ public AbstractSequence getSequence(String sequence, public AbstractSequence getSequence( List list) { AbstractSequence seq =super.getSequence(list); - Collection strCase = new ArrayList(seq.getLength()); + Collection strCase = new ArrayList<>(seq.getLength()); for(int i=0;i getSequence( * This list contains only Booleans. */ private static List getStringCase(String str) { - List types = new ArrayList(str.length()); + List types = new ArrayList<>(str.length()); for(int i=0;i getSequence( @Override public AbstractSequence getSequence( List list) { - ArrayListProxySequenceReader store = new ArrayListProxySequenceReader(); + ArrayListProxySequenceReader store = new ArrayListProxySequenceReader<>(); store.setCompoundSet(compoundSet); store.setContents(list); return new DNASequence(store); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java index d7c4bde215..bdcc197f7e 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java @@ -148,7 +148,7 @@ public LinkedHashMap process(int max) throws IOException { boolean keepGoing = true; - LinkedHashMap sequences = new LinkedHashMap(); + LinkedHashMap sequences = new LinkedHashMap<>(); do { line = line.trim(); // nice to have but probably not needed diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java index e250a8d4f9..d185a6f062 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java @@ -57,7 +57,7 @@ public static LinkedHashMap readFastaDNASequence(File file, } FastaReader fastaProxyReader = - new FastaReader( + new FastaReader<>( file, new GenericFastaHeaderParser(), new FileProxyDNASequenceCreator( @@ -85,7 +85,7 @@ public static LinkedHashMap readFastaRNASequence(File file, } FastaReader fastaProxyReader = - new FastaReader( + new FastaReader<>( file, new GenericFastaHeaderParser(), new FileProxyRNASequenceCreator( @@ -124,7 +124,7 @@ public static LinkedHashMap readFastaProteinSequence( */ public static LinkedHashMap readFastaProteinSequence( InputStream inStream) throws IOException { - FastaReader fastaReader = new FastaReader( + FastaReader fastaReader = new FastaReader<>( inStream, new GenericFastaHeaderParser(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())); @@ -139,7 +139,7 @@ public static LinkedHashMap readFastaProteinSequence( */ public static LinkedHashMap readFastaDNASequence( InputStream inStream) throws IOException { - FastaReader fastaReader = new FastaReader( + FastaReader fastaReader = new FastaReader<>( inStream, new GenericFastaHeaderParser(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())); @@ -168,7 +168,7 @@ public static LinkedHashMap readFastaDNASequence( */ public static LinkedHashMap readFastaRNASequence( InputStream inStream) throws IOException { - FastaReader fastaReader = new FastaReader( + FastaReader fastaReader = new FastaReader<>( inStream, new GenericFastaHeaderParser(), new RNASequenceCreator(RNACompoundSet.getRNACompoundSet())); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java index 966d723728..dfeae8a642 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java @@ -71,7 +71,7 @@ public static void writeProteinSequence(File file, public static void writeProteinSequence(OutputStream outputStream, Collection proteinSequences) throws Exception { - FastaWriter fastaWriter = new FastaWriter( + FastaWriter fastaWriter = new FastaWriter<>( outputStream, proteinSequences, new GenericFastaHeaderFormat()); fastaWriter.process(); @@ -132,7 +132,7 @@ public static void writeNucleotideSequence(File file, Collection dn */ public static void writeNucleotideSequence(OutputStream outputStream, Collection dnaSequences) throws Exception { - FastaWriter fastaWriter = new FastaWriter( + FastaWriter fastaWriter = new FastaWriter<>( outputStream, dnaSequences, new GenericFastaHeaderFormat()); fastaWriter.process(); @@ -170,7 +170,7 @@ public static void writeSequence(OutputStream outputStream, Sequence sequence */ private static Collection> singleSeqToCollection(Sequence sequence) { - Collection> sequences = new ArrayList>(); + Collection> sequences = new ArrayList<>(); sequences.add(sequence); return sequences; } @@ -199,7 +199,7 @@ public String getHeader(Sequence sequence) { }; FastaWriter, Compound> fastaWriter = - new FastaWriter, Compound>(outputStream, + new FastaWriter<>(outputStream, sequences, fhfi); fastaWriter.process(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java index fb89f1c4e3..21b0699ab6 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java @@ -78,7 +78,7 @@ public FileProxyDNASequenceCreator(File file, */ @Override public AbstractSequence getSequence(String sequence, long index ) throws CompoundNotFoundException, IOException { - SequenceFileProxyLoader sequenceFileProxyLoader = new SequenceFileProxyLoader( + SequenceFileProxyLoader sequenceFileProxyLoader = new SequenceFileProxyLoader<>( file, sequenceParser, index, diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java index 7db550683f..e45907a2ed 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java @@ -76,7 +76,7 @@ public FileProxyProteinSequenceCreator(File file, CompoundSet @Override public AbstractSequence getSequence(String sequence, long index) throws CompoundNotFoundException, IOException { SequenceFileProxyLoader sequenceFileProxyLoader = - new SequenceFileProxyLoader( + new SequenceFileProxyLoader<>( file, sequenceParser, index, diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java index 4be68696fb..58fe3f98d7 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java @@ -78,7 +78,7 @@ public FileProxyRNASequenceCreator(File file, */ @Override public AbstractSequence getSequence(String sequence, long index ) throws CompoundNotFoundException, IOException { - SequenceFileProxyLoader sequenceFileProxyLoader = new SequenceFileProxyLoader( + SequenceFileProxyLoader sequenceFileProxyLoader = new SequenceFileProxyLoader<>( file, sequenceParser, index, diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java index 638e570cc5..2a1d30f146 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java @@ -61,7 +61,7 @@ public static LinkedHashMap readGenbankDNASequence(File fil } GenbankReader GenbankProxyReader = - new GenbankReader( + new GenbankReader<>( file, new GenericGenbankHeaderParser(), new FileProxyDNASequenceCreator( @@ -89,7 +89,7 @@ public static LinkedHashMap readGenbankProteinSequence( } GenbankReader GenbankProxyReader = - new GenbankReader( + new GenbankReader<>( file, new GenericGenbankHeaderParser(), new FileProxyProteinSequenceCreator( @@ -117,7 +117,7 @@ public static LinkedHashMap readGenbankRNASequence(File fil } GenbankReader GenbankProxyReader = - new GenbankReader( + new GenbankReader<>( file, new GenericGenbankHeaderParser(), new FileProxyRNASequenceCreator( @@ -156,7 +156,7 @@ public static LinkedHashMap readGenbankProteinSequence( */ public static LinkedHashMap readGenbankProteinSequence( InputStream inStream) throws Exception { - GenbankReader GenbankReader = new GenbankReader( + GenbankReader GenbankReader = new GenbankReader<>( inStream, new GenericGenbankHeaderParser(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())); @@ -171,7 +171,7 @@ public static LinkedHashMap readGenbankProteinSequence( */ public static LinkedHashMap readGenbankDNASequence( InputStream inStream) throws Exception { - GenbankReader GenbankReader = new GenbankReader( + GenbankReader GenbankReader = new GenbankReader<>( inStream, new GenericGenbankHeaderParser(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())); @@ -199,7 +199,7 @@ public static LinkedHashMap readGenbankDNASequence( */ public static LinkedHashMap readGenbankRNASequence( InputStream inStream) throws Exception { - GenbankReader GenbankReader = new GenbankReader( + GenbankReader GenbankReader = new GenbankReader<>( inStream, new GenericGenbankHeaderParser(), new RNASequenceCreator(RNACompoundSet.getRNACompoundSet())); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java index a0ba83aec0..97cfe557ad 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.java @@ -76,7 +76,7 @@ public static void writeProteinSequence(File file, public static void writeProteinSequence(OutputStream outputStream, Collection proteinSequences) throws Exception { - GenbankWriter genbankWriter = new GenbankWriter( + GenbankWriter genbankWriter = new GenbankWriter<>( outputStream, proteinSequences, new GenericGenbankHeaderFormat()); @@ -126,10 +126,10 @@ public static void writeNucleotideSequence(OutputStream outputStream, public static void writeNucleotideSequence(OutputStream outputStream, Collection dnaSequences, String seqType) throws Exception { - GenericGenbankHeaderFormat genericGenbankHeaderFormat = new GenericGenbankHeaderFormat( + GenericGenbankHeaderFormat genericGenbankHeaderFormat = new GenericGenbankHeaderFormat<>( seqType); // genericGenbankHeaderFormat.setLineSeparator(lineSep); - GenbankWriter genbankWriter = new GenbankWriter( + GenbankWriter genbankWriter = new GenbankWriter<>( outputStream, dnaSequences, genericGenbankHeaderFormat); // genbankWriter.setLineSeparator(lineSep); genbankWriter.process(); @@ -146,9 +146,9 @@ public static void writeNucleotideSequence(OutputStream outputStream, public static void writeNucleotideSequenceOriginal(OutputStream outputStream, Collection dnaSequences) throws Exception { - GenericGenbankHeaderFormat genericGenbankHeaderFormat = new GenericGenbankHeaderFormat( + GenericGenbankHeaderFormat genericGenbankHeaderFormat = new GenericGenbankHeaderFormat<>( true); - GenbankWriter genbankWriter = new GenbankWriter( + GenbankWriter genbankWriter = new GenbankWriter<>( outputStream, dnaSequences, genericGenbankHeaderFormat); genbankWriter.process(); } @@ -189,7 +189,7 @@ public static void writeSequence(OutputStream outputStream, private static Collection> singleSeqToCollection( Sequence sequence) { - Collection> sequences = new ArrayList>(); + Collection> sequences = new ArrayList<>(); sequences.add(sequence); return sequences; } @@ -219,7 +219,7 @@ public String getHeader(Sequence sequence) { ; }; - GenbankWriter, Compound> genbankWriter = new GenbankWriter, Compound>( + GenbankWriter, Compound> genbankWriter = new GenbankWriter<>( outputStream, sequences, fhfi); genbankWriter.process(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java index 9acaf1d25c..d44468d554 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java @@ -71,7 +71,7 @@ public class GenericFastaHeaderParser, C extends C */ private String[] getHeaderValues(String header) { String[] data = new String[0]; - ArrayList values = new ArrayList(); + ArrayList values = new ArrayList<>(); StringBuffer sb = new StringBuffer(); //commented out 1/11/2012 to resolve an issue where headers do contain a length= at the end that are not recognized //if(header.indexOf("length=") != -1){ diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java index 9542710488..71e5f9379d 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java @@ -208,7 +208,7 @@ private String _insdc_feature_location_string(FeatureInterface locations = new ArrayList(); + ArrayList locations = new ArrayList<>(); for(Location l : feature.getLocations().getSubLocations()) { locations.add(_insdc_location_string_ignoring_strand_and_subfeatures((AbstractLocation) l, record_length)); } @@ -223,7 +223,7 @@ private String _insdc_feature_location_string(FeatureInterface locations = new ArrayList(); + ArrayList locations = new ArrayList<>(); for(Location l : feature.getLocations().getSubLocations()) { locations.add(_insdc_location_string_ignoring_strand_and_subfeatures((AbstractLocation) l, record_length)); } @@ -248,7 +248,7 @@ private String _insdc_feature_location_string(FeatureInterface locations = new ArrayList(); + ArrayList locations = new ArrayList<>(); for(FeatureInterface, C> f : feature.getChildrenFeatures()) { locations.add(_insdc_location_string_ignoring_strand_and_subfeatures(f.getLocations(), record_length)); } @@ -261,7 +261,7 @@ private String _insdc_feature_location_string(FeatureInterface locations = new ArrayList(); + ArrayList locations = new ArrayList<>(); for(FeatureInterface, C> f : feature.getChildrenFeatures()) { locations.add(_insdc_location_string_ignoring_strand_and_subfeatures(f.getLocations(), record_length)); } @@ -406,14 +406,14 @@ raise ValueError("Expected a SeqFeature position object.") */ protected ArrayList _split_multi_line(String text, int max_len) { // TODO Auto-generated method stub - ArrayList output = new ArrayList(); + ArrayList output = new ArrayList<>(); text = text.trim(); if(text.length() <= max_len) { output.add(text); return output; } - ArrayList words = new ArrayList(); + ArrayList words = new ArrayList<>(); Collections.addAll(words, text.split("\\s+")); while(!words.isEmpty()) { text = words.remove(0); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java index 96ff94ebfd..0f9b3ca950 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java @@ -134,8 +134,8 @@ public IUPACTable getTable(Integer id) { private void populateLookups() { if(nameLookup == null) { - nameLookup = new HashMap(); - idLookup = new HashMap(); + nameLookup = new HashMap<>(); + idLookup = new HashMap<>(); for(IUPACTable t: getTables()) { nameLookup.put(t.getName(), t); idLookup.put(t.getId(), t); @@ -144,7 +144,7 @@ private void populateLookups() { } private List parseTables() { - List localTables = new ArrayList(); + List localTables = new ArrayList<>(); List lines = IOUtils.getList(is); Integer id = null; String name, aa, starts, baseone, basetwo, basethree; @@ -198,7 +198,7 @@ public static class IUPACTable implements Table { private final String baseTwo; private final String baseThree; - private final List codons = new ArrayList(); + private final List codons = new ArrayList<>(); private CompoundSet compounds = null; public IUPACTable(String name, int id, String aminoAcidString, @@ -328,7 +328,7 @@ public CompoundSet getCodonCompoundSet( } private List> codonStrings() { - List> codons = new ArrayList>(); + List> codons = new ArrayList<>(); for (int i = 0; i < baseOne.length(); i++) { List codon = Arrays.asList(Character .toString(baseOne.charAt(i)), @@ -348,7 +348,7 @@ private List startCodons() { } private List split(String string) { - List split = new ArrayList(); + List split = new ArrayList<>(); for (int i = 0; i < string.length(); i++) { split.add(Character.toString(string.charAt(i))); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java index c40e3efa2a..1efebed609 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java @@ -70,7 +70,7 @@ public AbstractSequence getSequence(String sequence, @Override public AbstractSequence getSequence( List list) { - ArrayListProxySequenceReader store = new ArrayListProxySequenceReader(); + ArrayListProxySequenceReader store = new ArrayListProxySequenceReader<>(); store.setCompoundSet(compoundSet); store.setContents(list); return new ProteinSequence(store); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java index 96abe9cd35..0a691f1afa 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java @@ -78,7 +78,7 @@ public AbstractSequence getSequence( @Override public AbstractSequence getSequence(List list) { ArrayListProxySequenceReader store = - new ArrayListProxySequenceReader(); + new ArrayListProxySequenceReader<>(); store.setCompoundSet(compoundSet); store.setContents(list); return new RNASequence(store); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java index 4f807c5799..b60bc9eb00 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java @@ -110,7 +110,7 @@ public static void processReader(BufferedReader br, ReaderProcessor processor) { * @throws ParserException Can throw this if we cannot parse the given reader */ public static List getList(BufferedReader br) { - final List list = new ArrayList(); + final List list = new ArrayList<>(); processReader(br, new ReaderProcessor() { @Override public void process(String line) { diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java index 006827f321..d3e6c52661 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java @@ -74,7 +74,7 @@ public GenbankProxySequenceReader( String db = compoundSet instanceof AminoAcidCompoundSet ? "protein" : "nuccore"; InputStream inStream = getBufferedInputStream(accessionID, db); - genbankParser = new GenbankSequenceParser, C>(); + genbankParser = new GenbankSequenceParser<>(); setContents(genbankParser.getSequence(new BufferedReader(new InputStreamReader(inStream)), 0)); headerParser = genbankParser.getSequenceHeaderParser(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java index fa7d81f4e9..61df84f46d 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java @@ -57,7 +57,7 @@ public class SequenceFileProxyLoader implements ProxySequenc SequenceParserInterface sequenceParser; private CompoundSet compoundSet; - private List parsedCompounds = new ArrayList(); + private List parsedCompounds = new ArrayList<>(); File file; long sequenceStartIndex = -1; int sequenceLength = -1; @@ -204,7 +204,7 @@ public String getSequenceAsString() { */ public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand) { - SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper(); + SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper<>(); return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, bioBegin, bioEnd, strand); } @@ -260,7 +260,7 @@ public int hashCode(){ @Override public SequenceView getSubSequence(final Integer bioBegin, final Integer bioEnd) { - return new SequenceProxyView(SequenceFileProxyLoader.this, bioBegin, bioEnd); + return new SequenceProxyView<>(SequenceFileProxyLoader.this, bioBegin, bioEnd); } /** diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java index 57c793ddc1..7ae1fa1632 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java @@ -46,7 +46,7 @@ public class StringProxySequenceReader implements ProxySeque private String sequence; private CompoundSet compoundSet; - private List parsedCompounds = new ArrayList(); + private List parsedCompounds = new ArrayList<>(); public StringProxySequenceReader() {} @@ -126,13 +126,13 @@ public List getAsList() { public String getSequenceAsString(Integer bioBegin, Integer bioEnd,Strand strand) { - SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper(); + SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper<>(); return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, bioBegin, bioEnd, strand); } @Override public SequenceView getSubSequence(final Integer bioBegin, final Integer bioEnd) { - return new SequenceProxyView(StringProxySequenceReader.this,bioBegin,bioEnd); + return new SequenceProxyView<>(StringProxySequenceReader.this,bioBegin,bioEnd); } @Override diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java index 4ca7204bbd..020fee4a97 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java @@ -79,7 +79,7 @@ public class UniprotProxySequenceReader implements ProxySequ private static String uniprotDirectoryCache = null; private String sequence; private CompoundSet compoundSet; - private List parsedCompounds = new ArrayList(); + private List parsedCompounds = new ArrayList<>(); Document uniprotDoc; /** @@ -125,7 +125,7 @@ public UniprotProxySequenceReader(Document document, CompoundSet compoundSet) public static UniprotProxySequenceReader parseUniprotXMLString(String xml, CompoundSet compoundSet) { try { Document document = XMLHelper.inputStreamToDocument(new ByteArrayInputStream(xml.getBytes())); - return new UniprotProxySequenceReader(document, compoundSet); + return new UniprotProxySequenceReader<>(document, compoundSet); } catch (Exception e) { logger.error("Exception on xml parse of: {}", xml); } @@ -281,7 +281,7 @@ public SequenceView getInverse() { * @return */ public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand) { - SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper(); + SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper<>(); return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, bioBegin, bioEnd, strand); } @@ -293,7 +293,7 @@ public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand stran */ @Override public SequenceView getSubSequence(final Integer bioBegin, final Integer bioEnd) { - return new SequenceProxyView(UniprotProxySequenceReader.this, bioBegin, bioEnd); + return new SequenceProxyView<>(UniprotProxySequenceReader.this, bioBegin, bioEnd); } /** @@ -341,7 +341,7 @@ public AccessionID getAccession() { * @throws XPathExpressionException */ public ArrayList getAccessions() throws XPathExpressionException { - ArrayList accessionList = new ArrayList(); + ArrayList accessionList = new ArrayList<>(); if (uniprotDoc == null) { return accessionList; } @@ -373,7 +373,7 @@ public ArrayList getAliases() throws XPathExpressionException { * @throws XPathExpressionException */ public ArrayList getProteinAliases() throws XPathExpressionException { - ArrayList aliasList = new ArrayList(); + ArrayList aliasList = new ArrayList<>(); if (uniprotDoc == null) { return aliasList; } @@ -476,7 +476,7 @@ private void getProteinAliasesFromElement(ArrayList aliasList, Element e * @throws XPathExpressionException */ public ArrayList getGeneAliases() throws XPathExpressionException { - ArrayList aliasList = new ArrayList(); + ArrayList aliasList = new ArrayList<>(); if (uniprotDoc == null) { return aliasList; } @@ -609,7 +609,7 @@ private StringBuilder fetchUniprotXML(String uniprotURL) StringBuilder sb = new StringBuilder(); URL uniprot = new URL(uniprotURL); int attempt = 5; - List errorCodes = new ArrayList(); + List errorCodes = new ArrayList<>(); while(attempt > 0) { HttpURLConnection uniprotConnection = openURLConnection(uniprot); int statusCode = uniprotConnection.getResponseCode(); @@ -775,7 +775,7 @@ public String getOrganismName() { */ @Override public ArrayList getKeyWords() { - ArrayList keyWordsList = new ArrayList(); + ArrayList keyWordsList = new ArrayList<>(); if (uniprotDoc == null) { return keyWordsList; } @@ -789,7 +789,7 @@ public ArrayList getKeyWords() { } } catch (XPathExpressionException e) { logger.error("Problems while parsing keywords in UniProt XML: {}. No keywords will be available.",e.getMessage()); - return new ArrayList(); + return new ArrayList<>(); } return keyWordsList; @@ -815,7 +815,7 @@ public Map> getDatabaseReferences() { String id = element.getAttribute("id"); List idlist = databaseReferencesHashMap.get(type); if (idlist == null) { - idlist = new ArrayList(); + idlist = new ArrayList<>(); databaseReferencesHashMap.put(type, idlist); } DBReferenceInfo dbreferenceInfo = new DBReferenceInfo(type, id); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java index f670783a0c..e49bd22216 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java @@ -153,7 +153,7 @@ public Location parse(String locationString) { private List parseLocationString(String string, int versus) { Matcher m; - List boundedLocationsCollection = new ArrayList(); + List boundedLocationsCollection = new ArrayList<>(); List tokens = splitString(string); for (String t : tokens) { @@ -272,7 +272,7 @@ private List parseLocationString(String string, int versus) { private List splitString(String input) { - List result = new ArrayList(); + List result = new ArrayList<>(); int start = 0; int openedParenthesis = 0; for (int current = 0; current < input.length(); current++) { diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java index efb02f6c64..d36d882c98 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java @@ -153,7 +153,7 @@ public static Location circularLocation(int start, int end, Strand strand, int l end = (length * (numberOfPasses + 1)) + modEnd; } - List locations = new ArrayList(); + List locations = new ArrayList<>(); locations.add(new SimpleLocation(modStart, length, strand)); for (int i = 0; i < numberOfPasses; i++) { locations.add(new SimpleLocation(1, length, strand)); @@ -283,7 +283,7 @@ public static boolean detectCicular(List subLocations) { * @return Returns a boolean indicating if this is consistently accessioned */ public static boolean consistentAccessions(List subLocations) { - Set set = new HashSet(); + Set set = new HashSet<>(); for(Location sub: subLocations) { set.add(sub.getAccession()); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java index efe1cc6d6f..03dcf54a74 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java @@ -224,7 +224,7 @@ public Iterator iterator() { list = getSubLocations(); } else { - list = new ArrayList(); + list = new ArrayList<>(); list.add(this); } return list.iterator(); @@ -245,7 +245,7 @@ public List getRelevantSubLocations() { * Here to allow for recursion */ private List getAllSubLocations(Location location) { - List flatSubLocations = new ArrayList(); + List flatSubLocations = new ArrayList<>(); for (Location l : location.getSubLocations()) { if (l.isComplex()) { flatSubLocations.addAll(getAllSubLocations(l)); @@ -312,11 +312,11 @@ public boolean isBetweenCompounds() { @Override public Sequence getSubSequence(Sequence sequence) { if(isCircular()) { - List> sequences = new ArrayList>(); + List> sequences = new ArrayList<>(); for(Location l: this) { sequences.add(l.getSubSequence(sequence)); } - return new JoiningSequenceReader(sequence.getCompoundSet(), sequences); + return new JoiningSequenceReader<>(sequence.getCompoundSet(), sequences); } return reverseSequence(sequence.getSubSequence( getStart().getPosition(), getEnd().getPosition())); @@ -328,11 +328,11 @@ public Sequence getSubSequence(Sequence sequence) { @Override public Sequence getRelevantSubSequence(Sequence sequence) { - List> sequences = new ArrayList>(); + List> sequences = new ArrayList<>(); for(Location l: getRelevantSubLocations()) { sequences.add(l.getSubSequence(sequence)); } - return new JoiningSequenceReader(sequence.getCompoundSet(), sequences); + return new JoiningSequenceReader<>(sequence.getCompoundSet(), sequences); } /** @@ -346,12 +346,12 @@ protected Sequence reverseSequence(Sequence sequence) return sequence; } - Sequence reversed = new ReversedSequenceView(sequence); + Sequence reversed = new ReversedSequenceView<>(sequence); // "safe" operation as we have tried to check this if(canComplement(sequence)) { Sequence casted = (Sequence) reversed; ComplementSequenceView complement = - new ComplementSequenceView(casted); + new ComplementSequenceView<>(casted); return (Sequence)complement; } return reversed; diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java index 25cdf48f05..b0887bf706 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java @@ -206,7 +206,7 @@ public static Location circularLocation(int start, int end, Strand strand, int l end = (length * (numberOfPasses + 1)) + modEnd; } - List locations = new ArrayList(); + List locations = new ArrayList<>(); locations.add(new SimpleLocation(modStart, length, strand)); for (int i = 0; i < numberOfPasses; i++) { locations.add(new SimpleLocation(1, length, strand)); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java index 48ecb8aff4..5e499261c1 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java @@ -44,7 +44,7 @@ public class ArrayListSequenceReader implements SequenceReader { private CompoundSet compoundSet; - private ArrayList parsedCompounds = new ArrayList(); + private ArrayList parsedCompounds = new ArrayList<>(); private volatile Integer hashcode = null; @@ -95,7 +95,7 @@ public String getSequenceAsString() { */ public String getSequenceAsString(Integer begin, Integer end, Strand strand) { // TODO Optimise/cache. - SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper(); + SequenceAsStringHelper sequenceAsStringHelper = new SequenceAsStringHelper<>(); return sequenceAsStringHelper.getSequenceAsString(this.parsedCompounds, compoundSet, begin, end, strand); } @@ -232,7 +232,7 @@ public void setContents(List list) { */ @Override public SequenceView getSubSequence(final Integer bioBegin, final Integer bioEnd) { - return new SequenceProxyView(ArrayListSequenceReader.this, bioBegin, bioEnd); + return new SequenceProxyView<>(ArrayListSequenceReader.this, bioBegin, bioEnd); } /** diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java index 83f4c5dfd2..49e4c2f8ec 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.java @@ -114,7 +114,7 @@ protected int compoundsPerDatatype() { @Override protected Map generateCompoundsToIndex() { final CompoundSet cs = getCompoundSet(); - Map map = new HashMap(); + Map map = new HashMap<>(); int index = 0; for (C currentCompound : sortedCompounds(cs)) { C upperCasedCompound = getOptionalUpperCasedCompound(currentCompound, cs); @@ -143,7 +143,7 @@ private C getOptionalUpperCasedCompound(C currentCompound, CompoundSet cs) { } private List sortedCompounds(final CompoundSet cs) { - List compounds = new ArrayList(cs.getAllCompounds()); + List compounds = new ArrayList<>(cs.getAllCompounds()); Collections.sort(compounds, new Comparator() { @@ -165,7 +165,7 @@ public int compare(C o1, C o2) { protected List generateIndexToCompounds() { CompoundSet cs = getCompoundSet(); Map lookup = getCompoundsToIndexLookup(); - Map tempMap = new HashMap(); + Map tempMap = new HashMap<>(); //First get the reverse lookup working for (C compound : lookup.keySet()) { C upperCasedCompound = getOptionalUpperCasedCompound(compound, cs); @@ -174,8 +174,8 @@ protected List generateIndexToCompounds() { } //Then populate the results by going back through the sorted integer keys - List compounds = new ArrayList(); - List keys = new ArrayList(tempMap.keySet()); + List compounds = new ArrayList<>(); + List keys = new ArrayList<>(tempMap.keySet()); Collections.sort(keys); for (Integer key : keys) { compounds.add(tempMap.get(key)); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java index a18d406d73..46a0501b8a 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java @@ -86,7 +86,7 @@ public JoiningSequenceReader(CompoundSet compoundSet, List> seque } private List> grepSequences(List> sequences) { - List> seqs = new ArrayList>(); + List> seqs = new ArrayList<>(); for (Sequence s : sequences) { if (s.getLength() != 0) { seqs.add(s); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java index 554b7b8361..b02c1e0c77 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java @@ -146,7 +146,7 @@ public List getAsList() { @Override public SequenceView getSubSequence(Integer start, Integer end) { - return new SequenceProxyView(this, start, end); + return new SequenceProxyView<>(this, start, end); } /** @@ -182,7 +182,7 @@ public int countCompounds(C... compounds) { @Override public Iterator iterator() { - return new SequenceMixin.SequenceIterator(this); + return new SequenceMixin.SequenceIterator<>(this); } @Override diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java index 1d739905d0..6384638557 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.java @@ -133,7 +133,7 @@ protected Map generateCompoundsToIndex() { @Override protected List generateIndexToCompounds() { CompoundSet cs = getCompoundSet(); - List result = new ArrayList(); + List result = new ArrayList<>(); result.add( cs.getCompoundForString("T")); result.add( cs.getCompoundForString("C")); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java index 579153a2fd..f7be44c572 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java @@ -39,11 +39,11 @@ public abstract class AbstractCompoundSet implements Compoun private final static Logger logger = LoggerFactory.getLogger(AbstractCompoundSet.class); - private Map charSeqToCompound = new HashMap(); + private Map charSeqToCompound = new HashMap<>(); private int maxCompoundCharSequenceLength = -1; private Boolean compoundStringLengthEqual = null; - Map> equivalentsMap = new HashMap>(); + Map> equivalentsMap = new HashMap<>(); protected void addCompound(C compound, C lowerCasedCompound, Iterable equivalents) { addCompound(compound); @@ -61,7 +61,7 @@ protected void addCompound(C compound, C lowerCasedCompound, Iterable equival } protected void addCompound(C compound, C lowerCasedCompound, C... equivalents) { - List equiv = new ArrayList(equivalents.length); + List equiv = new ArrayList<>(equivalents.length); equiv.addAll(Arrays.asList(equivalents)); addCompound(compound, lowerCasedCompound, equiv); } @@ -69,7 +69,7 @@ protected void addCompound(C compound, C lowerCasedCompound, C... equivalents) { protected void addEquivalent(C compound, C equivalent) { Set s = equivalentsMap.get(compound); if ( s == null){ - s = new HashSet(); + s = new HashSet<>(); equivalentsMap.put(compound, s); } @@ -170,7 +170,7 @@ public boolean isValidSequence(Sequence sequence) { @Override public List getAllCompounds() { - return new ArrayList(charSeqToCompound.values()); + return new ArrayList<>(charSeqToCompound.values()); } private void assertCompound(C compound) { diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java index e11af2b1de..3320a5edc6 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java @@ -37,7 +37,7 @@ public abstract class AbstractCompoundTranslator creator, CompoundSet fromCompoundSet, CompoundSet toCompoundSet) { this.creator = creator; - this.mapper = new HashMap>(); + this.mapper = new HashMap<>(); this.fromCompoundSet = fromCompoundSet; this.toCompoundSet = toCompoundSet; } @@ -66,7 +66,7 @@ protected void addCompounds(F source, T... targets) { List l = mapper.get(source); if ( l == null) { - l = new ArrayList(); + l = new ArrayList<>(); mapper.put(source, l); } l.addAll(Arrays.asList(targets)); @@ -97,7 +97,7 @@ else if (compounds.size() > 1) { @Override public List> createSequences(Sequence originalSequence) { - List> workingList = new ArrayList>(); + List> workingList = new ArrayList<>(); for (F source : originalSequence) { List compounds = translateMany(source); @@ -126,7 +126,7 @@ public List> createSequences(Sequence originalSequence) { protected void addCompoundsToList(List compounds, List> workingList) { int size = compounds.size(); - List> currentWorkingList = new ArrayList>(); + List> currentWorkingList = new ArrayList<>(); for (int i = 0; i < size; i++) { boolean last = (i == (size - 1)); // If last run we add the compound to the top set of lists & then @@ -147,7 +147,7 @@ protected void addCompoundsToList(List compounds, List> workingList) } protected List> workingListToSequences(List> workingList) { - List> sequences = new ArrayList>(); + List> sequences = new ArrayList<>(); for (List seqList : workingList) { sequences.add(getCreator().getSequence(seqList)); } @@ -155,7 +155,7 @@ protected List> workingListToSequences(List> workingList) { } private List> duplicateList(List> incoming) { - List> outgoing = new ArrayList>(); + List> outgoing = new ArrayList<>(); for (List current : incoming) { outgoing.add(new ArrayList(current)); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java index af6a8768e3..27e9721182 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java @@ -46,7 +46,7 @@ protected void addNucleotideCompound(String base, String complement, String... e C upper = newNucleotideCompound(base.toUpperCase(), complement.toUpperCase(), upperEquivalents); C lower = newNucleotideCompound(base.toLowerCase(), complement.toLowerCase(), lowerEquivalents); - List equivalentCompounds = new ArrayList(); + List equivalentCompounds = new ArrayList<>(); for(int i=0; i> equivalentsMap = new HashMap>(); + Map> equivalentsMap = new HashMap<>(); List ambiguousCompounds = getAllCompounds().stream() .filter(compound -> compound.isAmbiguous()) @@ -116,7 +116,7 @@ private void checkAdd( List listS = equivalentsMap.get(key); if ( listS == null){ - listS = new ArrayList(); + listS = new ArrayList<>(); equivalentsMap.put(key, listS); } listS.add(value); @@ -137,7 +137,7 @@ private NucleotideCompound toLowerCase(NucleotideCompound compound) { * @return The ambiguity symbol which represents this set of nucleotides best */ public NucleotideCompound getAmbiguity(NucleotideCompound... compounds) { - Set settedCompounds = new HashSet(); + Set settedCompounds = new HashSet<>(); for(NucleotideCompound compound: compounds) { for(NucleotideCompound subCompound: compound.getConstituents()) { settedCompounds.add(getCompoundForString(subCompound.getBase().toUpperCase())); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java index f68d7614cb..5797df9502 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java @@ -65,15 +65,15 @@ public abstract class AbstractSequence implements Sequence parentSequence = null; private String source = null; - private ArrayList notesList = new ArrayList(); + private ArrayList notesList = new ArrayList<>(); private Double sequenceScore = null; private FeaturesKeyWordInterface featuresKeyWord = null; private DatabaseReferenceInterface databaseReferences = null; private FeatureRetriever featureRetriever = null; private ArrayList, C>> features = - new ArrayList, C>>(); + new ArrayList<>(); private LinkedHashMap, C>>> groupedFeatures = - new LinkedHashMap, C>>>(); + new LinkedHashMap<>(); private List comments = new ArrayList<>(); private List references; @@ -93,7 +93,7 @@ public AbstractSequence(String seqString, CompoundSet compoundSet) throws Com // so it can be called from subclass constructors protected void initSequenceStorage(String seqString) throws CompoundNotFoundException { - sequenceStorage = new ArrayListSequenceReader(); + sequenceStorage = new ArrayListSequenceReader<>(); sequenceStorage.setCompoundSet(this.getCompoundSet()); sequenceStorage.setContents(seqString); } @@ -354,7 +354,7 @@ public void setReferences(List references) { */ public List, C>> getFeatures(String featureType, int bioSequencePosition) { ArrayList, C>> featureHits = - new ArrayList, C>>(); + new ArrayList<>(); List, C>> features = getFeaturesByType(featureType); if (features != null) { for (FeatureInterface, C> feature : features) { @@ -373,7 +373,7 @@ public List, C>> getFeatures(String feature */ public List, C>> getFeatures(int bioSequencePosition) { ArrayList, C>> featureHits = - new ArrayList, C>>(); + new ArrayList<>(); if (features != null) { for (FeatureInterface, C> feature : features) { if (bioSequencePosition >= feature.getLocations().getStart().getPosition() && bioSequencePosition <= feature.getLocations().getEnd().getPosition()) { @@ -401,7 +401,7 @@ public List, C>> getFeatures() { */ public void addFeature(int bioStart, int bioEnd, FeatureInterface, C> feature) { SequenceLocation, C> sequenceLocation = - new SequenceLocation, C>(bioStart, bioEnd, this); + new SequenceLocation<>(bioStart, bioEnd, this); feature.setLocation(sequenceLocation); addFeature(feature); } @@ -416,7 +416,7 @@ public void addFeature(FeatureInterface, C> feature) { features.add(feature); ArrayList, C>> featureList = groupedFeatures.get(feature.getType()); if (featureList == null) { - featureList = new ArrayList, C>>(); + featureList = new ArrayList<>(); groupedFeatures.put(feature.getType(), featureList); } featureList.add(feature); @@ -447,7 +447,7 @@ public void removeFeature(FeatureInterface, C> feature) { public List, C>> getFeaturesByType(String type) { List, C>> features = groupedFeatures.get(type); if (features == null) { - features = new ArrayList, C>>(); + features = new ArrayList<>(); } return features; } @@ -609,7 +609,7 @@ private SequenceReader getSequenceStorage() { //return parentSequence.getSequenceStorage(); if ( this.compoundSet.equals(parentSequence.getCompoundSet())){ - sequenceStorage = new ArrayListSequenceReader(); + sequenceStorage = new ArrayListSequenceReader<>(); sequenceStorage.setCompoundSet(this.getCompoundSet()); try { sequenceStorage.setContents(parentSequence.getSequenceAsString()); @@ -706,7 +706,7 @@ public int getLength() { */ @Override public SequenceView getSubSequence(final Integer bioStart, final Integer bioEnd) { - return new SequenceProxyView(this, bioStart, bioEnd); + return new SequenceProxyView<>(this, bioStart, bioEnd); } /** diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java index d6efc03817..c3dec3d0bd 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java @@ -113,7 +113,7 @@ public static int countAT(Sequence sequence) { * sequence. Any compound not in the Map will return a fraction of 0. */ public static Map getDistribution(Sequence sequence) { - Map results = new HashMap(); + Map results = new HashMap<>(); Map composition = getComposition(sequence); double length = sequence.getLength(); for (Map.Entry entry : composition.entrySet()) { @@ -133,7 +133,7 @@ public static Map getDistribution(Sequence se * @return Counts for the instances of all compounds in the sequence */ public static Map getComposition(Sequence sequence) { - Map results = new HashMap(); + Map results = new HashMap<>(); for (C currentCompound : sequence) { Integer currentInteger = results.get(currentCompound); @@ -187,7 +187,7 @@ public static String toString(Sequence sequence) { * the Compounds of that {@link Sequence}. */ public static List toList(Sequence sequence) { - List list = new ArrayList(sequence.getLength()); + List list = new ArrayList<>(sequence.getLength()); for (C compound : sequence) { list.add(compound); } @@ -229,7 +229,7 @@ public static int lastIndexOf(Sequence sequence, */ public static Iterator createIterator( Sequence sequence) { - return new SequenceIterator(sequence); + return new SequenceIterator<>(sequence); } /** @@ -237,7 +237,7 @@ public static Iterator createIterator( */ public static SequenceView createSubSequence( Sequence sequence, int start, int end) { - return new SequenceProxyView(sequence, start, end); + return new SequenceProxyView<>(sequence, start, end); } /** @@ -250,7 +250,7 @@ public static SequenceView createSubSequence( public static Sequence shuffle(Sequence sequence) { List compounds = sequence.getAsList(); Collections.shuffle(compounds); - return new ArrayListSequenceReader(compounds, + return new ArrayListSequenceReader<>(compounds, sequence.getCompoundSet()); } @@ -275,8 +275,8 @@ public static String checksum(Sequence sequence) { * @return The list of non-overlapping K-mers */ public static List> nonOverlappingKmers(Sequence sequence, int kmer) { - List> l = new ArrayList>(); - WindowedSequence w = new WindowedSequence(sequence, kmer); + List> l = new ArrayList<>(); + WindowedSequence w = new WindowedSequence<>(sequence, kmer); for(SequenceView view: w) { l.add(view); } @@ -293,9 +293,9 @@ public static List> nonOverlappingKmers(Seq * @return The list of overlapping K-mers */ public static List> overlappingKmers(Sequence sequence, int kmer) { - List> l = new ArrayList>(); + List> l = new ArrayList<>(); List>> windows - = new ArrayList>>(); + = new ArrayList<>(); for(int i=1; i<=kmer; i++) { if(i == 1) { @@ -333,7 +333,7 @@ public static List> overlappingKmers(Sequen */ @SuppressWarnings({ "unchecked" }) public static SequenceView inverse(Sequence sequence) { - SequenceView reverse = new ReversedSequenceView(sequence); + SequenceView reverse = new ReversedSequenceView<>(sequence); if(sequence.getCompoundSet().isComplementable()) { return new ComplementSequenceView(reverse); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java index f6e51dfad7..92023bd44e 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java @@ -117,12 +117,12 @@ public CompoundSet getCompoundSet() { @Override public SequenceView getSubSequence(final Integer bioStart, final Integer bioEnd) { - return new SequenceProxyView(this, bioStart, bioEnd); + return new SequenceProxyView<>(this, bioStart, bioEnd); } @Override public Iterator iterator() { - return new SequenceMixin.SequenceIterator(this); + return new SequenceMixin.SequenceIterator<>(this); } @Override diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java index 0016c86507..baafa9419d 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.java @@ -65,7 +65,7 @@ public DNAToRNATranslator(SequenceCreatorInterface rnaCreato @Override public List> createSequences(Sequence originalSequence) { if(shortCutTranslation) { - List> result = new ArrayList>(1); + List> result = new ArrayList<>(1); result.add(wrapToRna(originalSequence)); return result; } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java index 8f35c0eb03..eb0f4a91c6 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Frame.java @@ -83,7 +83,7 @@ public static Frame[] getAllFrames() { public Sequence wrap(Sequence incoming) { Sequence reversed; if(reverse) { - reversed = new ComplementSequenceView(new ReversedSequenceView(incoming)); + reversed = new ComplementSequenceView<>(new ReversedSequenceView(incoming)); } else { reversed = incoming; diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java index e748b41387..f6d9f7ca84 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java @@ -81,9 +81,9 @@ public RNAToAminoAcidTranslator( this.initMetOnly = initMetOnly; this.translateNCodons = translateNCodons; - quickLookup = new HashMap(codons + quickLookup = new HashMap<>(codons .getAllCompounds().size()); - aminoAcidToCodon = new HashMap>(); + aminoAcidToCodon = new HashMap<>(); List codonList = table.getCodons(nucleotides, aminoAcids); for (Codon codon : codonList) { @@ -92,7 +92,7 @@ public RNAToAminoAcidTranslator( List codonL = aminoAcidToCodon.get(codon.getAminoAcid()); if (codonL == null) { - codonL = new ArrayList(); + codonL = new ArrayList<>(); aminoAcidToCodon.put(codon.getAminoAcid(), codonL); } codonL.add(codon); @@ -114,7 +114,7 @@ public RNAToAminoAcidTranslator( public List> createSequences( Sequence originalSequence) { - List> workingList = new ArrayList>(); + List> workingList = new ArrayList<>(); Iterable> iter = new WindowedSequence( originalSequence, 3); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java index 0ca5bc6f1a..162d760f05 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java @@ -125,7 +125,7 @@ public Sequence translate( */ public Map> multipleFrameTranslation( Sequence dna, Frame... frames) { - Map> results = new EnumMap>( + Map> results = new EnumMap<>( Frame.class); for (Frame frame : frames) { Sequence rna = getDnaRnaTranslator() diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java index b0c00d6a60..cdb08052fd 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/RnaSequenceView.java @@ -90,9 +90,9 @@ public Map getDnaToRna() { protected void buildTranslators() { Map localDnaToRna = - new HashMap(); + new HashMap<>(); Map localRnaToDna = - new HashMap(); + new HashMap<>(); NucleotideCompound thymine = getViewedSequence().getCompoundSet().getCompoundForString("T"); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java index 6808ef01fb..09f8a6760d 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java @@ -48,7 +48,7 @@ public class FlatFileCache { /** * The cache singleton. */ - private static SoftHashMap cache = new SoftHashMap(0); + private static SoftHashMap cache = new SoftHashMap<>(0); // no public constructor; diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java index 27485db5f5..437085866f 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java @@ -41,10 +41,10 @@ public class PrettyXMLWriter implements XMLWriter { private boolean afterNewline = true; private int indent = 0; - private Map namespacePrefixes = new HashMap(); + private Map namespacePrefixes = new HashMap<>(); private int namespaceSeed = 0; - private LinkedList> namespaceBindings = new LinkedList>(); - private List namespacesDeclared = new ArrayList(); + private LinkedList> namespaceBindings = new LinkedList<>(); + private List namespacesDeclared = new ArrayList<>(); public PrettyXMLWriter(PrintWriter writer) { this.writer = writer; @@ -113,7 +113,7 @@ private String allocPrefix(String nsURI) { namespacePrefixes.put(nsURI, prefix); List bindings = namespaceBindings.getLast(); if (bindings == null) { - bindings = new ArrayList(); + bindings = new ArrayList<>(); namespaceBindings.removeLast(); namespaceBindings.add(bindings); } diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java index eef144080a..1b395828b5 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java @@ -190,7 +190,7 @@ private double getDistance(int first, int second) { private void updateIndicesToCheck(int m) { if (indicesToCheck==null) { - indicesToCheck = new ArrayList(numItems); + indicesToCheck = new ArrayList<>(numItems); for (int i=0;i> getClusters(double cutoff) { clusterIt(); } - Map> clusters = new TreeMap>(); + Map> clusters = new TreeMap<>(); int clusterId = 1; @@ -276,7 +276,7 @@ public Map> getClusters(double cutoff) { if (firstClusterId==-1 && secondClusterId==-1) { // neither member is in a cluster yet, let's assign a new cluster and put them both in - Set members = new TreeSet(); + Set members = new TreeSet<>(); members.add(dendrogram[i].getFirst()); members.add(dendrogram[i].getSecond()); clusters.put(clusterId, members); @@ -319,7 +319,7 @@ public Map> getClusters(double cutoff) { } // reassigning cluster numbers by creating a new map (there can be gaps in the numbering if cluster-joining happened) - Map> finalClusters = new TreeMap>(); + Map> finalClusters = new TreeMap<>(); int newClusterId = 1; for (int oldClusterId:clusters.keySet()) { finalClusters.put(newClusterId, clusters.get(oldClusterId)); @@ -336,7 +336,7 @@ public Map> getClusters(double cutoff) { } } if (!isAlreadyClustered) { - Set members = new TreeSet(); + Set members = new TreeSet<>(); members.add(i); finalClusters.put(newClusterId, members); newClusterId++; diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java index b0ac87519c..f3bcef0468 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java @@ -46,16 +46,16 @@ public class SoftHashMap extends AbstractMap { public static final int DEFAULT_LIMIT = 1; /** The internal HashMap that stores SoftReference to actual data. */ - private final Map> map = new HashMap>(); + private final Map> map = new HashMap<>(); /** Maximum Number of references you dont want GC to collect. */ private final int max_limit; /** The FIFO list of hard references, order of last access. */ - private final LinkedList hardCache = new LinkedList(); + private final LinkedList hardCache = new LinkedList<>(); /** Reference queue for cleared SoftReference objects. */ - private final ReferenceQueue queue = new ReferenceQueue(); + private final ReferenceQueue queue = new ReferenceQueue<>(); public SoftHashMap() { this(1000); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java index d4eab71660..4344063e1d 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java @@ -207,7 +207,7 @@ public static Element selectSingleElement(Element element, String xpathExpressio * @throws XPathExpressionException */ public static ArrayList selectElements(Element element, String xpathExpression) throws XPathExpressionException { - ArrayList resultVector = new ArrayList(); + ArrayList resultVector = new ArrayList<>(); if (element == null) { return resultVector; } diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java index 7f7294801e..681ddb0910 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java @@ -42,7 +42,7 @@ public class GeneFeatureHelper { private static final Logger logger = LoggerFactory.getLogger(GeneFeatureHelper.class); static public LinkedHashMap loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File fastaSequenceFile, File uppercaseFastaFile, boolean throwExceptionGeneNotFound) throws Exception { - LinkedHashMap chromosomeSequenceList = new LinkedHashMap(); + LinkedHashMap chromosomeSequenceList = new LinkedHashMap<>(); LinkedHashMap dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile); for (String accession : dnaSequenceList.keySet()) { DNASequence contigSequence = dnaSequenceList.get(accession); @@ -91,7 +91,7 @@ static public LinkedHashMap loadFastaAddGeneFeatures dnaSequence.getAccession().toString(), contigDNASequence.getAccession().toString(), bioStart, bioEnd, strand); ChromosomeSequence chromosomeSequence = chromosomeSequenceList.get(accession); - ArrayList exonBoundries = new ArrayList(); + ArrayList exonBoundries = new ArrayList<>(); //look for transitions from lowercase to upper case for (int i = 0; i < geneSequence.length(); i++) { @@ -314,7 +314,7 @@ static public void addGeneIDGFF2GeneFeatures(LinkedHashMap getChromosomeSequenceFromDNASequence(LinkedHashMap dnaSequenceList) { - LinkedHashMap chromosomeSequenceList = new LinkedHashMap(); + LinkedHashMap chromosomeSequenceList = new LinkedHashMap<>(); for (String key : dnaSequenceList.keySet()) { DNASequence dnaSequence = dnaSequenceList.get(key); ChromosomeSequence chromosomeSequence = new ChromosomeSequence(dnaSequence.getProxySequenceReader()); //we want the underlying sequence but don't need storage @@ -836,7 +836,7 @@ static public void addGeneMarkGTFGeneFeatures(LinkedHashMap getProteinSequences(Collection chromosomeSequences) throws Exception { - LinkedHashMap proteinSequenceHashMap = new LinkedHashMap(); + LinkedHashMap proteinSequenceHashMap = new LinkedHashMap<>(); for (ChromosomeSequence dnaSequence : chromosomeSequences) { for (GeneSequence geneSequence : dnaSequence.getGeneSequences().values()) { for (TranscriptSequence transcriptSequence : geneSequence.getTranscripts().values()) { @@ -865,7 +865,7 @@ static public LinkedHashMap getProteinSequences(Collect } static public LinkedHashMap getGeneSequences(Collection chromosomeSequences) throws Exception { - LinkedHashMap geneSequenceHashMap = new LinkedHashMap(); + LinkedHashMap geneSequenceHashMap = new LinkedHashMap<>(); for (ChromosomeSequence chromosomeSequence : chromosomeSequences) { for (GeneSequence geneSequence : chromosomeSequence.getGeneSequences().values()) { geneSequenceHashMap.put(geneSequence.getAccession().getID(), geneSequence); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java index 88881b37eb..0d40fe835c 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java @@ -33,7 +33,7 @@ public class BlastHomologyHits { static public LinkedHashMap> getMatches(File xmlBlastHits, double ecutoff) throws Exception { - LinkedHashMap> homologyHits = new LinkedHashMap>(); + LinkedHashMap> homologyHits = new LinkedHashMap<>(); BlastXMLQuery blastXMLQuery = new BlastXMLQuery(xmlBlastHits.getAbsolutePath()); LinkedHashMap> hits = blastXMLQuery.getHitsQueryDef(ecutoff); for (String accessionid : hits.keySet()) { diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java index 7b7111c6a6..e8d7666348 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java @@ -79,7 +79,7 @@ public void process(LinkedHashMap> hits, LinkedHashMap } ArrayList uniprotProteinHits = hits.get(accessionid); String uniprotBestHit = uniprotProteinHits.get(0); - UniprotProxySequenceReader uniprotSequence = new UniprotProxySequenceReader(uniprotBestHit, AminoAcidCompoundSet.getAminoAcidCompoundSet()); + UniprotProxySequenceReader uniprotSequence = new UniprotProxySequenceReader<>(uniprotBestHit, AminoAcidCompoundSet.getAminoAcidCompoundSet()); ProteinSequence proteinSequence = new ProteinSequence(uniprotSequence); String hitSequence = proteinSequence.getSequenceAsString(); @@ -89,7 +89,7 @@ public void process(LinkedHashMap> hits, LinkedHashMap String predictedProteinSequence = transcriptSequence.getProteinSequence().getSequenceAsString(); ArrayList cdsProteinList = transcriptSequence.getProteinCDSSequences(); - ArrayList cdsSequenceList = new ArrayList(transcriptSequence.getCDSSequences().values()); + ArrayList cdsSequenceList = new ArrayList<>(transcriptSequence.getCDSSequences().values()); String testSequence = ""; for (ProteinSequence cdsProteinSequence : cdsProteinList) { testSequence = testSequence + cdsProteinSequence.getSequenceAsString(); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java index 437d7bd435..78191a7655 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqTools.java @@ -133,7 +133,7 @@ public static QualityFeature, NucleotideCom { throw new IllegalArgumentException("fastq must not be null"); } - QualityFeature, NucleotideCompound> qualityScores = new QualityFeature, NucleotideCompound>("qualityScores", "sequencing"); + QualityFeature, NucleotideCompound> qualityScores = new QualityFeature<>("qualityScores", "sequencing"); qualityScores.setQualities(toList(qualityScores(fastq))); return qualityScores; } @@ -153,7 +153,7 @@ public static QuantityFeature, NucleotideCo { throw new IllegalArgumentException("fastq must not be null"); } - QuantityFeature, NucleotideCompound> errorProbabilities = new QuantityFeature, NucleotideCompound>("errorProbabilities", "sequencing"); + QuantityFeature, NucleotideCompound> errorProbabilities = new QuantityFeature<>("errorProbabilities", "sequencing"); errorProbabilities.setQuantities(toList(errorProbabilities(fastq))); return errorProbabilities; } diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java index efffbf4f78..3a93c5c057 100755 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/io/fastq/FastqVariant.java @@ -186,7 +186,7 @@ public double errorProbability(final int qualityScore) /** Map of FASTQ sequence format variants keyed by name and lowercase-with-dashes name. */ - private static final Map FASTQ_VARIANTS = new HashMap(6); + private static final Map FASTQ_VARIANTS = new HashMap<>(6); static { diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java index 560566b0b2..d7ab896b8a 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.java @@ -52,7 +52,7 @@ public static void main(String[] args) { try { SortedSet cytobands = me.getAllCytobands(new URL( DEFAULT_LOCATION)); - SortedSet types = new TreeSet(); + SortedSet types = new TreeSet<>(); for (Cytoband c : cytobands) { logger.info("Cytoband: {}", c); if (!types.contains(c.getType())) @@ -77,7 +77,7 @@ public SortedSet getAllCytobands(InputStream instream) BufferedReader reader = new BufferedReader(new InputStreamReader( instream)); String line = null; - SortedSet cytobands = new TreeSet(); + SortedSet cytobands = new TreeSet<>(); while ((line = reader.readLine()) != null) { String[] spl = line.split("\t"); if (spl.length != 5) { diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java index a573a7062d..b509f73ab7 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java @@ -51,7 +51,7 @@ public GeneIDXMLReader(String geneidXMLFile) throws Exception { } public LinkedHashMap getProteinSequences() throws Exception { - LinkedHashMap proteinSequenceList = new LinkedHashMap(); + LinkedHashMap proteinSequenceList = new LinkedHashMap<>(); ArrayList elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/protein"); logger.info("{} hits", elementList.size()); @@ -68,7 +68,7 @@ public LinkedHashMap getProteinSequences() throws Excep } public LinkedHashMap getDNACodingSequences() throws Exception { - LinkedHashMap dnaSequenceList = new LinkedHashMap(); + LinkedHashMap dnaSequenceList = new LinkedHashMap<>(); ArrayList elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/cDNA"); logger.info("{} hits", elementList.size()); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java index d7a06070c7..0ced7c5e00 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.java @@ -79,7 +79,7 @@ public static List getChromosomeMappings() throws IOExce public static List getChromosomeMappings(InputStream inStream) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(inStream)); - ArrayList gcps = new ArrayList(); + ArrayList gcps = new ArrayList<>(); String line = null; while ((line = reader.readLine()) != null) { @@ -126,7 +126,7 @@ private static GeneChromosomePosition getGeneChromosomePosition(String line) { private static List getIntegerList(String lst){ String[] spl = lst.split(","); - ArrayList l = new ArrayList(); + ArrayList l = new ArrayList<>(); for (String s : spl){ l.add(Integer.parseInt(s)); } diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java index e39a34fd92..1ffba84b52 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java @@ -92,7 +92,7 @@ public static List getGeneNames() throws IOException{ */ public static List getGeneNames(InputStream inStream) throws IOException{ - ArrayList geneNames = new ArrayList(); + ArrayList geneNames = new ArrayList<>(); BufferedReader reader = new BufferedReader(new InputStreamReader(inStream)); // skip reading first line (it is the legend) diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java index 9d750f850e..c5c9e07e1e 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java @@ -153,7 +153,7 @@ public Feature(Feature feature) { mFrame = feature.mFrame; mAttributes = feature.mAttributes; initAttributeHashMap(); - mUserMap = new HashMap(feature.mUserMap); + mUserMap = new HashMap<>(feature.mUserMap); } /** @@ -177,7 +177,7 @@ public Feature(String seqname, String source, String type, Location location, Do mFrame = frame; mAttributes = attributes; initAttributeHashMap(); - mUserMap = new HashMap(); + mUserMap = new HashMap<>(); } @@ -199,7 +199,7 @@ public HashMap userData() { return mUserMap; } - HashMap attributeHashMap = new HashMap(); + HashMap attributeHashMap = new HashMap<>(); private void initAttributeHashMap(){ String[] values = mAttributes.split(";"); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java index 1383276ce2..bcdc0bc32b 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java @@ -38,7 +38,7 @@ public class FeatureHelper { */ static public LinkedHashMap buildFeatureAtrributeIndex(String attribute,FeatureList list){ - LinkedHashMap featureHashMap = new LinkedHashMap(); + LinkedHashMap featureHashMap = new LinkedHashMap<>(); FeatureList featureList = list.selectByAttribute(attribute); for(FeatureI feature : featureList){ String value = feature.getAttribute(attribute); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java index 19b7afec93..344fe34141 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java @@ -40,7 +40,7 @@ @SuppressWarnings("serial") public class FeatureList extends ArrayList { - Map>> featindex = new HashMap>>(); + Map>> featindex = new HashMap<>(); Location mLocation; //genomic location (union of feature locations) /** @@ -81,11 +81,11 @@ public boolean add(FeatureI feature) { if (featindex.containsKey(entry.getKey())){ Map> feat = featindex.get(entry.getKey()); if (feat==null){ - feat= new HashMap>(); + feat= new HashMap<>(); } List features = feat.get(entry.getValue()); if (features==null){ - features = new ArrayList(); + features = new ArrayList<>(); } features.add(feature); feat.put(entry.getValue(), features); @@ -185,7 +185,7 @@ public String splice(DNASequence sequence) { * the order of features in the list. */ public Collection groupValues() { - Set set = new HashSet(); + Set set = new HashSet<>(); for (FeatureI f : this) { //enter in a set -- removes duplicates set.add(f.group()); @@ -207,10 +207,10 @@ public Collection attributeValues(String key) { if (featindex.containsKey(key)){ Map> map = featindex.get(key); Collection result = map.keySet(); - if (result == null) result = new HashSet(); + if (result == null) result = new HashSet<>(); return Collections.unmodifiableCollection(result); } - LinkedHashMap hash = new LinkedHashMap(); + LinkedHashMap hash = new LinkedHashMap<>(); for (FeatureI f : this) { //enter as a key -- removes duplicates hash.put(f.getAttribute(key), null); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java index 6378a846c5..4d5980fa23 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java @@ -91,7 +91,7 @@ public void write(OutputStream outputStream, LinkedHashMap cdsSequenceList = new ArrayList(transcriptSequence.getCDSSequences().values()); + ArrayList cdsSequenceList = new ArrayList<>(transcriptSequence.getCDSSequences().values()); Collections.sort(cdsSequenceList, new SequenceComparator()); for (CDSSequence cdsSequence : cdsSequenceList) { gff3line = key + "\t" + cdsSequence.getSource() + "\t" + "CDS" + "\t" + cdsSequence.getBioBegin() + "\t" + cdsSequence.getBioEnd() + "\t"; diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java index 7818b93996..122dc4e6c8 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java @@ -52,7 +52,7 @@ public class TwoBitParser extends InputStream { private File f; private boolean reverse = false; private String[] seq_names; - private HashMap seq2pos = new HashMap(); + private HashMap seq2pos = new HashMap<>(); private String cur_seq_name; private long[][] cur_nn_blocks; private long[][] cur_mask_blocks; diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java index ff5e1318d0..3f3cccf654 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java @@ -47,7 +47,7 @@ public BlastXMLQuery(String blastFile) throws Exception { } public LinkedHashMap> getHitsQueryDef(double maxEScore) throws Exception { - LinkedHashMap> hitsHashMap = new LinkedHashMap>(); + LinkedHashMap> hitsHashMap = new LinkedHashMap<>(); logger.info("Query for hits"); ArrayList elementList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]"); logger.info("{} hits", elementList.size()); @@ -69,7 +69,7 @@ public LinkedHashMap> getHitsQueryDef(double maxEScore if (evalue <= maxEScore) { ArrayList hits = hitsHashMap.get(querydef); if (hits == null) { - hits = new ArrayList(); + hits = new ArrayList<>(); hitsHashMap.put(querydef, hits); } hits.add(hitaccession); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java index 66a9d2a086..2806e83d9d 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/uniprot/UniprotToFasta.java @@ -67,10 +67,10 @@ public void process( String uniprotDatFileName,String fastaFileName ) throws Exc String line = br.readLine(); String id = ""; StringBuffer sequence = new StringBuffer(); - ArrayList seqCodingRegionsList = new ArrayList(); + ArrayList seqCodingRegionsList = new ArrayList<>(); int count = 0; - HashMap uniqueGenes = new HashMap(); - HashMap uniqueSpecies = new HashMap(); + HashMap uniqueGenes = new HashMap<>(); + HashMap uniqueSpecies = new HashMap<>(); while(line != null){ if(line.startsWith("ID")){ String[] data = line.split(" "); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java index 4948a62c76..9018749f33 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java @@ -52,7 +52,7 @@ public void processNucleotides(File fastaFileName,String uniqueid, File outputDi }else{ fileName = fileName + uniqueid + dnaSequence.getAccession().getID() + ".fna"; } - ArrayList dnaList = new ArrayList(); + ArrayList dnaList = new ArrayList<>(); dnaList.add(dnaSequence); FastaWriterHelper.writeNucleotideSequence(new File(fileName), dnaList); } diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java index ff4b0abb82..4a35ff5218 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java @@ -50,10 +50,10 @@ public final class Component { */ private static void lazyInit() { if (components==null) { - components = new HashSet(); - nonTerminalComps = new HashMap, Component>(); - nTerminalAminoAcids = new HashMap, Component>(); - cTerminalAminoAcids = new HashMap, Component>(); + components = new HashSet<>(); + nonTerminalComps = new HashMap<>(); + nTerminalAminoAcids = new HashMap<>(); + cTerminalAminoAcids = new HashMap<>(); } } diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java index 89d9bd9720..8dcadab400 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationCategory.java @@ -108,7 +108,7 @@ public static ModificationCategory getByLabel(String label) { private static Map mapLabelCat; static { - mapLabelCat = new HashMap(); + mapLabelCat = new HashMap<>(); for (ModificationCategory cat:ModificationCategory.values()) { mapLabelCat.put(cat.label, cat); } diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java index 2af28ed33f..5cb7857bdd 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationConditionImpl.java @@ -49,7 +49,7 @@ public ModificationConditionImpl(final List components, if (components.size() > 1) { - Set indices = new HashSet(); + Set indices = new HashSet<>(); for (ModificationLinkage linkage : linkages) { indices.add(linkage.getIndexOfComponent1()); indices.add(linkage.getIndexOfComponent2()); diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java index 30a4bad4e0..3fdcef1e0a 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationOccurrenceType.java @@ -73,7 +73,7 @@ public static ModificationOccurrenceType getByLabel(String label) { private static Map mapLabelOcc; static { - mapLabelOcc = new HashMap(); + mapLabelOcc = new HashMap<>(); for (ModificationOccurrenceType occ:ModificationOccurrenceType.values()) { mapLabelOcc.put(occ.label, occ); } diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java index a06ee41936..dd4f11d41f 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationImpl.java @@ -251,7 +251,7 @@ public static class Builder { private String sysName = null; private String formula = null; - private Set keywords = new LinkedHashSet(); + private Set keywords = new LinkedHashSet<>(); /** * @@ -289,7 +289,7 @@ public Builder(final ProteinModification copyFrom) { this.sysName = copyFrom.getSystematicName(); this.formula = copyFrom.getFormula(); - this.keywords = new LinkedHashSet(copyFrom.getKeywords()); + this.keywords = new LinkedHashSet<>(copyFrom.getKeywords()); } public Builder setCategory(final ModificationCategory cat) { @@ -448,7 +448,7 @@ private ProteinModificationImpl(Builder builder) { this.sysName = builder.sysName; this.formula = builder.formula; - this.keywords = new LinkedHashSet(builder.keywords); + this.keywords = new LinkedHashSet<>(builder.keywords); } @Override diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java index 54babab8e1..043aa3d779 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java @@ -109,19 +109,19 @@ private static synchronized void lazyInit() { private static synchronized void lazyInit(InputStream inStream) { if (registry==null) { - registry = new HashSet(); - byId = new HashMap(); - byResidId = new HashMap>(); - byPsimodId = new HashMap>(); - byPdbccId = new HashMap>(); - byKeyword = new HashMap>(); - byComponent = new HashMap>(); - byCategory = new EnumMap>( + registry = new HashSet<>(); + byId = new HashMap<>(); + byResidId = new HashMap<>(); + byPsimodId = new HashMap<>(); + byPdbccId = new HashMap<>(); + byKeyword = new HashMap<>(); + byComponent = new HashMap<>(); + byCategory = new EnumMap<>( ModificationCategory.class); for (ModificationCategory cat:ModificationCategory.values()) { byCategory.put(cat, new HashSet()); } - byOccurrenceType = new EnumMap>( + byOccurrenceType = new EnumMap<>( ModificationOccurrenceType.class); for (ModificationOccurrenceType occ:ModificationOccurrenceType.values()) { byOccurrenceType.put(occ, new HashSet()); @@ -158,7 +158,7 @@ public static void register(final ProteinModification modification) { for (Component comp:comps) { Set mods = byComponent.get(comp); if (mods==null) { - mods = new HashSet(); + mods = new HashSet<>(); byComponent.put(comp, mods); } mods.add(modification); @@ -168,7 +168,7 @@ public static void register(final ProteinModification modification) { if (pdbccId!=null) { Set mods = byPdbccId.get(pdbccId); if (mods==null) { - mods = new HashSet(); + mods = new HashSet<>(); byPdbccId.put(pdbccId, mods); } mods.add(modification); @@ -178,7 +178,7 @@ public static void register(final ProteinModification modification) { if (residId!=null) { Set mods = byResidId.get(residId); if (mods==null) { - mods = new HashSet(); + mods = new HashSet<>(); byResidId.put(residId, mods); } mods.add(modification); @@ -188,7 +188,7 @@ public static void register(final ProteinModification modification) { if (psimodId!=null) { Set mods = byPsimodId.get(psimodId); if (mods==null) { - mods = new HashSet(); + mods = new HashSet<>(); byPsimodId.put(psimodId, mods); } mods.add(modification); @@ -197,7 +197,7 @@ public static void register(final ProteinModification modification) { for (String keyword : modification.getKeywords()) { Set mods = byKeyword.get(keyword); if (mods==null) { - mods = new HashSet(); + mods = new HashSet<>(); byKeyword.put(keyword, mods); } mods.add(modification); @@ -308,7 +308,7 @@ public static Set getByComponent(final Component comp1, if (comps.length==0) { return Collections.unmodifiableSet(mods); } else { - Set ret = new HashSet(mods); + Set ret = new HashSet<>(mods); for (Component comp:comps) { mods = byComponent.get(comp); if (mods==null) { diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java index 67f1ce5eee..15d635f4da 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ComponentXMLConverter.java @@ -74,7 +74,7 @@ public static Component fromXML(Node componentN) { boolean isNTerminal = Boolean.parseBoolean(nTerminalS); boolean isCTerminal = Boolean.parseBoolean(cTerminalS); - SetpdbccIds = new HashSet(); + SetpdbccIds = new HashSet<>(); NodeList valList = componentN.getChildNodes(); int numChildren = valList.getLength(); diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java index b408c3cc9a..187e113924 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java @@ -110,7 +110,7 @@ public static ModifiedCompound fromXML(String xml){ ProteinModification modification = null; //Collection linkages = new ArrayList(); StructureAtomLinkage[] linkages = null; - List structureGroups = new ArrayList(); + List structureGroups = new ArrayList<>(); try { //Convert string to XML document diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java index f1769b816d..598cd17835 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java @@ -121,14 +121,14 @@ public static void registerProteinModificationFromXml(InputStream isXml) Node compsNode = nodes.get(0); // keep track of the labels of component indices - Map mapLabelComp = new HashMap(); + Map mapLabelComp = new HashMap<>(); Map> compInfoNodes = getChildNodes(compsNode); // components List compNodes = compInfoNodes.get("Component"); int sizeComp = compNodes.size(); - List comps = new ArrayList(sizeComp); + List comps = new ArrayList<>(sizeComp); for (int iComp=0; iComp compIds = new HashSet(); + Set compIds = new HashSet<>(); List compIdNodes = getChildNodes(compNode).get("Id"); if (compIdNodes!=null) { for (Node compIdNode : compIdNodes) { @@ -199,7 +199,7 @@ public static void registerProteinModificationFromXml(InputStream isXml) List linkages = null; if (bondNodes!=null) { int sizeBonds = bondNodes.size(); - linkages = new ArrayList(sizeBonds); + linkages = new ArrayList<>(sizeBonds); for (int iBond=0; iBond> bondChildNodes = getChildNodes(bondNode); @@ -342,7 +342,7 @@ private static Map> getChildNodes(Node parent) { if (parent==null) return Collections.emptyMap(); - Map> children = new HashMap>(); + Map> children = new HashMap<>(); NodeList nodes = parent.getChildNodes(); int nNodes = nodes.getLength(); @@ -354,7 +354,7 @@ private static Map> getChildNodes(Node parent) { String name = node.getNodeName(); List namesakes = children.get(name); if (namesakes==null) { - namesakes = new ArrayList(); + namesakes = new ArrayList<>(); children.put(name, namesakes); } namesakes.add(node); diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java index e42d987e61..889d3948b2 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java @@ -75,7 +75,7 @@ public ModifiedCompoundImpl ( throw new IllegalArgumentException("Null argument(s)"); } - groups = new HashSet(1); + groups = new HashSet<>(1); groups.add(modifiedResidue); // is it possible that components be added by addLinkage later? @@ -101,7 +101,7 @@ public ModifiedCompoundImpl( ProteinModification modification, throw new IllegalArgumentException("at least one linkage."); } - this.groups = new HashSet(); + this.groups = new HashSet<>(); addAtomLinkages(linkages); @@ -128,7 +128,7 @@ else if (originalModification.getCategory()!=ModificationCategory.UNDEFINED) modification = originalModification; else { int nRes = 0; - Set ligands = new HashSet(); + Set ligands = new HashSet<>(); for (StructureGroup group : groups) { if (group.isAminoAcid()) { nRes ++; @@ -174,7 +174,7 @@ public Set getGroups() { @Override public Set getGroups(boolean isAminoAcid) { - Set result = new HashSet(); + Set result = new HashSet<>(); for (StructureGroup group : groups) { if (group.isAminoAcid() == isAminoAcid) { result.add(group); @@ -194,7 +194,7 @@ public Set getAtomLinkages() { if (atomLinkages==null) { return Collections.emptySet(); } else { - Set result = new HashSet(); + Set result = new HashSet<>(); for (Set linkages : atomLinkages.values()) { result.addAll(linkages); } @@ -218,17 +218,17 @@ public boolean addAtomLinkage(StructureAtomLinkage linkage) { throw new IllegalArgumentException("Null linkage"); } - Set gs = new HashSet(2); + Set gs = new HashSet<>(2); gs.add(linkage.getAtom1().getGroup()); gs.add(linkage.getAtom2().getGroup()); if (atomLinkages==null) { - atomLinkages = new HashMap, Set>(); + atomLinkages = new HashMap<>(); } Set linkages = atomLinkages.get(gs); if (linkages == null) { - linkages = new HashSet(); + linkages = new HashSet<>(); atomLinkages.put(gs, linkages); groups.addAll(gs); // it's possible of new groups }; diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java index f4a0a693a8..c9575a5444 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java @@ -267,9 +267,9 @@ public void identify(final List chains, } - residues = new ArrayList(); - List ligands = new ArrayList(); - Map> mapCompGroups = new HashMap>(); + residues = new ArrayList<>(); + List ligands = new ArrayList<>(); + Map> mapCompGroups = new HashMap<>(); for (Chain chain : chains) { @@ -292,7 +292,7 @@ public void identify(final List chains, } logger.warn("No amino acids found for {}. Either you did not parse the PDB file with alignSEQRES records, or this record does not contain any amino acids.", pdbId); } - List modComps = new ArrayList(); + List modComps = new ArrayList<>(); for (ProteinModification mod : potentialModifications) { ModificationCondition condition = mod.getCondition(); @@ -333,10 +333,10 @@ public void identify(final List chains, } private void reset() { - identifiedModifiedCompounds = new LinkedHashSet(); + identifiedModifiedCompounds = new LinkedHashSet<>(); if (recordUnidentifiableModifiedCompounds) { - unidentifiableAtomLinkages = new LinkedHashSet(); - unidentifiableModifiedResidues = new LinkedHashSet(); + unidentifiableAtomLinkages = new LinkedHashSet<>(); + unidentifiableModifiedResidues = new LinkedHashSet<>(); } } @@ -392,7 +392,7 @@ private void identifyAdditionalAttachments(ModifiedCompound mc, // ligands to amino acid bonds for same modification of unknown category // will be combined in mergeModComps() // TODO: how about chain-chain links? - List identifiedGroups = new ArrayList(); + List identifiedGroups = new ArrayList<>(); for (StructureGroup num : mc.getGroups(false)) { Group group; try { @@ -464,7 +464,7 @@ private Group getGroup(StructureGroup num, List chains) throws StructureE * Merge identified modified compounds if linked. */ private void mergeModComps(List modComps) { - TreeSet remove = new TreeSet(); + TreeSet remove = new TreeSet<>(); int n = modComps.size(); for (int icurr=1; icurr modComps, List ligands) { // first put identified linkages in a map for fast query - Set identifiedLinkages = new HashSet(); + Set identifiedLinkages = new HashSet<>(); for (ModifiedCompound mc : modComps) { identifiedLinkages.addAll(mc.getAtomLinkages()); } @@ -555,7 +555,7 @@ private void recordUnidentifiableAtomLinkages(List modComps, } private void recordUnidentifiableModifiedResidues(List modComps) { - Set identifiedComps = new HashSet(); + Set identifiedComps = new HashSet<>(); for (ModifiedCompound mc : modComps) { identifiedComps.addAll(mc.getGroups(true)); } @@ -592,7 +592,7 @@ private void addModificationGroups( throw new IllegalArgumentException("Null argument(s)."); } - Map> mapSingleMultiComps = new HashMap>(); + Map> mapSingleMultiComps = new HashMap<>(); for (ProteinModification mod : modifications) { ModificationCondition condition = mod.getCondition(); for (Component comp : condition.getComponents()) { @@ -601,7 +601,7 @@ private void addModificationGroups( comp.isNTerminal(), comp.isCTerminal()); Set mult = mapSingleMultiComps.get(single); if (mult == null) { - mult = new HashSet(); + mult = new HashSet<>(); mapSingleMultiComps.put(single, mult); } mult.add(comp); @@ -621,7 +621,7 @@ private void addModificationGroups( for (Component comp : unionComponentSet(ligandsWildCard, comps)) { Set gs = saveTo.get(comp); if (gs==null) { - gs = new LinkedHashSet(); + gs = new LinkedHashSet<>(); saveTo.put(comp, gs); } gs.add(group); @@ -647,7 +647,7 @@ private void addModificationGroups( for (Component comp : unionComponentSet(residuesWildCard, comps)) { Set gs = saveTo.get(comp); if (gs==null) { - gs = new LinkedHashSet(); + gs = new LinkedHashSet<>(); saveTo.put(comp, gs); } gs.add(group); @@ -671,7 +671,7 @@ private void addModificationGroups( for (Component comp : unionComponentSet(nTermWildCard, comps)) { Set gs = saveTo.get(comp); if (gs==null) { - gs = new LinkedHashSet(); + gs = new LinkedHashSet<>(); saveTo.put(comp, gs); } gs.add(res); @@ -693,7 +693,7 @@ private void addModificationGroups( for (Component comp : unionComponentSet(cTermWildCard, comps)) { Set gs = saveTo.get(comp); if (gs==null) { - gs = new LinkedHashSet(); + gs = new LinkedHashSet<>(); saveTo.put(comp, gs); } gs.add(res); @@ -712,7 +712,7 @@ private Set unionComponentSet(Set set1, Set set if (set2 == null) return set1; - Set set = new HashSet(set1.size()+set2.size()); + Set set = new HashSet<>(set1.size()+set2.size()); set.addAll(set1); set.addAll(set2); @@ -728,7 +728,7 @@ private List> getMatchedAtomsOfLinkages( int nLink = linkages.size(); List> matchedAtomsOfLinkages = - new ArrayList>(nLink); + new ArrayList<>(nLink); for (int iLink=0; iLink> getMatchedAtomsOfLinkages( Set groups1 = mapCompGroups.get(comp1); Set groups2 = mapCompGroups.get(comp2); - List list = new ArrayList(); + List list = new ArrayList<>(); List potentialNamesOfAtomOnGroup1 = linkage.getPDBNameOfPotentialAtomsOnComponent1(); for (String name : potentialNamesOfAtomOnGroup1) { @@ -810,9 +810,9 @@ private void assembleLinkages(List> matchedAtomsOfLinkages, int nLink = matchedAtomsOfLinkages.size(); int[] indices = new int[nLink]; - Set identifiedCompounds = new HashSet(); + Set identifiedCompounds = new HashSet<>(); while (indices[0] atomLinkages = new ArrayList(nLink); + List atomLinkages = new ArrayList<>(nLink); for (int iLink=0; iLink> matchedAtomsOfLinkages, // matched int n = atomLinkages.size(); - List linkages = new ArrayList(n); + List linkages = new ArrayList<>(n); for (int i=0; i findAtomLinkages(final Group group1, throw new IllegalArgumentException("bondLengthTolerance cannot be negative."); } - List ret = new ArrayList(); + List ret = new ArrayList<>(); if (potentialNamesOfAtomOnGroup1 == null) { // if empty name, search for all atoms @@ -323,7 +323,7 @@ public static List getAtomNames(Group group) { } int n = atoms.size(); - List ret = new ArrayList(n); + List ret = new ArrayList<>(n); for (int i=0; i(); - triples = new HashSet(); - subjectTriples = new HashMap>(); - objectTriples = new HashMap>(); - relationTriples = new HashMap>(); - remoteTerms = new HashMap(); - localRemoteTerms = new HashSet(); + terms = new HashMap<>(); + triples = new HashSet<>(); + subjectTriples = new HashMap<>(); + objectTriples = new HashMap<>(); + relationTriples = new HashMap<>(); + remoteTerms = new HashMap<>(); + localRemoteTerms = new HashSet<>(); } public Impl(String name, String description) { @@ -337,7 +337,7 @@ public void setDescription(String description){ @Override public Set getTerms() { - return new HashSet(terms.values()); + return new HashSet<>(terms.values()); } @Override @@ -384,7 +384,7 @@ private Set filterTriples(Set base, Term subject, Term object, T return Collections.unmodifiableSet(new HashSet(base)); } - Set retval = new HashSet(); + Set retval = new HashSet<>(); for (Iterator i = base.iterator(); i.hasNext(); ) { Triple t = i.next(); if (subject != null && t.getSubject() != subject) { @@ -566,7 +566,7 @@ private void addTriple(Triple t) { private void pushTriple(Map> m, Term key, Triple t) { Set s = m.get(key); if (s == null) { - s = new HashSet(); + s = new HashSet<>(); m.put(key, s); } s.add(t); diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java index 387aa7c17a..209c76414f 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java @@ -155,7 +155,7 @@ public Impl(Ontology ontology, String name, String description, Object[] synonym this.description = description; this.ontology = ontology; - this.synonyms = new TreeSet(); + this.synonyms = new TreeSet<>(); if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms)); } diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java index 550c4d5651..a265f2ff56 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java @@ -182,7 +182,7 @@ public Impl(Term subject, this.name = name; this.description = description; - this.synonyms = new TreeSet(); + this.synonyms = new TreeSet<>(); if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms)); } diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java index d314b907ba..000d69740c 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/GOParser.java @@ -48,7 +48,7 @@ public Ontology parseGO(BufferedReader goFile, Ontology onto = factory.createOntology(ontoName, ontoDescription); Term isa = onto.importTerm(OntoTools.IS_A, null); Term partof = null; // fixme: onto.importTerm(OntoTools.PART_OF, null); - List termStack = new ArrayList(); + List termStack = new ArrayList<>(); String line; while ((line = goFile.readLine()) != null) { int leadSpaces = 0; @@ -122,7 +122,7 @@ private Term parseTerm(Ontology onto, String s) } else { Term t = onto.createTerm(termName, termDesc); if (toke.hasMoreTokens()) { - List secondaries = new ArrayList(); + List secondaries = new ArrayList<>(); while (toke.hasMoreTokens()) { secondaries.add(toke.nextToken()); } diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java index aeee6aa627..116ee735d2 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java @@ -90,7 +90,7 @@ public void documentEnd() { @Override public void documentStart() { - termStack = new ArrayList(); + termStack = new ArrayList<>(); } @Override diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java index 57b36bc600..96474a5385 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java @@ -61,10 +61,10 @@ public class OboFileParser { protected static final Map escapeChars = - new HashMap(); + new HashMap<>(); protected static final Map unescapeChars = - new HashMap(); + new HashMap<>(); static { escapeChars.put('n', '\n'); @@ -114,7 +114,7 @@ public SOPair(String str, int index, int endIndex) { public OboFileParser(){ - listeners = new ArrayList(); + listeners = new ArrayList<>(); } @@ -316,7 +316,7 @@ else if ("NARROW".equals(token)) } protected Map[] getDbxrefList(String line, int startoffset, int endoffset) throws IOException { - Vector> temp = new Vector>(); + Vector> temp = new Vector<>(); boolean stop = false; while (!stop) { int braceIndex = findUnescaped(line, '{', startoffset, endoffset); @@ -381,7 +381,7 @@ protected Map parseXref(String line, } - Map m = new HashMap(); + Map m = new HashMap<>(); m.put("xref",xref_str); m.put("desc",desc_str); return m; diff --git a/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java b/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java index f6013dadd2..cb8c0fa98e 100644 --- a/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java +++ b/biojava-protein-disorder/src/main/java/demo/PredictDisorder.java @@ -59,7 +59,7 @@ public static void main(String[] args) throws Exception{ private static ProteinSequence getUniprot(String uniProtID) throws Exception { AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet(); - UniprotProxySequenceReader uniprotSequence = new UniprotProxySequenceReader(uniProtID,set); + UniprotProxySequenceReader uniprotSequence = new UniprotProxySequenceReader<>(uniProtID,set); ProteinSequence seq = new ProteinSequence(uniprotSequence); diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java index 55b9bc5cc6..de53ae084d 100644 --- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java +++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java @@ -250,7 +250,7 @@ public static void writeFasta(final OutputStream outstream, */ public static List readFasta(final InputStream inStream) throws IOException { - final List seqs = new ArrayList(); + final List seqs = new ArrayList<>(); final BufferedReader infasta = new BufferedReader( new InputStreamReader(inStream, "UTF8"), 16000); diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java index 058e47546d..ccb85292b8 100644 --- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java +++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java @@ -214,7 +214,7 @@ public static Range[] scoresToRanges(float[] scores, float probability) { int count=0; int regionLen=0; - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); for(float score: scores) { count++; // Round to 2 decimal points before comparison @@ -245,7 +245,7 @@ public static Range[] scoresToRanges(float[] scores, float probability) { * @see #getDisorder(FastaSequence) */ public static Map getDisorderScores(List sequences) { - Map results = new TreeMap(); + Map results = new TreeMap<>(); results = sequences.stream().collect(Collectors.toMap(fastaSequence -> fastaSequence, fastaSequence -> predictSerial(fastaSequence))); return results; } @@ -258,7 +258,7 @@ public static Map getDisorderScores(List s * @see #getDisorder(FastaSequence) */ public static Map getDisorder(List sequences) { - Map disorderRanges = new TreeMap(); + Map disorderRanges = new TreeMap<>(); disorderRanges = sequences.stream().collect(Collectors.toMap(fastaSequence -> fastaSequence, fastaSequence -> getDisorder(fastaSequence) )); return disorderRanges; } diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java index e9db4ebdde..ff636c0710 100644 --- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java +++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java @@ -155,7 +155,7 @@ public String toString() { } - private static final Map models = new HashMap(); + private static final Map models = new HashMap<>(); public Model getModel(final int modelNum) { return ModelLoader.models.get(modelNum); diff --git a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java index fbd3ecc74d..9bd3e71af4 100644 --- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java +++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java @@ -81,7 +81,7 @@ public static void getAlignmentFromFasta() throws StructureException { // "4HHB.A:1-15" (residue range) // For this example, the built-in fasta parser will extract the correct accession. SequenceHeaderParserInterface headerParser; - headerParser = new GenericFastaHeaderParser(); + headerParser = new GenericFastaHeaderParser<>(); // Create AtomCache to fetch structures from the PDB AtomCache cache = new AtomCache(); diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java index 062bc6d8d7..a609d925e3 100644 --- a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java +++ b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java @@ -97,9 +97,9 @@ public static void main(String[] args) throws IOException, StructureException, I //Load the CA atoms of the structures AtomCache cache = new AtomCache(); - List identifiers = new ArrayList(); + List identifiers = new ArrayList<>(); - List atomArrays = new ArrayList(); + List atomArrays = new ArrayList<>(); for (String name:names) { atomArrays.add(cache.getAtoms(name)); identifiers.add(new SubstructureIdentifier(name)); diff --git a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java index c99678d4b9..fd2c15d28a 100644 --- a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java +++ b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java @@ -73,7 +73,7 @@ public static void getStructureFromFasta() { // "4HHB.A:1-15" (residue range) // For this example, the built-in fasta parser will extract the correct accession. SequenceHeaderParserInterface headerParser; - headerParser = new GenericFastaHeaderParser(); + headerParser = new GenericFastaHeaderParser<>(); // Create AtomCache to fetch structures from the PDB AtomCache cache = new AtomCache(); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java index 03aa7d5084..ff710bafb8 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java @@ -56,7 +56,7 @@ public class DisplayAFP { //TODO: same as getEqrPos??? !!! public static final List getEQRAlignmentPos(AFPChain afpChain){ - List lst = new ArrayList(); + List lst = new ArrayList<>(); char[] s1 = afpChain.getAlnseq1(); char[] s2 = afpChain.getAlnseq2(); @@ -107,7 +107,7 @@ private static boolean isAlignedPosition(int i, char c1, char c2, boolean isFatC * @param ca */ public static final List getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca){ - List lst = new ArrayList(); + List lst = new ArrayList<>(); if ( aligPos > 1) { System.err.println("multiple alignments not supported yet!"); return lst; @@ -407,7 +407,7 @@ private static final int getUngappedFatCatPos(AFPChain afpChain, int chainNr, in * @throws StructureException */ public static final Atom[] getAtomArray(Atom[] ca,List hetatms ) throws StructureException{ - List atoms = new ArrayList(); + List atoms = new ArrayList<>(); Collections.addAll(atoms, ca); logger.debug("got {} hetatoms", hetatms.size()); @@ -436,7 +436,7 @@ public static final Atom[] getAtomArray(Atom[] ca,List hetatms ) throws S public static final StructureAlignmentJmol display(AFPChain afpChain,Group[] twistedGroups, Atom[] ca1, Atom[] ca2,List hetatms1, List hetatms2 ) throws StructureException { - List twistedAs = new ArrayList(); + List twistedAs = new ArrayList<>(); for ( Group g: twistedGroups){ if ( g == null ) @@ -560,7 +560,7 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain,ca1, ca2); - List twistedAs = new ArrayList(); + List twistedAs = new ArrayList<>(); for ( Group g: twistedGroups){ if ( g == null ) diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java index 22f4ad1822..0532d91498 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java @@ -76,7 +76,7 @@ public DotPlotPanel(AFPChain alignment ){ int[][][] optAln = alignment.getOptAln(); // [block #][{0,1} chain index][pos] for(;alignNumber < optAln.length;alignNumber++) { - List alignPairs = new ArrayList(); + List alignPairs = new ArrayList<>(); for(int pos = 0; pos atomArrays = new ArrayList(); + List atomArrays = new ArrayList<>(); for (Structure s:structures){ Atom[] ca = StructureTools.getRepresentativeAtomArray(s); atomArrays.add(ca); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java index fac312875f..a0b6111a0e 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java @@ -76,7 +76,7 @@ public class MultipleAlignmentJmolDisplay { public static List getPDBresnum(int structNum, MultipleAlignment multAln, Atom[] ca){ - List lst = new ArrayList(); + List lst = new ArrayList<>(); for(Block block : multAln.getBlocks() ) { diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java index fe43530bed..ca983d3452 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ParameterGUI.java @@ -82,7 +82,7 @@ public ParameterGUI(ConfigStrucAligParams params, String algorithm) { assert(names.size() == types.size()); assert(names.size() == helps.size()); - textFields = new ArrayList(); + textFields = new ArrayList<>(); Box vBox = Box.createVerticalBox(); for (int i = 0 ; i < keys.size(); i++){ diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java index 9914f07d2a..83f1dda632 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.java @@ -44,7 +44,7 @@ public class AligPanelMouseMotionListener implements MouseMotionListener, MouseL public AligPanelMouseMotionListener(AligPanel parent){ this.parent = parent; - aligPosListeners = new ArrayList(); + aligPosListeners = new ArrayList<>(); prevPos = -1; isDragging = false; selectionStart = null; diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java index 1387bbd417..483df6f2df 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java @@ -139,7 +139,7 @@ public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, this.multAln = ensemble.getMultipleAlignment(0); //Create the sequence alignment and the structure-sequence mapping. - this.mapSeqToStruct = new ArrayList(); + this.mapSeqToStruct = new ArrayList<>(); this.alnSeq = MultipleAlignmentTools.getSequenceAlignment( this.multAln, this.mapSeqToStruct); @@ -162,7 +162,7 @@ public MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm) { this.multAln = msa; //Create the sequence alignment and the structure-sequence mapping. - this.mapSeqToStruct = new ArrayList(); + this.mapSeqToStruct = new ArrayList<>(); this.alnSeq = MultipleAlignmentTools.getSequenceAlignment( this.multAln, this.mapSeqToStruct); @@ -225,7 +225,7 @@ public void paintComponent(Graphics g){ else isGapped = true; //Loop through every structure to get all the points - List points = new ArrayList(); + List points = new ArrayList<>(); for (int str=0; str(); + aligPosListeners = new ArrayList<>(); prevPos = -1; isDragging = false; selectionStart = null; diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java index 045ff5ce8d..1a87aa786a 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.java @@ -30,7 +30,7 @@ public class DefaultAutoSuggestProvider implements AutoSuggestProvider { @Override public Vector getSuggestion(String userInput) { - Vector data = new Vector(); + Vector data = new Vector<>(); data.add(userInput + " no AutoSuggestProvider registered yet!"); return data; diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java index ff1e31b2d8..9e3c825910 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java @@ -247,7 +247,7 @@ private void init(){ lastWord = ""; regular = getFont(); busy = new Font(getFont().getName(), Font.ITALIC, getFont().getSize()); - suggestions = new Vector(); + suggestions = new Vector<>(); defaultText = DEFAULT_TEXT; diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java index d90fd0380f..136f184584 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java @@ -47,7 +47,7 @@ public Vector getSuggestion(String userInput) { long timeS = System.currentTimeMillis(); - List domains = new ArrayList(); + List domains = new ArrayList<>(); domains = getPossibleScopDomains(userInput); @@ -55,7 +55,7 @@ public Vector getSuggestion(String userInput) { // convert domains to Strings - Vector v=new Vector(); + Vector v=new Vector<>(); int counter = 0; for ( ScopDomain d : domains){ @@ -82,7 +82,7 @@ public Vector getSuggestion(String userInput) { private List getPossibleScopDomains(String userInput) { - List domains = new ArrayList(); + List domains = new ArrayList<>(); ScopDatabase scop = ScopFactory.getSCOP(); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java index fc7d209312..a9d65c3948 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java @@ -113,7 +113,7 @@ public MultipleAlignmentJmol(MultipleAlignment msa, frame.setJMenuBar(menu); this.multAln = msa; this.transformedAtoms = rotatedAtoms; - this.selectedStructures = new ArrayList(); + this.selectedStructures = new ArrayList<>(); frame.addWindowListener(new WindowAdapter() { @@ -432,7 +432,7 @@ public static String getJmolString(MultipleAlignment multAln, // Color the equivalent residues of every structure StringBuffer sel = new StringBuffer(); sel.append("select *; color lightgrey; backbone 0.1; "); - List> allPDB = new ArrayList>(); + List> allPDB = new ArrayList<>(); // Get the aligned residues of every structure for (int i = 0; i < multAln.size(); i++) { @@ -508,7 +508,7 @@ private static void printJmolScript4Block(Atom[] atoms, int str, int colorPos, int blockNum) { // Obtain the residues aligned in this block of the structure - List pdb = new ArrayList(); + List pdb = new ArrayList<>(); for (int i = 0; i < alignRes.get(str).size(); i++) { // Handle gaps - only color if it is not null diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java index 6a81491f82..d1ce5c0e30 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java @@ -50,7 +50,7 @@ public class RasmolCommandListener public RasmolCommandListener(JmolPanel panel, JTextField field){ textfield = field; jmolPanel = panel; - history = new ArrayList(); + history = new ArrayList<>(); historyPosition = -2; // -2 = history = empty; } diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java index c25336ab71..7a87f6cbb9 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java @@ -256,7 +256,7 @@ public void itemStateChanged(ItemEvent e) { zoomSlider.setMajorTickSpacing(100); zoomSlider.setPaintTicks(true); - Hashtable labelTable = new Hashtable(); + Hashtable labelTable = new Hashtable<>(); labelTable.put(0,new JLabel("0%")); labelTable.put(100,new JLabel("100%")); labelTable.put(200,new JLabel("200%")); @@ -559,8 +559,8 @@ private static void printJmolScript4Block(Atom[] ca1, Atom[] ca2, int blockNum, c1 = ColorUtils.getIntermediate(ColorUtils.orange, end1, blockNum, bk); c2 = ColorUtils.getIntermediate(ColorUtils.cyan, end2, blockNum, bk); - List pdb1 = new ArrayList(); - List pdb2 = new ArrayList(); + List pdb1 = new ArrayList<>(); + List pdb2 = new ArrayList<>(); for (int i = 0; i < optLen[bk]; i++) { /// int pos1 = optAln[bk][0][i]; diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java index b2c6917559..37a0133e78 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.java @@ -198,7 +198,7 @@ public ScaleableMatrixPanel(){ protected static Map createGradients() { - SortedMap gradients = new TreeMap(); + SortedMap gradients = new TreeMap<>(); int i = 0; //prepend number, since sorted alphabetically ColorSpace hsv = HSVColorSpace.getHSVColorSpace(); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java index 0aada492fb..93c7757201 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java @@ -232,7 +232,7 @@ public SequenceDisplay(StructurePairAligner structurePairAligner){ this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); - apos = new ArrayList(); + apos = new ArrayList<>(); } public void clearListeners(){ diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java index 7805df236a..70d69d03c5 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/PDBUploadPanel.java @@ -79,7 +79,7 @@ public class PDBUploadPanel public static JComboBox getFileFormatSelect(){ JComboBox fileType = new JComboBox<>(); - fileType = new JComboBox(new String[] {UserConfiguration.PDB_FORMAT,UserConfiguration.MMCIF_FORMAT}); + fileType = new JComboBox<>(new String[] {UserConfiguration.PDB_FORMAT,UserConfiguration.MMCIF_FORMAT}); fileType.setSelectedIndex(0); fileType.setMaximumSize(new Dimension(10,50)); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java index ae8d859951..c651b0deca 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java @@ -90,7 +90,7 @@ private Box getDomainPanel(JTextField f){ public List getStructures() throws StructureException { - List structures = new ArrayList(); + List structures = new ArrayList<>(); for (StructureIdentifier name:getNames()){ structures.add(getStructure(name)); @@ -100,7 +100,7 @@ public List getStructures() throws StructureException { public List getNames() { - List names = new ArrayList(); + List names = new ArrayList<>(); String raw = input.getText().trim(); String[] split = raw.split(" "); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java index e10331b9d5..11d7f2fd31 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java @@ -86,7 +86,7 @@ public SequenceMouseListener(SequenceDisplay parent) { coordManager = new CoordManager(); - alignmentPositionListeners = new ArrayList(); + alignmentPositionListeners = new ArrayList<>(); //renderer.getLayeredPane().addMouseListener(popupFrame); } diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java index bc29425c07..06542e5271 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java @@ -105,7 +105,7 @@ public SequenceScalePanel(int position) { setPrefSize(); coordManager = new CoordManager(); - apos = new ArrayList(); + apos = new ArrayList<>(); } diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java index 4678d68707..55ab77d2ad 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/GradientMapper.java @@ -61,7 +61,7 @@ public GradientMapper(Color negInf, Color posInf) { this(negInf,posInf,ColorSpace.getInstance(ColorSpace.CS_sRGB)); } public GradientMapper(Color negInf, Color posInf, ColorSpace cspace) { - mapping = new TreeMap(); + mapping = new TreeMap<>(); mapping.put(Double.NEGATIVE_INFINITY, negInf); mapping.put(Double.POSITIVE_INFINITY, posInf); interpolator = new LinearColorInterpolator(cspace); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java index f5fc7da991..52df113942 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java @@ -239,7 +239,7 @@ public static String printSymmetryAxes(CeSymmResult symm,boolean allAxes) for (Axis a : symmAxes) { RotationAxis rot = a.getRotationAxis(); List> cyclicForm = axes.getRepeatsCyclicForm(a); - List repAtoms = new ArrayList(); + List repAtoms = new ArrayList<>(); for(List cycle : cyclicForm) { for(Integer repeat : cycle) { repAtoms.addAll(Arrays.asList(repeats.get(repeat))); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java index 428635c78b..7686b98ac0 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java @@ -423,7 +423,7 @@ public String colorBySubunit() { Color4f c = colors[i]; List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } String id = getChainSpecification(modelNumbers, chainIds, j); @@ -454,7 +454,7 @@ public String colorBySequenceCluster() { Color4f c = colors[seqClusterIds.get(i)]; List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } String id = getChainSpecification(modelNumbers, chainIds, i); @@ -504,7 +504,7 @@ public String colorBySymmetry() { c.scale(scale); List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } String id = getChainSpecification(modelNumbers, chainIds, subunit); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java index 3ee6734d75..7fd90d2497 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java @@ -332,7 +332,7 @@ public String colorBySubunit() { Color4f c = colors[colorIndex]; List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } String id = getChainSpecification(modelNumbers, chainIds, subunit); @@ -362,7 +362,7 @@ public String colorBySequenceCluster() { Color4f c = colors[seqClusterIds.get(i)]; List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } String id = getChainSpecification(modelNumbers, chainIds, i); @@ -414,7 +414,7 @@ public String colorBySymmetry() { Color4f c = colors[colorIndex]; List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } for (int subunit: orbits.get(i)) { @@ -431,7 +431,7 @@ public String colorBySymmetry() { Color4f c = new Color4f(colors[i]); List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } List orbit = orbits.get(i); @@ -542,7 +542,7 @@ private Map> getCnColorMap() { Color4f c = colors[i]; List ids = colorMap.get(c); if (ids == null) { - ids = new ArrayList(); + ids = new ArrayList<>(); colorMap.put(c, ids); } ids.add(id); @@ -947,7 +947,7 @@ private static Vector3d[] getC2PolygonVertices(Vector3d axis, Vector3d reference private List getUniqueAxes() { - List uniqueRotations = new ArrayList(); + List uniqueRotations = new ArrayList<>(); for (int i = 0, n = rotationGroup.getOrder(); i < n; i++) { Rotation rotationI = rotationGroup.getRotation(i); diff --git a/biojava-structure/src/main/java/demo/DemoMultipleMC.java b/biojava-structure/src/main/java/demo/DemoMultipleMC.java index 4ca84f0174..6a60c454e6 100644 --- a/biojava-structure/src/main/java/demo/DemoMultipleMC.java +++ b/biojava-structure/src/main/java/demo/DemoMultipleMC.java @@ -92,9 +92,9 @@ public static void main(String[] args) throws IOException, StructureException, I //Load the CA atoms of the structures AtomCache cache = new AtomCache(); - List atomArrays = new ArrayList(); + List atomArrays = new ArrayList<>(); - List ids = new ArrayList(); + List ids = new ArrayList<>(); for (String name:names) { StructureIdentifier id = new StructureName(name); ids.add(id); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java index efe8822397..41021e0045 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java @@ -153,7 +153,7 @@ public AtomPositionMap(Atom[] atoms) { * @param atoms */ public AtomPositionMap(Atom[] atoms, GroupMatcher matcher) { - hashMap = new HashMap(); + hashMap = new HashMap<>(); for (int i = 0; i < atoms.length; i++) { Group group = atoms[i].getGroup(); ResidueNumber rn = group.getResidueNumber(); @@ -164,7 +164,7 @@ public AtomPositionMap(Atom[] atoms, GroupMatcher matcher) { } } Comparator vc = new ValueComparator(hashMap); - treeMap = new TreeMap(vc); + treeMap = new TreeMap<>(vc); treeMap.putAll(hashMap); } @@ -341,7 +341,7 @@ public List getRanges() { String currentChain = ""; ResidueNumber first = null; ResidueNumber prev = null; - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); for (ResidueNumber rn : treeMap.keySet()) { if (!rn.getChainName().equals(currentChain)) { if (first != null) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java index e6a243d7cf..3c5fd7af68 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java @@ -90,7 +90,7 @@ public BondImpl(Atom atomA, Atom atomB, int bondOrder, boolean addSelfToAtoms) { private void addSelfToAtoms() { List bonds = atomA.getBonds(); if (bonds==null) { - bonds = new ArrayList(AtomImpl.BONDS_INITIAL_CAPACITY); + bonds = new ArrayList<>(AtomImpl.BONDS_INITIAL_CAPACITY); atomA.setBonds(bonds); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java index 510230ccf6..2f534b2828 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java @@ -191,7 +191,7 @@ public enum Element { private static final Map allElements ; static { - allElements = new HashMap(); + allElements = new HashMap<>(); for (Element e : Element.values()){ allElements.put(e.toString().toLowerCase(), e); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java index 829e8abfc7..61300fe451 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java @@ -159,11 +159,11 @@ public EntityInfo (EntityInfo c) { this.title = c.title; if (c.synonyms!=null) { - this.synonyms = new ArrayList(); + this.synonyms = new ArrayList<>(); synonyms.addAll(c.synonyms); } if (c.ecNums!=null) { - this.ecNums = new ArrayList(); + this.ecNums = new ArrayList<>(); ecNums.addAll(c.ecNums); } @@ -380,7 +380,7 @@ private void initResSerialsMap(Chain c) { return; } - Map resNums2ResSerials = new HashMap(); + Map resNums2ResSerials = new HashMap<>(); chains2pdbResNums2ResSerials.put(c.getId(), resNums2ResSerials); for (int i=0;i initExpTechStr2Value() { - HashMap expTechStr2Value = new HashMap(); + HashMap expTechStr2Value = new HashMap<>(); for(ExperimentalTechnique exp:ExperimentalTechnique.values()) { expTechStr2Value.put(exp.getName(), exp); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java index 7fa92f7363..e6c3373b9d 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java @@ -95,7 +95,7 @@ public Set getResidueTypes() { * @return */ private static Set matchPolymerTypes(Set allowedTypes) { - Set matched = new HashSet(); + Set matched = new HashSet<>(); for(ResidueType restype : ResidueType.values()) { if(allowedTypes.contains(restype.polymerType)) { matched.add(restype); @@ -109,7 +109,7 @@ private static Set matchPolymerTypes(Set allowedTypes) * @return */ private static Set getHetatmTypes() { - Set unmatched = new HashSet(); + Set unmatched = new HashSet<>(); for(ResidueType restype : ResidueType.values()) { if(!AMINOACID.getResidueTypes().contains(restype) && !NUCLEOTIDE.getResidueTypes().contains(restype) ) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java index a4c77badd2..5e4052a1dc 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java @@ -32,8 +32,8 @@ public class JournalArticle implements Serializable { private static final long serialVersionUID = 5062668226159515468L; - private List authorList = new ArrayList(); - private List editorList = new ArrayList(); + private List authorList = new ArrayList<>(); + private List editorList = new ArrayList<>(); private String title = ""; private String ref = ""; private String journalName = ""; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java index 42e4662689..a26745f9a5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java @@ -59,7 +59,7 @@ public class Mutator{ List supportedAtoms; public Mutator(){ - supportedAtoms = new ArrayList(); + supportedAtoms = new ArrayList<>(); supportedAtoms.add("N"); supportedAtoms.add("CA"); supportedAtoms.add("C"); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java index 216f0b2476..f3cc2d8d16 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java @@ -104,7 +104,7 @@ public PDBHeader(){ rFree = DEFAULT_RFREE; rWork = DEFAULT_RFREE; - bioAssemblies = new LinkedHashMap(); + bioAssemblies = new LinkedHashMap<>(); crystallographicInfo = new PDBCrystallographicInfo(); keywords = new ArrayList<>(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java index 79dbedbdfc..05fb941fc8 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRange.java @@ -137,7 +137,7 @@ public static List parseMultiple(String s) { } String[] parts = s.split(","); - List list = new ArrayList(parts.length); + List list = new ArrayList<>(parts.length); for (String part : parts) { list.add(parse(part)); } @@ -352,7 +352,7 @@ public static Iterator multiIterator(AtomPositionMap map, List parseMultiple(List ranges) { - List rrs = new ArrayList(ranges.size()); + List rrs = new ArrayList<>(ranges.size()); for (String range : ranges) { ResidueRange rr = ResidueRange.parse(range); if (rr != null) rrs.add(rr); @@ -361,7 +361,7 @@ public static List parseMultiple(List ranges) { } public static List toStrings(List ranges) { - List list = new ArrayList(ranges.size()); + List list = new ArrayList<>(ranges.size()); for (ResidueRange range : ranges) { list.add(range.toString()); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java index fbf9cb07bf..d9769d0134 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java @@ -129,7 +129,7 @@ public static ResidueRangeAndLength parse(String s, AtomPositionMap map) { public static List parseMultiple(List ranges, AtomPositionMap map) { - List rrs = new ArrayList(ranges.size()); + List rrs = new ArrayList<>(ranges.size()); for (String range : ranges) { ResidueRangeAndLength rr = ResidueRangeAndLength.parse(range, map); if (rr != null) rrs.add(rr); @@ -145,7 +145,7 @@ public static List parseMultiple(List ranges, Ato */ public static List parseMultiple(String s, AtomPositionMap map) { String[] parts = s.split(","); - List list = new ArrayList(parts.length); + List list = new ArrayList<>(parts.length); for (String part : parts) { list.add(parse(part, map)); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java index 306b3a2cee..9158906d23 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java @@ -42,7 +42,7 @@ public class Site implements PDBRecord, Comparable { private static final String lineEnd = System.getProperty("line.separator"); private String siteID = ""; - private List groups = new ArrayList(); + private List groups = new ArrayList<>(); //variables for REMARK 800 private String evCode = ""; private String description = ""; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java index d52d358385..731267aafa 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java @@ -64,7 +64,7 @@ private StandardAminoAcid() { * @author Tamas Horvath provided the standard amino acids */ static { - aminoAcids = new HashMap(); + aminoAcids = new HashMap<>(); InputStream fileStream = StandardAminoAcid.class.getClassLoader().getResourceAsStream(STANDARD_AMINOS_FILE); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java index 08b7ebceb0..4fce5b853e 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java @@ -126,7 +126,7 @@ public Structure clone() { // go through each chain and clone chain for (int i=0;i cloned_model = new ArrayList(); + List cloned_model = new ArrayList<>(); for (int j=0;j AMINOACID_BACKBONE_ATOMS; static { - nucleotides30 = new HashMap(); + nucleotides30 = new HashMap<>(); nucleotides30.put("DA", 'A'); nucleotides30.put("DC", 'C'); nucleotides30.put("DG", 'G'); @@ -215,14 +215,14 @@ public class StructureTools { // store nucleic acids (C, G, A, T, U, and I), and // the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), // and - nucleotides23 = new HashMap(); + nucleotides23 = new HashMap<>(); String[] names = { "C", "G", "A", "T", "U", "I", "+C", "+G", "+A", "+T", "+U", "+I" }; for (String n : names) { nucleotides23.put(n, n.charAt(n.length() - 1)); } - aminoAcids = new HashMap(); + aminoAcids = new HashMap<>(); aminoAcids.put("GLY", 'G'); aminoAcids.put("ALA", 'A'); aminoAcids.put("VAL", 'V'); @@ -254,7 +254,7 @@ public class StructureTools { aminoAcids.put("PYH", 'O'); aminoAcids.put("PYL", 'O'); - hBondDonorAcceptors = new HashSet(); + hBondDonorAcceptors = new HashSet<>(); hBondDonorAcceptors.add(Element.N); hBondDonorAcceptors.add(Element.O); hBondDonorAcceptors.add(Element.S); @@ -320,7 +320,7 @@ public static int getNrGroups(Structure s) { public static Atom[] getAtomArray(Structure s, String[] atomNames) { List chains = s.getModel(0); - List atoms = new ArrayList(); + List atoms = new ArrayList<>(); extractAtoms(atomNames, chains, atoms); return atoms.toArray(new Atom[0]); @@ -787,7 +787,7 @@ private static void extractAtoms(String[] atomNames, List chains, List thisGroupAtoms = new ArrayList(); + List thisGroupAtoms = new ArrayList<>(); // flag to check if this group contains all the requested atoms. boolean thisGroupAllAtoms = true; for (String atomName : atomNames) { @@ -927,7 +927,7 @@ public static Atom[] getRepresentativeAtomArray(Chain c) { public static Atom[] cloneAtomArray(Atom[] ca) { Atom[] newCA = new Atom[ca.length]; - List model = new ArrayList(); + List model = new ArrayList<>(); int apos = -1; for (Atom a : ca) { apos++; @@ -973,7 +973,7 @@ public static Atom[] cloneAtomArray(Atom[] ca) { public static Group[] cloneGroups(Atom[] ca) { Group[] newGroup = new Group[ca.length]; - List model = new ArrayList(); + List model = new ArrayList<>(); int apos = -1; for (Atom a : ca) { apos++; @@ -1081,7 +1081,7 @@ public static Atom[] duplicateCA2(Atom[] ca2) { */ public static Atom[] getAtomCAArray(Structure s) { - List atoms = new ArrayList(); + List atoms = new ArrayList<>(); for (Chain c : s.getChains()) { for (Group g : c.getAtomGroups()) { @@ -1460,12 +1460,12 @@ public static Map getGroupDistancesWithinShell( // for speed, we avoid calculating square roots radius = radius * radius; - Map distances = new HashMap(); + Map distances = new HashMap<>(); // we only need this if we're averaging distances // note that we can't use group.getAtoms().size() because some the // group's atoms be outside the shell - Map atomCounts = new HashMap(); + Map atomCounts = new HashMap<>(); for (Chain chain : structure.getChains()) { groupLoop: for (Group chainGroup : chain.getAtomGroups()) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java index 49789d2fc9..6419603c64 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java @@ -109,7 +109,7 @@ public SubstructureIdentifier(String id) { this.ranges = ResidueRange.parseMultiple(rangeStr); } else { - this.ranges = new LinkedList(); + this.ranges = new LinkedList<>(); } } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java index 3718259c56..0b2d21ae82 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java @@ -295,7 +295,7 @@ private static void transformOrigPDB(int n, int[] res1, int[] res2, private static Atom[] getAtoms(Atom[] ca, int[] positions, int length, boolean clone) { - List atoms = new ArrayList(); + List atoms = new ArrayList<>(); for (int i = 0; i < length; i++) { int p = positions[i]; Atom a; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java index 8b1c2629ef..956529262c 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java @@ -135,7 +135,7 @@ public static StructureAlignment[] getAllAlgorithms(){ public static String[] getAllAlgorithmNames(){ StructureAlignment[] algos = getAllAlgorithms(); - List names = new ArrayList(); + List names = new ArrayList<>(); for (StructureAlignment alg : algos){ names.add(alg.getAlgorithmName()); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java index fb7382cf71..20bc11827e 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java @@ -82,7 +82,7 @@ public abstract class AbstractUserArgumentProcessor implements UserArgumentProce protected StartupParameters params ; - public static final List mandatoryArgs= new ArrayList(); + public static final List mandatoryArgs= new ArrayList<>(); protected AbstractUserArgumentProcessor(){ params = getStartupParametersInstance(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java index 7e88bcb0b2..6c045ba48e 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java @@ -118,7 +118,7 @@ public CECalculator(CeParameters params){ dist1= new double[0][0]; dist2= new double[0][0]; this.params = params; - matrixListeners = new ArrayList(); + matrixListeners = new ArrayList<>(); } @@ -1143,7 +1143,7 @@ private void checkBestTraces( AFPChain afpChain, } // start to convert CE internal datastructure to generic AFPChain one... - List afpSet = new ArrayList(); + List afpSet = new ArrayList<>(); for (int afp=0;afp atoms = new ArrayList(); + List atoms = new ArrayList<>(); for ( int i = 0 ; i < length ; i++){ Atom a; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java index 2d7e76cf77..881fc224b4 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java @@ -415,8 +415,8 @@ public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCal // Fix numbering: // First, split up the atoms into left and right blocks - List< ResiduePair > left = new ArrayList(); // residues from left of duplication - List< ResiduePair > right = new ArrayList(); // residues from right of duplication + List< ResiduePair > left = new ArrayList<>(); // residues from left of duplication + List< ResiduePair > right = new ArrayList<>(); // residues from right of duplication for(int i=0;i= firstRes && optAln[0][1][i] <= lastRes ) { // not trimmed @@ -432,7 +432,7 @@ public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCal alignLen = 0; // Now we don't care about left/right, so just call them "blocks" - List> blocks = new ArrayList>(2); + List> blocks = new ArrayList<>(2); if( !left.isEmpty() ) { blocks.add(left); alignLen += left.size(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java index 05db803cf0..4f57161268 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java @@ -116,7 +116,7 @@ public CeCalculatorEnhanced(CeParameters params){ dist1= new double[0][0]; dist2= new double[0][0]; this.params = params; - matrixListeners = new ArrayList(); + matrixListeners = new ArrayList<>(); } @@ -1134,7 +1134,7 @@ private void checkBestTraces( AFPChain afpChain, } // start to convert CE internal datastructure to generic AFPChain one... - List afpSet = new ArrayList(); + List afpSet = new ArrayList<>(); for (int afp=0;afp atoms = new ArrayList(); + List atoms = new ArrayList<>(); for ( int i = 0 ; i < length ; i++){ Atom a; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java index 8383acf585..106aa08090 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java @@ -205,7 +205,7 @@ public Integer getMaxGapSize() { @Override public List getUserConfigHelp() { - List params =new ArrayList(); + List params =new ArrayList<>(); String helpMaxGap = "This parameter configures the maximum gap size G, that is applied during the AFP extension. The larger the value, the longer the calculation time can become, Default value is 30. Set to 0 for no limit. " ; //String helpRmsdThr = "This configures the RMSD threshold applied during the trace of the fragment matrix."; String helpWinSize = "This configures the fragment size m of Aligned Fragment Pairs (AFPs)."; @@ -222,7 +222,7 @@ public List getUserConfigHelp() { @Override public List getUserConfigParameters() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("MaxGapSize"); //params.add("RmsdThr"); params.add("WinSize"); @@ -236,7 +236,7 @@ public List getUserConfigParameters() { @Override public List getUserConfigParameterNames(){ - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("max. gap size G (during AFP extension)."); //params.add("RMSD threshold during trace of the fragment matrix."); params.add("fragment size m"); @@ -250,7 +250,7 @@ public List getUserConfigParameterNames(){ @Override @SuppressWarnings("rawtypes") public List getUserConfigTypes() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add(Integer.class); //params.add(Double.class); params.add(Integer.class); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java index b10e09fbfd..7fa9c4cf28 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java @@ -126,7 +126,7 @@ private static void permuteArray(T[] arr, int cp) { "Permutation point ("+cp+") must be between -ca2.length and ca2.length-1" ); } - List temp = new ArrayList(cp); + List temp = new ArrayList<>(cp); // shift residues left for(int i=0;i>> blocks = new ArrayList>>(afpChain.getBlockNum()*2); + List>> blocks = new ArrayList<>(afpChain.getBlockNum()*2); //Update residue indices // newi = (oldi-cp) % N @@ -342,7 +342,7 @@ private static void permuteOptAln(AFPChain afpChain, int cp) continue; // set up storage for the current block - List> currBlock = new ArrayList>(2); + List> currBlock = new ArrayList<>(2); currBlock.add( new ArrayList()); currBlock.add( new ArrayList()); blocks.add(currBlock); @@ -356,7 +356,7 @@ private static void permuteOptAln(AFPChain afpChain, int cp) //this happens when the new alignment crosses the protein terminus if( optAln[block][1][pos-1]+cp= ca2len) { - currBlock = new ArrayList>(2); + currBlock = new ArrayList<>(2); currBlock.add( new ArrayList()); currBlock.add( new ArrayList()); blocks.add(currBlock); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java index 0d9428a6b7..c7d68f2d04 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java @@ -329,7 +329,7 @@ private boolean initFromFile() { } private static Set getChainNames(SubstructureIdentifier si) { - Set chains = new TreeSet(); + Set chains = new TreeSet<>(); List ranges = si.getResidueRanges(); for(ResidueRange range : ranges) { String chainName = range.getChainName(); @@ -604,7 +604,7 @@ public int compareTo(StructureName o) { * @return The best match for name among the domains of scopDB, or null if none match. */ public static ScopDomain guessScopDomain(String name, ScopDatabase scopDB) { - List matches = new LinkedList(); + List matches = new LinkedList<>(); // Try exact match first ScopDomain domain = scopDB.getDomainByScopID(name); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java index a672cc9831..52b903189d 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java @@ -48,7 +48,7 @@ public class AFPCalculator public static void extractAFPChains(FatCatParameters params, AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws StructureException { - List afpSet = new ArrayList(); + List afpSet = new ArrayList<>(); afpChain.setAfpSet(afpSet); if ( debug ) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java index 760b196bd5..bee2eb4df5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java @@ -366,7 +366,7 @@ public void setSparse(int sparse) @Override public List getUserConfigHelp() { - List params = new ArrayList(); + List params = new ArrayList<>(); String fragLen = "The length of the fragments."; String rmsdCutHelp = "The RMSD cutoff to be used during AFP detection."; String disCutHelp = "The distance cutoff used when calculate the connectivity of AFP pairs"; @@ -382,7 +382,7 @@ public List getUserConfigHelp() { @Override public List getUserConfigParameterNames() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("Fragment Length"); params.add("RMSD Cutoff"); params.add("AFP Distance Cutoff"); @@ -393,7 +393,7 @@ public List getUserConfigParameterNames() { @Override public List getUserConfigParameters() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("FragLen"); params.add("RmsdCut"); params.add("DisCut"); @@ -406,7 +406,7 @@ public List getUserConfigParameters() { @SuppressWarnings({ "rawtypes" }) public List getUserConfigTypes() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add(Integer.class); params.add(Double.class); params.add(Double.class); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java index 862e7d8d50..05cc643aa8 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/JointFragments.java @@ -40,7 +40,7 @@ public class JointFragments { List idxlist; public JointFragments(){ - idxlist = new ArrayList(); + idxlist = new ArrayList<>(); rms = 999; } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java index d06f91e7d9..41cef89031 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java @@ -180,7 +180,7 @@ public AFPChain(AFPChain o) { this.alignScoreUpdate = o.alignScoreUpdate; this.afpChainTwiNum = o.afpChainTwiNum; this.minLen = o.minLen; - this.afpSet = new ArrayList(o.afpSet); + this.afpSet = new ArrayList<>(o.afpSet); this.afpIndex = o.afpIndex == null? null: o.afpIndex.clone(); this.afpAftIndex = o.afpAftIndex == null? null: o.afpAftIndex.clone(); this.afpBefIndex = o.afpBefIndex == null? null: o.afpBefIndex.clone(); @@ -440,7 +440,7 @@ private void init(){ blockResSize = new int[maxTra+1]; - afpSet = new ArrayList(); + afpSet = new ArrayList<>(); totalLenIni = totalLenOpt = 0; totalRmsdIni = totalRmsdOpt = 0.0; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java index b1ae2bf543..796da8382b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.java @@ -48,7 +48,7 @@ protected AbstractScoresCache(AbstractScoresCache cache) { @Override public void putScore(String property, Double score) { if(scores == null) { - scores = new TreeMap(); + scores = new TreeMap<>(); } scores.put(property, score); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java index 402aa5984e..becc817e85 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java @@ -80,7 +80,7 @@ public BlockImpl(BlockImpl b) { this.alignRes = null; if (b.alignRes != null) { // Make a deep copy of everything - alignRes = new ArrayList>(); + alignRes = new ArrayList<>(); for (int k = 0; k < b.size(); k++) { alignRes.add(new ArrayList(b.alignRes.get(k))); } @@ -188,7 +188,7 @@ public List getAlignResCounts() { if (alignResCounts != null) return alignResCounts; - alignResCounts = new ArrayList(size()); + alignResCounts = new ArrayList<>(size()); for (int s = 0; s < size(); s++) { int count = 0; for (int r = 0; r < length(); r++) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java index c817853634..5282f83b31 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java @@ -98,7 +98,7 @@ public BlockSetImpl(BlockSetImpl bs) { blocks = null; if (bs.blocks != null) { // Make a deep copy of everything - this.blocks = new ArrayList(); + this.blocks = new ArrayList<>(); for (Block b : bs.blocks) { Block newB = b.clone(); newB.setBlockSet(this); @@ -143,7 +143,7 @@ public void setMultipleAlignment(MultipleAlignment parent) { @Override public List getBlocks() { if (blocks == null) - blocks = new ArrayList(); + blocks = new ArrayList<>(); return blocks; } @@ -232,7 +232,7 @@ public List getAlignResCounts() { if (alignResCounts != null) return alignResCounts; - alignResCounts = new ArrayList(size()); + alignResCounts = new ArrayList<>(size()); for (int s = 0; s < size(); s++) alignResCounts.add(0); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java index 04b31447b0..a6df171705 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java @@ -115,7 +115,7 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) { distanceMatrix = null; if (e.distanceMatrix != null) { // Make a deep copy of everything - distanceMatrix = new ArrayList(); + distanceMatrix = new ArrayList<>(); for (Matrix mat : e.distanceMatrix) { distanceMatrix.add((Matrix) mat.clone()); } @@ -124,7 +124,7 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) { multipleAlignments = null; if (e.multipleAlignments != null) { // Make a deep copy of everything - multipleAlignments = new ArrayList(); + multipleAlignments = new ArrayList<>(); for (MultipleAlignment msa : e.multipleAlignments) { MultipleAlignment newMSA = msa.clone(); newMSA.setEnsemble(this); @@ -133,10 +133,10 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) { } if (e.atomArrays != null) { - atomArrays = new ArrayList(e.atomArrays); + atomArrays = new ArrayList<>(e.atomArrays); } if (e.structureIdentifiers != null) { - structureIdentifiers = new ArrayList( + structureIdentifiers = new ArrayList<>( e.structureIdentifiers); } } @@ -326,7 +326,7 @@ public void setAtomArrays(List atomArrays) { */ public void updateAtomArrays() throws IOException, StructureException { AtomCache cache = new AtomCache(); - atomArrays = new ArrayList(); + atomArrays = new ArrayList<>(); for (StructureIdentifier name : getStructureIdentifiers()) { Atom[] array = cache.getRepresentativeAtoms(name); atomArrays.add(array); @@ -346,7 +346,7 @@ public List getDistanceMatrix() { public void updateDistanceMatrix() { // Reset the distance Matrix variable - distanceMatrix = new ArrayList(); + distanceMatrix = new ArrayList<>(); for (int s = 0; s < size(); s++) { Atom[] ca = atomArrays.get(s); @@ -359,7 +359,7 @@ public void updateDistanceMatrix() { public List getMultipleAlignments() { if (multipleAlignments == null) { - multipleAlignments = new ArrayList(); + multipleAlignments = new ArrayList<>(); } return multipleAlignments; } @@ -377,7 +377,7 @@ public void setMultipleAlignments(List alignments) { @Override public void addMultipleAlignment(MultipleAlignment alignment) { if (multipleAlignments == null) { - multipleAlignments = new ArrayList(); + multipleAlignments = new ArrayList<>(); } multipleAlignments.add(alignment); alignment.setEnsemble(this); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java index 91d087b8b8..7f55f1c2f0 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java @@ -100,7 +100,7 @@ public MultipleAlignmentImpl(MultipleAlignmentImpl ma) { blockSets = null; if (ma.blockSets != null) { // Make a deep copy of everything - this.blockSets = new ArrayList(); + this.blockSets = new ArrayList<>(); for (BlockSet bs : ma.blockSets) { BlockSet newBS = bs.clone(); newBS.setMultipleAlignment(this); @@ -127,7 +127,7 @@ public MultipleAlignmentImpl clone() { @Override public String toString() { - List ids = new ArrayList(parent + List ids = new ArrayList<>(parent .getStructureIdentifiers().size()); for (StructureIdentifier i : parent.getStructureIdentifiers()) { ids.add(i.getIdentifier()); @@ -147,13 +147,13 @@ public String toString() { @Override public List getBlockSets() { if (blockSets == null) - blockSets = new ArrayList(); + blockSets = new ArrayList<>(); return blockSets; } @Override public List getBlocks() { - List blocks = new ArrayList(); + List blocks = new ArrayList<>(); for (BlockSet bs : getBlockSets()) { blocks.addAll(bs.getBlocks()); } @@ -263,7 +263,7 @@ public List getAlignResCounts() { if (alignResCounts != null) return alignResCounts; - alignResCounts = new ArrayList(size()); + alignResCounts = new ArrayList<>(size()); for (int s = 0; s < size(); s++) alignResCounts.add(0); @@ -282,7 +282,7 @@ public List getCoverages() { return coverages; List counts = getAlignResCounts(); - coverages = new ArrayList(size()); + coverages = new ArrayList<>(size()); for (int s = 0; s < size(); s++) coverages.add(counts.get(s) / (double) getAtomArrays().get(s).length); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java index dcc843d791..702ed1d6a5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java @@ -124,7 +124,7 @@ private MultipleAlignment generateSeed(List atomArrays) int size = atomArrays.size(); //List to store the all-to-all alignments - List> afpAlignments = new ArrayList>(); + List> afpAlignments = new ArrayList<>(); for (int i=0; i()); for (int j=0; j atomArrays) int threads = params.getNrThreads(); ExecutorService executor = Executors.newFixedThreadPool(threads); - List> afpFuture = new ArrayList>(); + List> afpFuture = new ArrayList<>(); //Create all the possible protein pairwise combinations //(N*(N-1)/2) and call the pairwise alignment algorithm @@ -184,7 +184,7 @@ private static int chooseReferenceRMSD(List> afpAlignments){ int size = afpAlignments.size(); - List RMSDs = new ArrayList(); + List RMSDs = new ArrayList<>(); for (int i=0; i flexibleBoundaries = new TreeSet(); + SortedSet flexibleBoundaries = new TreeSet<>(); //Stores the equivalencies of all the structures as a double List - List> equivalencies = new ArrayList>(); + List> equivalencies = new ArrayList<>(); for (int str=0; str()); for (int res=0; res> alnRes = - new ArrayList>(size); + new ArrayList<>(size); for (int k=0; k()); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java index 0845c61300..83b2247bbe 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java @@ -125,7 +125,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln, imposer = new CoreSuperimposer(reference); if (params.getConvergenceSteps() == 0) { - List lens = new ArrayList(); + List lens = new ArrayList<>(); for (int i = 0; i < size; i++) lens.add(atomArrays.get(i).length); convergenceSteps = Collections.min(lens) * size; @@ -142,8 +142,8 @@ public MultipleMcOptimizer(MultipleAlignment seedAln, Lmin = params.getMinBlockLen(); // Delete all shorter than Lmin blocks, and empty blocksets - List toDelete = new ArrayList(); - List emptyBs = new ArrayList(); + List toDelete = new ArrayList<>(); + List emptyBs = new ArrayList<>(); for (Block b : msa.getBlocks()) { if (b.getCoreLength() < Lmin) { @@ -183,12 +183,12 @@ public MultipleAlignment call() throws Exception { private void initialize() throws StructureException { // Initialize alignment variables - freePool = new ArrayList>(); - List> aligned = new ArrayList>(); + freePool = new ArrayList<>(); + List> aligned = new ArrayList<>(); // Generate freePool residues from the ones not aligned for (int i = 0; i < size; i++) { - List residues = new ArrayList(); + List residues = new ArrayList<>(); for (BlockSet bs : msa.getBlockSets()) { for (Block b : bs.getBlocks()) { for (int l = 0; l < b.length(); l++) { @@ -219,9 +219,9 @@ private void initialize() throws StructureException { // Initialize the history variables if (history) { - lengthHistory = new ArrayList(); - rmsdHistory = new ArrayList(); - scoreHistory = new ArrayList(); + lengthHistory = new ArrayList<>(); + rmsdHistory = new ArrayList<>(); + scoreHistory = new ArrayList<>(); } } @@ -249,9 +249,9 @@ public MultipleAlignment optimize() throws StructureException { // Save the state of the system MultipleAlignment lastMSA = msa.clone(); - List> lastFreePool = new ArrayList>(); + List> lastFreePool = new ArrayList<>(); for (int k = 0; k < size; k++) { - SortedSet p = new TreeSet(); + SortedSet p = new TreeSet<>(); for (Integer l : freePool.get(k)) p.add(l); lastFreePool.add(p); @@ -349,10 +349,10 @@ private boolean checkGaps() { boolean shrinkedAny = false; - List> shrinkColumns = new ArrayList>(); + List> shrinkColumns = new ArrayList<>(); // Loop for each Block for (Block b : msa.getBlocks()) { - List shrinkCol = new ArrayList(); + List shrinkCol = new ArrayList<>(); // Loop for each column in the Block for (int res = 0; res < b.length(); res++) { int gapCount = 0; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java index a49d9febc3..cc42754463 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.java @@ -54,7 +54,7 @@ public MultipleMcParameters(){ @Override public List getUserConfigParameters() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("RandomSeed"); params.add("MinBlockLen"); params.add("MinAlignedStructures"); @@ -69,7 +69,7 @@ public List getUserConfigParameters() { @Override public List getUserConfigParameterNames() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("Random Seed"); params.add("Minimum Block Length"); params.add("Minimum Structures per Column"); @@ -85,7 +85,7 @@ public List getUserConfigParameterNames() { @SuppressWarnings("rawtypes") public List getUserConfigTypes() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add(Integer.class); params.add(Integer.class); params.add(Integer.class); @@ -100,7 +100,7 @@ public List getUserConfigTypes() { @Override public List getUserConfigHelp() { - List params =new ArrayList(); + List params =new ArrayList<>(); String randomSeed = "Random seed for the optimizer random number generator."; String minBlockLen = diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java index 097615a554..56a8be3687 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.java @@ -127,8 +127,8 @@ public void superimpose(MultipleAlignment alignment) Atom[] ref = atomArrays.get(reference); Atom[] curr = atomArrays.get(i); - List atomSet1 = new ArrayList(); - List atomSet2 = new ArrayList(); + List atomSet1 = new ArrayList<>(); + List atomSet2 = new ArrayList<>(); for( Block blk : bs.getBlocks() ) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java index ad5b1dd83f..d3fe14ba20 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.java @@ -69,7 +69,7 @@ public static List getRotatedAtoms(MultipleAlignment multAln) + atomArrays.get(i).length); } - List rotatedAtoms = new ArrayList(); + List rotatedAtoms = new ArrayList<>(); // TODO implement independent BlockSet superposition of the structure List transf = multAln.getBlockSet(0).getTransformations(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java index 1422348e6d..1a9642e251 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java @@ -66,7 +66,7 @@ public static void calculateScores(MultipleAlignment alignment) alignment.putScore(RMSD, getRMSD(trans)); // Put AvgTM-Score - List lengths = new ArrayList(alignment.size()); + List lengths = new ArrayList<>(alignment.size()); for (Atom[] atoms : alignment.getAtomArrays()) { lengths.add(atoms.length); } @@ -237,7 +237,7 @@ public static double getAvgTMScore(MultipleAlignment alignment) List trans = MultipleAlignmentTools.transformAtoms(alignment); - List lengths = new ArrayList(alignment.size()); + List lengths = new ArrayList<>(alignment.size()); for (Atom[] atoms : alignment.getAtomArrays()) { lengths.add(atoms.length); } @@ -314,7 +314,7 @@ public static double getRefTMScore(MultipleAlignment alignment, int ref) List trans = MultipleAlignmentTools.transformAtoms(alignment); - List lengths = new ArrayList(alignment.size()); + List lengths = new ArrayList<>(alignment.size()); for (Atom[] atoms : alignment.getAtomArrays()) { lengths.add(atoms.length); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java index d790eec19c..836d5c922a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java @@ -108,7 +108,7 @@ public static List getSequenceAlignment( MultipleAlignment alignment, final List mapSeqToStruct) { // Initialize sequence variables - List alnSequences = new ArrayList(); + List alnSequences = new ArrayList<>(); for (int str = 0; str < alignment.size(); str++) alnSequences.add(""); mapSeqToStruct.clear(); @@ -116,13 +116,13 @@ public static List getSequenceAlignment( int globalPos = -1; // Initialize helper variables in constucting the sequence alignment - List> freePool = new ArrayList>(); - List> blockStarts = new ArrayList>(); - List> aligned = new ArrayList>(); + List> freePool = new ArrayList<>(); + List> blockStarts = new ArrayList<>(); + List> aligned = new ArrayList<>(); // Generate freePool residues from the ones not aligned for (int i = 0; i < alignment.size(); i++) { - List residues = new ArrayList(); + List residues = new ArrayList<>(); freePool.add(new TreeSet()); blockStarts.add(new TreeSet()); for (BlockSet bs : alignment.getBlockSets()) { @@ -346,7 +346,7 @@ public static List getBlockSequenceAlignment( MultipleAlignment alignment, List mapSeqToStruct) { // Initialize sequence variables - List alnSequences = new ArrayList(); + List alnSequences = new ArrayList<>(); for (int str = 0; str < alignment.size(); str++) alnSequences.add(""); mapSeqToStruct.clear(); @@ -661,7 +661,7 @@ public static List transformAtoms(MultipleAlignment alignment) { } List atomArrays = alignment.getAtomArrays(); - List transformed = new ArrayList(atomArrays.size()); + List transformed = new ArrayList<>(atomArrays.size()); // Loop through structures for (int i = 0; i < atomArrays.size(); i++) { @@ -729,7 +729,7 @@ public static List transformAtoms(MultipleAlignment alignment) { */ public static List getCorePositions(Block block) { - List corePositions = new ArrayList(); + List corePositions = new ArrayList<>(); for (int col = 0; col < block.length(); col++) { boolean core = true; @@ -800,9 +800,9 @@ public static MultipleSequenceAlignment toPr + "the structures aligned are not proteins"); } - MultipleSequenceAlignment msa = new MultipleSequenceAlignment(); + MultipleSequenceAlignment msa = new MultipleSequenceAlignment<>(); - Map uniqueID = new HashMap(); + Map uniqueID = new HashMap<>(); List seqs = getSequenceAlignment(msta); for (int i = 0; i < msta.size(); i++) { // Make sure the identifiers are unique (required by AccessionID) @@ -875,7 +875,7 @@ public static Matrix getRMSDMatrix(MultipleAlignment msa) { for (int j = i; j < msa.size(); j++) { if (i == j) rmsdMat.set(i, j, 0.0); - List compared = new ArrayList(); + List compared = new ArrayList<>(); compared.add(superposed.get(i)); compared.add(superposed.get(j)); double rmsd = MultipleAlignmentScorer.getRMSD(compared); @@ -947,7 +947,7 @@ public static Phylogeny getStructuralTree(MultipleAlignment msta) { BasicSymmetricalDistanceMatrix rmsdDist = (BasicSymmetricalDistanceMatrix) DistanceMatrixCalculator .structuralDistance(rmsdMat, 1, 5, 0.4); // Set the identifiers of the matrix - Map alreadySeen = new HashMap(); + Map alreadySeen = new HashMap<>(); for (int i = 0; i < msta.size(); i++) { // Make sure the identifiers are unique String id = msta.getStructureIdentifier(i).toString(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java index 70482a8c78..7db5d2e714 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java @@ -95,7 +95,7 @@ public static String toFatCat(MultipleAlignment alignment) { fatcat.append(alignment.toString() + "\n\n"); // Get the alignment sequences and the mapping - List mapSeqToStruct = new ArrayList(); + List mapSeqToStruct = new ArrayList<>(); List alnSequences = MultipleAlignmentTools .getSequenceAlignment(alignment, mapSeqToStruct); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java index 0285f8a90d..24fe3abe9c 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.java @@ -125,8 +125,8 @@ public void superimpose(MultipleAlignment alignment) Atom[] ref = atomArrays.get(reference); Atom[] curr = atomArrays.get(i); - List atomSet1 = new ArrayList(); - List atomSet2 = new ArrayList(); + List atomSet1 = new ArrayList<>(); + List atomSet2 = new ArrayList<>(); for( Block blk : bs.getBlocks() ) { if( blk.size() != atomArrays.size()) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java index cb9b870111..87f51844ec 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java @@ -118,7 +118,7 @@ public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] frag StrucAligParameters params) throws StructureException { //the final list of joined fragments stores as apairs - List fll = new ArrayList(); + List fll = new ArrayList<>(); FragmentPair[] tmpfidx = new FragmentPair[fraglst.length]; for ( int i=0 ; i < fraglst.length; i++){ @@ -203,7 +203,7 @@ public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] frag Collections.sort(fll,comp); Collections.reverse(fll); int m = Math.min(params.getMaxrefine(),fll.size()); - List retlst = new ArrayList(); + List retlst = new ArrayList<>(); for ( int i = 0 ; i < m ; i++){ JointFragments jf = fll.get(i); retlst.add(jf); @@ -372,7 +372,7 @@ public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDi int[] used = new int[n]; //the final list of joined fragments stores as apairs - List fll = new ArrayList(); + List fll = new ArrayList<>(); double adiff = angleDiff * Math.PI / 180d; logger.debug("addiff{}", adiff); @@ -443,7 +443,7 @@ public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDi Collections.sort(fll,comp); Collections.reverse(fll); int m = Math.min(maxRefine,fll.size()); - List retlst = new ArrayList(); + List retlst = new ArrayList<>(); for ( int i = 0 ; i < m ; i++){ JointFragments jf = fll.get(i); retlst.add(jf); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java index d0b9752519..83ed3ffaae 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.java @@ -209,7 +209,7 @@ private void setPath(){ int n; IndexPair[] backId = new IndexPair[a.getRows()+1+a.getCols()+1]; - List path = new ArrayList(); + List path = new ArrayList<>(); backId[0] = new IndexPair((short)(a.getRows()),(short)(a.getCols())); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java index d7dcade047..2b92f3330d 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java @@ -94,7 +94,7 @@ public static QsAlignResult align(List s1, List s2, List c2 = SubunitClusterer.cluster(s2, cParams).getClusters(); // STEP 2: match each subunit cluster between groups O(N^2*L^2) - inter - Map clusterMap = new HashMap(); + Map clusterMap = new HashMap<>(); for (int i = 0; i < c1.size(); i++) { for (int j = 0; j < c2.size(); j++) { @@ -123,15 +123,15 @@ public static QsAlignResult align(List s1, List s2, // Take a cluster match as reference int index1 = 0; int index2 = clust1.size() - clust2.size(); - Map subunitMap = new HashMap(); + Map subunitMap = new HashMap<>(); subunitMap.put(index1, index2); // Map cluster id to their subunit matching - Map> clustSubunitMap = new HashMap>(); + Map> clustSubunitMap = new HashMap<>(); clustSubunitMap.put(globalKey, subunitMap); // Change order of key set so that globalKey is first - List keySet = new ArrayList(clusterMap.keySet()); + List keySet = new ArrayList<>(clusterMap.keySet()); keySet.remove((Integer) globalKey); keySet.add(0, globalKey); @@ -141,7 +141,7 @@ public static QsAlignResult align(List s1, List s2, if (key == globalKey) subunitMap = clustSubunitMap.get(key); else - subunitMap = new HashMap(); + subunitMap = new HashMap<>(); // Obtain the clusters of each subunit group clust1 = c1.get(key); @@ -224,11 +224,11 @@ public static QsAlignResult align(List s1, List s2, logger.info("Cluster Subunit Map: " + clustSubunitMap.toString()); // Unfold the nested map into subunit map and alignment - subunitMap = new HashMap(); - List alignRes1 = new ArrayList(); - List alignRes2 = new ArrayList(); - List atomArray1 = new ArrayList(); - List atomArray2 = new ArrayList(); + subunitMap = new HashMap<>(); + List alignRes1 = new ArrayList<>(); + List alignRes2 = new ArrayList<>(); + List atomArray1 = new ArrayList<>(); + List atomArray2 = new ArrayList<>(); for (int key : clustSubunitMap.keySet()) { @@ -274,7 +274,7 @@ public static QsAlignResult align(List s1, List s2, // Fill in the alignment information BlockSet bs = new BlockSetImpl(msa); Block b = new BlockImpl(bs); - List> alignRes = new ArrayList>(2); + List> alignRes = new ArrayList<>(2); alignRes.add(alignRes1); alignRes.add(alignRes2); b.setAlignRes(alignRes); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java index 986bf3a8d3..74b8b891d5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.java @@ -42,7 +42,7 @@ public SmithWaterman3DParameters() { @Override public List getUserConfigHelp() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("The Gap open penalty"); params.add("The Gap extension penalty"); params.add("The maximum RMSD of superposition allowed"); @@ -54,7 +54,7 @@ public List getUserConfigHelp() { @Override public List getUserConfigParameterNames() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("Gap Open"); params.add("Gap Extension"); params.add("Maximum RMSD"); @@ -65,7 +65,7 @@ public List getUserConfigParameterNames() { @Override public List getUserConfigParameters() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add("GapOpen"); params.add("GapExtend"); params.add("MaxRmsd"); @@ -77,7 +77,7 @@ public List getUserConfigParameters() { @Override @SuppressWarnings("rawtypes") public List getUserConfigTypes() { - List params = new ArrayList(); + List params = new ArrayList<>(); params.add(Short.class); params.add(Short.class); params.add(Double.class); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java index cdde7480a3..11f36456ab 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java @@ -90,7 +90,7 @@ public static Atom getTranslation(AFPChain afpChain,Atom[] ca1,Atom[] ca2) throw } public static Atom[] getAlignedAtoms1(AFPChain afpChain,Atom[] ca1){ - List atoms = new ArrayList(); + List atoms = new ArrayList<>(); int blockNum = afpChain.getBlockNum(); @@ -111,7 +111,7 @@ public static Atom[] getAlignedAtoms1(AFPChain afpChain,Atom[] ca1){ } public static Atom[] getAlignedAtoms2(AFPChain afpChain,Atom[] ca2){ - List atoms = new ArrayList(); + List atoms = new ArrayList<>(); int blockNum = afpChain.getBlockNum(); @@ -329,7 +329,7 @@ public static Map calcIdSimilarity(char[] seq1, char[] seq2, int if ( seq1 == null || seq2 == null){ logger.warn("Can't calc %ID for an empty alignment! "); - Map m = new HashMap(); + Map m = new HashMap<>(); m.put("similarity", similarity); m.put("identity", identity); return m; @@ -369,7 +369,7 @@ public static Map calcIdSimilarity(char[] seq1, char[] seq2, int similarity = (similarity) / eqr; identity = identity/eqr; } - Map m = new HashMap(); + Map m = new HashMap<>(); m.put("similarity", similarity); m.put("identity", identity); @@ -400,7 +400,7 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain,ca1, ca2); - List twistedAs = new ArrayList(); + List twistedAs = new ArrayList<>(); for ( Group g: twistedGroups){ if ( g == null ) @@ -412,8 +412,8 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, } Atom[] twistedAtoms = twistedAs.toArray(new Atom[twistedAs.size()]); - List hetatms = new ArrayList(); - List nucs1 = new ArrayList(); + List hetatms = new ArrayList<>(); + List nucs1 = new ArrayList<>(); Group g1 = ca1[0].getGroup(); Chain c1 = null; if ( g1 != null) { @@ -423,8 +423,8 @@ public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, nucs1 = c1.getAtomGroups(GroupType.NUCLEOTIDE); } } - List hetatms2 = new ArrayList(); - List nucs2 = new ArrayList(); + List hetatms2 = new ArrayList<>(); + List nucs2 = new ArrayList<>(); Group g2 = ca2[0].getGroup(); Chain c2 = null; if ( g2 != null){ diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java index f7660e2097..82d38d010c 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java @@ -157,7 +157,7 @@ public static boolean isSequentialAlignment(AFPChain afpChain, boolean checkWith * @throws StructureException If afpChain is not one-to-one */ public static Map alignmentAsMap(AFPChain afpChain) throws StructureException { - Map map = new HashMap(); + Map map = new HashMap<>(); if( afpChain.getAlnLength() < 1 ) { return map; @@ -223,11 +223,11 @@ public static Map applyAlignment(Map alignmentMap, Map ide if(k<0) throw new IllegalArgumentException("k must be positive"); if(k==1) { - return new HashMap(alignmentMap); + return new HashMap<>(alignmentMap); } // Convert to lists to establish a fixed order - List preimage = new ArrayList(alignmentMap.keySet()); // currently unmodified - List image = new ArrayList(preimage); + List preimage = new ArrayList<>(alignmentMap.keySet()); // currently unmodified + List image = new ArrayList<>(preimage); for(int n=1;n Map applyAlignment(Map alignmentMap, Map ide - Map imageMap = new HashMap(alignmentMap.size()); + Map imageMap = new HashMap<>(alignmentMap.size()); //TODO handle nulls consistently. // assure that all the residues in the domain are valid keys @@ -321,8 +321,8 @@ public static int getSymmetryOrder(Map alignment, */ public static int getSymmetryOrder(Map alignment, Map identity, final int maxSymmetry, final float minimumMetricChange) { - List preimage = new ArrayList(alignment.keySet()); // currently unmodified - List image = new ArrayList(preimage); + List preimage = new ArrayList<>(alignment.keySet()); // currently unmodified + List image = new ArrayList<>(preimage); int bestSymmetry = 1; double bestMetric = Double.POSITIVE_INFINITY; //lower is better @@ -443,10 +443,10 @@ public static int getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float min */ public static Map guessSequentialAlignment( Map alignment, boolean inverseAlignment) { - Map identity = new HashMap(); + Map identity = new HashMap<>(); - SortedSet aligned1 = new TreeSet(); - SortedSet aligned2 = new TreeSet(); + SortedSet aligned1 = new TreeSet<>(); + SortedSet aligned2 = new TreeSet<>(); for(Entry pair : alignment.entrySet()) { aligned1.add(pair.getKey()); @@ -480,18 +480,18 @@ public static Map guessSequentialAlignment( public static List>> getOptAlnAsList(AFPChain afpChain) { int[][][] optAln = afpChain.getOptAln(); int[] optLen = afpChain.getOptLen(); - List>> blocks = new ArrayList>>(afpChain.getBlockNum()); + List>> blocks = new ArrayList<>(afpChain.getBlockNum()); for(int blockNum=0;blockNum align1 = new ArrayList(optLen[blockNum]); - List align2 = new ArrayList(optLen[blockNum]); + List align1 = new ArrayList<>(optLen[blockNum]); + List align2 = new ArrayList<>(optLen[blockNum]); for(int pos=0;pos> block = new ArrayList>(2); + List> block = new ArrayList<>(2); block.add(align1); block.add(align2); blocks.add(block); @@ -627,7 +627,7 @@ public static AFPChain splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2) // Determine block lengths // Split blocks if residue indices don't increase monotonically - List newBlkLen = new ArrayList(); + List newBlkLen = new ArrayList<>(); boolean blockChanged = false; for(int blk=0;blk blocks = new ArrayList( newBlkLen.size() ); + List blocks = new ArrayList<>( newBlkLen.size() ); int oldBlk = 0; int pos = 0; @@ -758,7 +758,7 @@ public static AFPChain replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, // increasing monotonically. Integer[] res1 = alignment.keySet().toArray(new Integer[0]); Arrays.sort(res1); - List blockLens = new ArrayList(2); + List blockLens = new ArrayList<>(2); int optLength = 0; Integer lastRes = alignment.get(res1[0]); int blkLen = lastRes==null?0:1; @@ -989,17 +989,17 @@ public static Object resizeArray (Object oldArray, int newSize) { */ public static String toConciseAlignmentString(Map alignment, Map identity) { // Clone input to prevent changes - Map alig = new HashMap(alignment); + Map alig = new HashMap<>(alignment); // Generate inverse alignment - Map> inverse = new HashMap>(); + Map> inverse = new HashMap<>(); for(Entry e: alig.entrySet()) { S val = identity.get(e.getValue()); if( inverse.containsKey(val) ) { List l = inverse.get(val); l.add(e.getKey()); } else { - List l = new ArrayList(); + List l = new ArrayList<>(); l.add(e.getKey()); inverse.put(val,l); } @@ -1058,7 +1058,7 @@ public static String toConciseAlignmentString(Map alignment) { * @see #toConciseAlignmentString(Map, Map) */ public static Map fromConciseAlignmentString(String string) { - Map map = new HashMap(); + Map map = new HashMap<>(); boolean matches = true; while (matches) { Pattern pattern = Pattern.compile("(\\d+)>(\\d+)"); @@ -1201,7 +1201,7 @@ public static void alignmentToSIF(Writer out,AFPChain afpChain, */ public static final List getAlignedModel(Atom[] ca){ - List model = new ArrayList(); + List model = new ArrayList<>(); for ( Atom a: ca){ Group g = a.getGroup(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java index 513b2bdf5d..8b8af2539a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java @@ -100,14 +100,14 @@ public static String[] configureBean(Object bean, String[] args) throw new ConfigurationException("Couldn't get information for target bean " + ex.getMessage()); } - Map propertiesByName = new HashMap(); + Map propertiesByName = new HashMap<>(); for (PropertyDescriptor pd : bi.getPropertyDescriptors() ) { propertiesByName.put(pd.getName(), pd); } - List anonArgs = new ArrayList(); - Map> arrayProps = new HashMap>(); - Set usedProps = new HashSet(); + List anonArgs = new ArrayList<>(); + Map> arrayProps = new HashMap<>(); + Set usedProps = new HashSet<>(); boolean stdInUsed = false; boolean stdOutUsed = false; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java index d803ad1a80..282e971c84 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java @@ -223,7 +223,7 @@ public static void rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2){ } public static AFPChain[] parseMultiXML(String xml) throws IOException { - List afpChains = new ArrayList(); + List afpChains = new ArrayList<>(); try { @@ -316,7 +316,7 @@ public static AFPChain[] parseMultiXML(String xml) throws IOException { a.setBlockShiftVector(blockShiftVector); int afpNum = Integer.parseInt(getAttribute(rootElement,"afpNum")); - List afpSet = new ArrayList(); + List afpSet = new ArrayList<>(); for (int afp=0;afp parseXMLfile(String xml) throws ParserConfigurationException, SAXException, IOException { List ensembles = - new ArrayList(); + new ArrayList<>(); //Convert string to XML document DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); @@ -178,7 +178,7 @@ else if ("ScoresCache".equals(child.getNodeName())){ private static Block parseBlock(Node root, BlockSet blockSet) { Block b = new BlockImpl(blockSet); - List> alignRes = new ArrayList>(); + List> alignRes = new ArrayList<>(); b.setAlignRes(alignRes); NodeList children = root.getChildNodes(); @@ -276,7 +276,7 @@ private static void parseHeader(Node node, private static void parseStructures(Node root, MultipleAlignmentEnsemble ensemble) { - List names = new ArrayList(); + List names = new ArrayList<>(); ensemble.setStructureIdentifiers(names); NamedNodeMap atts = root.getAttributes(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java index 433e053a3c..afcc4f95ac 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.java @@ -44,7 +44,7 @@ public class PdbPairXMLConverter { public static final String DEFAULT_METHOD_NAME = FatCatRigid.algorithmName; public static PdbPairsMessage convertXMLtoPairs(String xml) { - SortedSet pairs = new TreeSet(); + SortedSet pairs = new TreeSet<>(); PdbPairsMessage message = new PdbPairsMessage(); try { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java index 170ee5ff47..6aa415a8d9 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PdbPairsMessage.java @@ -40,7 +40,7 @@ public PdbPairsMessage(){ method = PdbPairXMLConverter.DEFAULT_METHOD_NAME; - pairs = new TreeSet(); + pairs = new TreeSet<>(); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java index 05d34b8d21..6c8be18ed9 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/GroupAsa.java @@ -44,7 +44,7 @@ public class GroupAsa implements Serializable { private static HashMap initTriPeptAsas() { // ASA in extended tripeptide conformation (GLY-X-GLY) from Miller et al JMB 1987 (for calculation of relative ASAs) - HashMap map = new HashMap(); + HashMap map = new HashMap<>(); map.put('A', 113.0); map.put('R', 241.0); map.put('N', 158.0); @@ -223,8 +223,8 @@ public Object clone() { GroupAsa n = new GroupAsa(this.g); n.setAsaC(this.getAsaC()); n.setAsaU(this.getAsaU()); - n.atomAsaUs = new ArrayList(this.atomAsaUs.size()); - n.atomAsaCs = new ArrayList(this.atomAsaCs.size()); + n.atomAsaUs = new ArrayList<>(this.atomAsaUs.size()); + n.atomAsaCs = new ArrayList<>(this.atomAsaCs.size()); for (int i=0;i getChains() throws StructureException { - Set chains = new HashSet(); + Set chains = new HashSet<>(); List rrs = toCanonical().getResidueRanges(); for (ResidueRange rr : rrs) chains.add(rr.getChainName()); return chains; @@ -436,7 +436,7 @@ public String getIdentifier() { @Override public SubstructureIdentifier toCanonical() throws StructureException{ - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); String chain = String.valueOf(getDomainName().charAt(getDomainName().length() - 3)); for (CathSegment segment : this.getSegments()) { ranges.add(new ResidueRange(chain, segment.getStart(), segment.getStop())); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java index 77fe36fd8e..4a7796e6af 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java @@ -45,7 +45,7 @@ public class CathFactory { private static CathDatabase cath; - private static Map versions = new HashMap(); + private static Map versions = new HashMap<>(); /** * Sets the default (singleton) CathDatabase. diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java index acf1489a02..3f0f44158b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java @@ -97,11 +97,11 @@ public CathInstallation(String cacheLocation, boolean usingCDDF, boolean parseCF cathVersion = DEFAULT_VERSION; cathDownloadUrl = CATH_DOWNLOAD_URL; - pdbMap = new HashMap>(); - domainMap = new HashMap(); - cathTree = new HashMap(); + pdbMap = new HashMap<>(); + domainMap = new HashMap< >(); + cathTree = new HashMap<>(); - if (parseCathFragments) fragmentMap = new HashMap>(); + if (parseCathFragments) fragmentMap = new HashMap<>(); } @@ -207,7 +207,7 @@ public List getByCategory(CathCategory category) { ensureDomallInstalled(); } ensureNodeListInstalled(); - List matches = new ArrayList(); + List matches = new ArrayList<>(); CathNode node; for ( String nodeId : cathTree.keySet() ) { if ( (node = cathTree.get(nodeId)).getCategory() == category ) { @@ -224,7 +224,7 @@ public List filterByCathCode(String query) { } else { ensureDomallInstalled(); } - List matches = new ArrayList(); + List matches = new ArrayList<>(); for ( String k : domainMap.keySet() ) { if ( domainMap.get(k).getCATH().startsWith(query) ) { matches.add( domainMap.get(k) ); @@ -236,7 +236,7 @@ public List filterByCathCode(String query) { @Override public List getTree(CathDomain domain) { CathNode node = getCathNode( domain.getCATH() ); - List tree = new ArrayList(); + List tree = new ArrayList<>(); while (node != null) { node = getCathNode( node.getParentId() ); if (node != null) tree.add(node); @@ -248,14 +248,14 @@ public List getTree(CathDomain domain) { @Override public List filterByNodeName(String query) { ensureNodeListInstalled(); - List matchingNodes = new ArrayList(); + List matchingNodes = new ArrayList<>(); CathNode node; for ( String nodeId : cathTree.keySet() ) { if ( (node = cathTree.get(nodeId) ).getDescription().startsWith(query) ) { matchingNodes.add(node); } } - List matches = new ArrayList(); + List matches = new ArrayList<>(); for (CathNode n : matchingNodes) { matches.addAll(getDomainsByNodeId(n.getNodeId())); } @@ -269,7 +269,7 @@ public List filterByDescription(String query) { } else { ensureDomallInstalled(); } - List matches = new ArrayList(); + List matches = new ArrayList<>(); for ( String k : domainMap.keySet() ) { if ( domainMap.get(k).getName().startsWith(query) ) { matches.add( domainMap.get(k) ); @@ -328,7 +328,7 @@ public List getDomainsByNodeId(String nodeId) { } else { ensureDomallInstalled(); } - List domains = new ArrayList(); + List domains = new ArrayList<>(); for (String domainName : domainMap.keySet()) { CathDomain description = domainMap.get(domainName); if ( description.getCATH().startsWith(nodeId) ) { @@ -366,7 +366,7 @@ private void parseCathDomainList(BufferedReader bufferedReader) throws IOExcepti if ( pdbMap.containsKey(pdbId)){ domainList = pdbMap.get(pdbId); } else { - domainList = new ArrayList(); + domainList = new ArrayList<>(); pdbMap.put(pdbId,domainList); } @@ -447,7 +447,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw } else if ( line.startsWith("DSEQS") ) { seqs = seqs.append( line.substring(10) ); } else if ( line.startsWith("NSEGMENTS") ) { - segments = new ArrayList(); + segments = new ArrayList<>(); } else if ( line.startsWith("SEGMENT") ) { segment = new CathSegment(); sseqh = new StringBuilder(); @@ -484,7 +484,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw if ( pdbMap.containsKey(pdbId)){ domainList = pdbMap.get(pdbId); } else { - domainList = new ArrayList(); + domainList = new ArrayList<>(); pdbMap.put(pdbId,domainList); } @@ -584,7 +584,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{ continue; } - List segments = new ArrayList(numberOfSegments); + List segments = new ArrayList<>(numberOfSegments); segIdx = 1; // Offset from domIdx. for (int j=1; j<=numberOfSegments; j++) { CathSegment segment = new CathSegment(); @@ -611,7 +611,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{ domIdx += 6*numberOfSegments + 1; } if (parseCathFragments) { - List fragments = new ArrayList(numberOfFragments); + List fragments = new ArrayList<>(numberOfFragments); for (int i=1; i<=numberOfFragments; i++) { CathFragment fragment = new CathFragment(); fragment.setFragmentId(i); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java index d73d747cb6..7851b8dbf3 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java @@ -679,9 +679,9 @@ public boolean divideInternally(SubunitClustererParameters clusterParams) } // Divide the Subunits in their repeats - List newSubunits = new ArrayList(subunits.size() + List newSubunits = new ArrayList<>(subunits.size() * columns.size()); - List> newSubunitEQR = new ArrayList>( + List> newSubunitEQR = new ArrayList<>( subunits.size() * columns.size()); for (int s = 0; s < subunits.size(); s++) { @@ -700,7 +700,7 @@ public boolean divideInternally(SubunitClustererParameters clusterParams) .get(s).getStructure())); // Recalculate equivalent residues - List eqr = new ArrayList(); + List eqr = new ArrayList<>(); for (int p = 0; p < columns.get(r).size(); p++) { eqr.add(subunitEQR.get(s).get(columns.get(r).get(p)) - start); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java index 487a51b564..45641d1e58 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java @@ -66,7 +66,7 @@ public static List extractSubunits(Structure structure, int absMinLen, double fraction, int minLen) { // The extracted subunit container - List subunits = new ArrayList(); + List subunits = new ArrayList<>(); for (Chain c : structure.getPolyChains()) { // Only take protein chains @@ -107,7 +107,7 @@ private static int calcAdjustedMinimumSequenceLength( int minLength = Integer.MAX_VALUE; // Extract the length List, the min and the max - List lengths = new ArrayList(); + List lengths = new ArrayList<>(); for (int i = 0; i < subunits.size(); i++) { if (subunits.get(i).size() >= absMinLen) { maxLength = Math.max(subunits.get(i).size(), maxLength); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java index e1297faec9..34de552786 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/AtomContactSet.java @@ -42,7 +42,7 @@ public class AtomContactSet implements Serializable, Iterable { public AtomContactSet(double cutoff) { this.cutoff = cutoff; - this.contacts = new HashMap,AtomContact>(); + this.contacts = new HashMap<>(); } public void add(AtomContact contact) { @@ -87,7 +87,7 @@ public Iterator iterator() { } private Pair getAtomIdPairFromContact(AtomContact contact) { - Pair pair = new Pair( + Pair pair = new Pair<>( new AtomIdentifier(contact.getPair().getFirst().getPDBserial(),contact.getPair().getFirst().getGroup().getChainId()), new AtomIdentifier(contact.getPair().getSecond().getPDBserial(),contact.getPair().getSecond().getGroup().getChainId())); @@ -132,7 +132,7 @@ public List getContactsWithinDistance(double distance) { String.format("%.2f", distance)+" is larger than contacts' distance cutoff "+ String.format("%.2f", cutoff)); - List list = new ArrayList(); + List list = new ArrayList<>(); for (AtomContact contact:this.contacts.values()) { if (contact.getDistance() getIndexPair() { - return new Pair(i,j); + return new Pair<>(i,j); } public int getI() { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java index 5123831ec6..11e2a59283 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java @@ -40,8 +40,8 @@ public class GridCell { private ArrayList jIndices; public GridCell(Grid parent){ - iIndices = new ArrayList(); - jIndices = new ArrayList(); + iIndices = new ArrayList<>(); + jIndices = new ArrayList<>(); this.grid = parent; } @@ -70,7 +70,7 @@ public int getNumJindices() { */ public List getContactsWithinCell(){ - List contacts = new ArrayList(); + List contacts = new ArrayList<>(); Point3d[] iAtoms = grid.getIAtoms(); Point3d[] jAtoms = grid.getJAtoms(); @@ -110,7 +110,7 @@ public List getContactsWithinCell(){ */ public List getContactsToOtherCell(GridCell otherCell){ - List contacts = new ArrayList(); + List contacts = new ArrayList<>(); Point3d[] iAtoms = grid.getIAtoms(); Point3d[] jAtoms = grid.getJAtoms(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java index 16c0eb08c5..07b163730d 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java @@ -41,7 +41,7 @@ public class GroupContact implements Serializable { private List atomContacts; public GroupContact() { - atomContacts = new ArrayList(); + atomContacts = new ArrayList<>(); } public void addAtomContact(AtomContact atomContact) { @@ -82,7 +82,7 @@ public List getAtomContacts() { */ public List getContactsWithinDistance(double distance) { - List list = new ArrayList(); + List list = new ArrayList<>(); for (AtomContact contact:this.atomContacts) { if (contact.getDistance(){ private HashMap, GroupContact> contacts; public GroupContactSet() { - contacts = new HashMap, GroupContact>(); + contacts = new HashMap<>(); } /** @@ -52,7 +52,7 @@ public GroupContactSet() { * @param atomContacts */ public GroupContactSet(AtomContactSet atomContacts) { - contacts = new HashMap, GroupContact>(); + contacts = new HashMap<>(); atoms2groups(atomContacts); } @@ -69,8 +69,8 @@ private void atoms2groups(AtomContactSet atomContacts) { // we skip the self-residue contacts if (iResidue.equals(jResidue)) continue; - Pair residuePair = new Pair (iResidue, jResidue); - Pair pair = new Pair(new ResidueIdentifier(iResidue), new ResidueIdentifier(jResidue)); + Pair residuePair = new Pair<> (iResidue, jResidue); + Pair pair = new Pair<>(new ResidueIdentifier(iResidue), new ResidueIdentifier(jResidue)); if (!contacts.containsKey(pair)) { @@ -152,7 +152,7 @@ public Iterator iterator() { } private Pair getResIdPairFromContact(GroupContact groupContact) { - return new Pair( + return new Pair<>( new ResidueIdentifier(groupContact.getPair().getFirst()), new ResidueIdentifier(groupContact.getPair().getSecond()) ); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java index b26275cde8..351e00f25b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java @@ -522,7 +522,7 @@ public Pair> getRimResidues(double bsaToAsaCutoff, double minAsaForS } } - return new Pair>(rim1, rim2); + return new Pair<>(rim1, rim2); } /** @@ -613,8 +613,8 @@ public double getContactOverlapScore(StructureInterface other, boolean invert) { return 0; } - Pair thisCompounds = new Pair(thisChains.getFirst().getEntityInfo(), thisChains.getSecond().getEntityInfo()); - Pair otherCompounds = new Pair(otherChains.getFirst().getEntityInfo(), otherChains.getSecond().getEntityInfo()); + Pair thisCompounds = new Pair<>(thisChains.getFirst().getEntityInfo(), thisChains.getSecond().getEntityInfo()); + Pair otherCompounds = new Pair<>(otherChains.getFirst().getEntityInfo(), otherChains.getSecond().getEntityInfo()); if (checkMolIdMatch(thisCompounds,otherCompounds)) { @@ -706,7 +706,7 @@ public Pair getParentCompounds() { logger.warn("Could not find parents chains, compounds will be null"); return null; } - return new Pair(chains.getFirst().getEntityInfo(), chains.getSecond().getEntityInfo()); + return new Pair<>(chains.getFirst().getEntityInfo(), chains.getSecond().getEntityInfo()); } private Structure getParentStructure() { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java index 5b1699bf8a..8743cdff9a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java @@ -40,7 +40,7 @@ public class StructureInterfaceCluster implements Serializable { public StructureInterfaceCluster() { - this.members = new ArrayList(); + this.members = new ArrayList<>(); } public List getMembers() { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java index 0f03a5a31c..bbb0323ce9 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/SerializableCache.java @@ -117,7 +117,7 @@ public Map reloadFromFile() { File f = getCacheFile(); - serializedCache = new HashMap(); + serializedCache = new HashMap<>(); // has never been cached here before if( ! f.exists()) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java index b771e0f09a..6cdc379da4 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/ClusterDomains.java @@ -228,7 +228,7 @@ private static List combine(List domains,int Si, int Sj, double if ( verbose) System.out.println(" +++ combining domains " + Si + " " + Sj); - List newdoms = new ArrayList(); + List newdoms = new ArrayList<>(); //int ndom = domains.size(); for(int i=0;i(); + domains = new ArrayList<>(); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java index 635f8bad94..6586c9f941 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/Domain.java @@ -48,7 +48,7 @@ public class Domain implements Comparable, Serializable{ int nseg; double score; - Listsegments = new ArrayList(); + Listsegments = new ArrayList<>(); public Domain(){ diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java index 66d6ae615c..7e0ab2c16a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java @@ -150,7 +150,7 @@ public EcodDomain(EcodDomain o) { this.tGroupName = o.tGroupName; this.fGroupName = o.fGroupName; this.assemblyId = o.assemblyId; - this.ligands = new HashSet(o.ligands); + this.ligands = new HashSet<>(o.ligands); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java index efa042edcf..2f9d27997a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java @@ -153,7 +153,7 @@ public List getDomainsForPdb(String id) throws IOException { return null; } // Deep clone - List clonedDoms = new ArrayList(doms.size()); + List clonedDoms = new ArrayList<>(doms.size()); for(EcodDomain d : doms) { clonedDoms.add( new EcodDomain(d) ); } @@ -178,7 +178,7 @@ public List filterByHierarchy(String hierarchy) throws IOException { Integer hGroup = xhtGroup.length>1 ? Integer.parseInt(xhtGroup[1]) : null; Integer tGroup = xhtGroup.length>2 ? Integer.parseInt(xhtGroup[2]) : null; - List filtered = new ArrayList(); + List filtered = new ArrayList<>(); for(EcodDomain d: getAllDomains()) { boolean match = true; if(xhtGroup.length>0) { @@ -485,7 +485,7 @@ private void indexDomains() throws IOException { } // Leave enough space for all PDBs as of 2015 - domainMap = new HashMap>((int) (150000/.85),.85f); + domainMap = new HashMap<>((int) (150000/.85),.85f); // Index with domainMap for(EcodDomain d : allDomains) { @@ -504,7 +504,7 @@ private void indexDomains() throws IOException { if( domainMap.containsKey(pdbId) ) { currDomains = domainMap.get(pdbId); } else { - currDomains = new LinkedList(); + currDomains = new LinkedList<>(); domainMap.put(pdbId,currDomains); } currDomains.add(d); @@ -582,7 +582,7 @@ public EcodParser(BufferedReader reader) throws IOException { private void parse(BufferedReader in) throws IOException { try { // Allocate plenty of space for ECOD as of 2015 - ArrayList domainsList = new ArrayList(500000); + ArrayList domainsList = new ArrayList<>(500000); Pattern versionRE = Pattern.compile("^\\s*#.*ECOD\\s*version\\s+(\\S+).*"); Pattern commentRE = Pattern.compile("^\\s*#.*"); @@ -705,7 +705,7 @@ private void parse(BufferedReader in) throws IOException { ligands = Collections.emptySet(); } else { String[] ligSplit = ligandStr.split(","); - ligands = new LinkedHashSet(ligSplit.length); + ligands = new LinkedHashSet<>(ligSplit.length); for(String s : ligSplit) { ligands.add(s.intern()); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java index 7d638bce65..8cfd032daa 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java @@ -47,7 +47,7 @@ public class MomentsOfInertia { private List points = new ArrayList(); - private List masses = new ArrayList(); + private List masses = new ArrayList<>(); private boolean modified = true; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java index 6f57eb3a46..1634988665 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/CAConverter.java @@ -42,7 +42,7 @@ public class CAConverter { * @since Biojava 4.1.0 */ public static List getRepresentativeAtomsOnly(List chains){ - List newChains = new ArrayList(); + List newChains = new ArrayList<>(); for (Chain chain : chains){ Chain newChain = getRepresentativeAtomsOnly(chain); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java index 6c6506504c..b0a8ab0bfb 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java @@ -85,8 +85,8 @@ public static AFPChain cpFastaToAfpChain(String first, String second, Structure public static AFPChain cpFastaToAfpChain(File fastaFile, Structure structure, int cpSite) throws IOException, StructureException { InputStream inStream = new FileInputStream(fastaFile); SequenceCreatorInterface creator = new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()); - SequenceHeaderParserInterface headerParser = new GenericFastaHeaderParser(); - FastaReader fastaReader = new FastaReader(inStream, headerParser, creator); + SequenceHeaderParserInterface headerParser = new GenericFastaHeaderParser<>(); + FastaReader fastaReader = new FastaReader<>(inStream, headerParser, creator); LinkedHashMap sequences = fastaReader.process(); inStream.close(); Iterator iter = sequences.values().iterator(); @@ -196,8 +196,8 @@ public static AFPChain fastaFileToAfpChain(File fastaFile, Structure structure1, InputStream inStream = new FileInputStream(fastaFile); SequenceCreatorInterface creator = new CasePreservingProteinSequenceCreator( AminoAcidCompoundSet.getAminoAcidCompoundSet()); - SequenceHeaderParserInterface headerParser = new GenericFastaHeaderParser(); - FastaReader fastaReader = new FastaReader( + SequenceHeaderParserInterface headerParser = new GenericFastaHeaderParser<>(); + FastaReader fastaReader = new FastaReader<>( inStream, headerParser, creator); LinkedHashMap sequences = fastaReader.process(); inStream.close(); @@ -236,8 +236,8 @@ public static AFPChain fastaToAfpChain(Map sequences, S throw new IllegalArgumentException("A structure is null"); } - List seqs = new ArrayList(); - List names = new ArrayList(2); + List seqs = new ArrayList<>(); + List names = new ArrayList<>(2); for (Map.Entry entry : sequences.entrySet()) { seqs.add(entry.getValue()); names.add(entry.getKey()); @@ -321,7 +321,7 @@ public static AFPChain fastaToAfpChain(SequencePair, sb1.append(a.getBase()); } ProteinSequence seq2 = new ProteinSequence(sb2.toString()); - LinkedHashMap map = new LinkedHashMap(); + LinkedHashMap map = new LinkedHashMap<>(); map.put(structure1.getName(), seq1); map.put(structure2.getName(), seq2); return fastaToAfpChain(map, structure1, structure2); @@ -349,8 +349,8 @@ private static AFPChain buildAlignment(Atom[] ca1, Atom[] ca2, ResidueNumber[] r // remove any gap // this includes the ones introduced by the nullifying above - List alignedResiduesList1 = new ArrayList(); - List alignedResiduesList2 = new ArrayList(); + List alignedResiduesList1 = new ArrayList<>(); + List alignedResiduesList2 = new ArrayList<>(); for (int i = 0; i < residues1.length; i++) { if (residues1[i] != null && residues2[i] != null) { alignedResiduesList1.add(residues1[i]); @@ -379,7 +379,7 @@ private static AFPChain buildAlignment(Atom[] ca1, Atom[] ca2, ResidueNumber[] r * @param sequence Make sure not to use {@link ProteinSequence#getSequenceAsString()} for this, as it won't preserve upper- and lower-case */ public static List getAlignedUserCollection(String sequence) { - List aligned = new ArrayList(sequence.length()); + List aligned = new ArrayList<>(sequence.length()); for (char c : sequence.toCharArray()) { aligned.add(Character.isUpperCase(c)); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java index bbc277b89f..108a65f4a3 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java @@ -130,7 +130,7 @@ private Object getCharges(Group thisGroup) { private static List getAtomCharges(Group group) { // The list to store the answer - List outArr = new ArrayList(); + List outArr = new ArrayList<>(); // Get the atom charge Information for(Atom a: group.getAtoms()){ outArr.add(a.getCharge()); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java index 1ce5300b28..5de75efee5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java @@ -174,7 +174,7 @@ public static enum FetchBehavior { * @param path Path to the PDB file directory */ public LocalPDBDirectory(String path) { - extensions = new ArrayList(); + extensions = new ArrayList<>(); params = new FileParsingParameters(); @@ -677,7 +677,7 @@ public File getLocalFile(PdbId pdbId) throws IOException { // Search directories: // 1) LOCAL_MMCIF_SPLIT_DIR//(pdb)?. // 2) LOCAL_MMCIF_ALL_DIR//(pdb)?. - LinkedList searchdirs = new LinkedList(); + LinkedList searchdirs = new LinkedList<>(); String middle = id.substring(offset, offset+2).toLowerCase(); File splitdir = new File(splitDirPath, middle); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java index 22462bafe1..d40bef1ec3 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java @@ -41,10 +41,10 @@ public class PDBBioAssemblyParser { //private static final Logger logger = LoggerFactory.getLogger(PDBBioAssemblyParser.class); private Integer currentBioMolecule = null; - private List currentChainIDs = new ArrayList(); + private List currentChainIDs = new ArrayList<>(); private Matrix currentMatrix = null; private double[] shift = null; - private Map transformationMap = new HashMap(); + private Map transformationMap = new HashMap<>(); private int modelNumber = 1; private List transformations; @@ -159,7 +159,7 @@ private void addToCurrentChainList(String line) { } private void initialize() { - transformations = new ArrayList(); + transformations = new ArrayList<>(); currentMatrix = Matrix.identity(3,3); currentBioMolecule = null; shift = new double[3]; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java index a9e30f6aac..176459bbf2 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java @@ -177,15 +177,15 @@ public class PDBFileParser { private boolean isLastCompndLine = false; private boolean isLastSourceLine = false; private EntityInfo current_compound; - private List entities = new ArrayList(); - private HashMap> compoundMolIds2chainIds = new HashMap>(); - private List compndLines = new ArrayList(); - private List sourceLines = new ArrayList(); - private List journalLines = new ArrayList(); - private List keywordsLines = new ArrayList(); + private List entities = new ArrayList<>(); + private HashMap> compoundMolIds2chainIds = new HashMap<>(); + private List compndLines = new ArrayList<>(); + private List sourceLines = new ArrayList<>(); + private List journalLines = new ArrayList<>(); + private List keywordsLines = new ArrayList<>(); private List dbrefs; - private Map siteMap = new LinkedHashMap(); - private Map> siteToResidueMap = new LinkedHashMap>(); + private Map siteMap = new LinkedHashMap<>(); + private Map> siteToResidueMap = new LinkedHashMap<>(); private List ssbonds = new ArrayList<>(); @@ -207,7 +207,7 @@ public class PDBFileParser { private float rfreeStandardLine = -1; private float rfreeNoCutoffLine = -1; - private static final List compndFieldValues = new ArrayList( + private static final List compndFieldValues = new ArrayList<>( Arrays.asList( "MOL_ID:", "MOLECULE:", "CHAIN:", "SYNONYM:", "EC:", "FRAGMENT:", "ENGINEERED:", "MUTATION:", @@ -215,14 +215,14 @@ public class PDBFileParser { )); - private static final List ignoreCompndFieldValues = new ArrayList( + private static final List ignoreCompndFieldValues = new ArrayList<>( Arrays.asList( "HETEROGEN:","ENGINEEREED:","FRAGMENT,", "MUTANT:","SYNTHETIC:" )); // ENGINEEREED in pdb219d - private static final List sourceFieldValues = new ArrayList( + private static final List sourceFieldValues = new ArrayList<>( Arrays.asList("ENGINEERED:", "MOL_ID:", "SYNTHETIC:", "FRAGMENT:", "ORGANISM_SCIENTIFIC:", "ORGANISM_COMMON:", "ORGANISM_TAXID:","STRAIN:", @@ -274,14 +274,14 @@ public PDBFileParser() { pdbHeader = new PDBHeader(); crystallographicInfo = new PDBCrystallographicInfo(); - connects = new ArrayList>() ; + connects = new ArrayList<>() ; - helixList = new ArrayList>(); - strandList = new ArrayList>(); - turnList = new ArrayList>(); + helixList = new ArrayList<>(); + strandList = new ArrayList<>(); + turnList = new ArrayList<>(); current_compound = null; - dbrefs = new ArrayList(); + dbrefs = new ArrayList<>(); siteMap = null; dateFormat = new SimpleDateFormat("dd-MMM-yy", Locale.US); atomCount = 0; @@ -294,7 +294,7 @@ public PDBFileParser() { loadMaxAtoms = params.getMaxAtoms(); atomCAThreshold = params.getAtomCaThreshold(); - linkRecords = new ArrayList(); + linkRecords = new ArrayList<>(); blankChainIdsPresent = false; @@ -486,7 +486,7 @@ private void pdb_HELIX_Handler(String line){ //System.out.println(initResName + " " + initChainId + " " + initSeqNum + " " + initICode + " " + // endResName + " " + endChainId + " " + endSeqNum + " " + endICode); - Map m = new HashMap(); + Map m = new HashMap<>(); m.put("initResName",initResName); m.put("initChainId", initChainId); @@ -573,7 +573,7 @@ private void pdb_SHEET_Handler( String line){ //System.out.println(initResName + " " + initChainId + " " + initSeqNum + " " + initICode + " " + // endResName + " " + endChainId + " " + endSeqNum + " " + endICode); - Map m = new HashMap(); + Map m = new HashMap<>(); m.put("initResName",initResName); m.put("initChainId", initChainId); @@ -638,7 +638,7 @@ private void pdb_TURN_Handler( String line){ //System.out.println(initResName + " " + initChainId + " " + initSeqNum + " " + initICode + " " + // endResName + " " + endChainId + " " + endSeqNum + " " + endICode); - Map m = new HashMap(); + Map m = new HashMap<>(); m.put("initResName",initResName); m.put("initChainId", initChainId); @@ -1055,7 +1055,7 @@ private void compndValueSetter(String field, String value) { if ("CHAIN:".equals(field)) { //System.out.println(value); StringTokenizer chainTokens = new StringTokenizer(value, ","); - List chains = new ArrayList(); + List chains = new ArrayList<>(); while (chainTokens.hasMoreTokens()) { String chainID = chainTokens.nextToken().trim(); @@ -1070,7 +1070,7 @@ private void compndValueSetter(String field, String value) { if ("SYNONYM:".equals(field)) { StringTokenizer synonyms = new StringTokenizer(value, ","); - List names = new ArrayList(); + List names = new ArrayList<>(); while (synonyms.hasMoreTokens()) { names.add(synonyms.nextToken()); @@ -1083,7 +1083,7 @@ private void compndValueSetter(String field, String value) { if ("EC:".equals(field)) { StringTokenizer ecNumTokens = new StringTokenizer(value, ","); - List ecNums = new ArrayList(); + List ecNums = new ArrayList<>(); while (ecNumTokens.hasMoreTokens()) { ecNums.add(ecNumTokens.nextToken()); @@ -2079,7 +2079,7 @@ private void pdb_CONECT_Handler(String line) { //System.out.println(atomserial+ " "+ bond1 +" "+bond2+ " " +bond3+" "+bond4+" "+ // hyd1+" "+hyd2 +" "+salt1+" "+hyd3+" "+hyd4+" "+salt2); - HashMap cons = new HashMap(); + HashMap cons = new HashMap<>(); cons.put("atomserial",atomserial); if ( bond1 != null) cons.put("bond1",bond1); @@ -2383,7 +2383,7 @@ private void pdb_SITE_Handler(String line){ //if the siteResidues doesn't yet exist, make a new one. if (siteResidues == null || ! siteToResidueMap.containsKey(siteID.trim())){ - siteResidues = new ArrayList(); + siteResidues = new ArrayList<>(); siteToResidueMap.put(siteID.trim(), siteResidues); logger.debug(String.format("New Site made: %s %s", siteID, siteResidues)); @@ -2600,10 +2600,10 @@ public Structure parsePDBFile(BufferedReader buf) startOfMolecule = true; startOfModel = true; - seqResChains = new ArrayList(); - siteMap = new LinkedHashMap(); + seqResChains = new ArrayList<>(); + siteMap = new LinkedHashMap<>(); pdbHeader = new PDBHeader(); - connects = new ArrayList>(); + connects = new ArrayList<>(); previousContinuationField = ""; continuationField = ""; continuationString = ""; @@ -2621,7 +2621,7 @@ public Structure parsePDBFile(BufferedReader buf) lengthCheck = -1; atomCount = 0; atomOverflow = false; - linkRecords = new ArrayList(); + linkRecords = new ArrayList<>(); siteToResidueMap.clear(); blankChainIdsPresent = false; @@ -2812,7 +2812,7 @@ private void handlePDBKeywords(List lines) { } String fulllengthList = fullList.toString(); keywords = fulllengthList.split("( )*,( )*"); - ArrayList lst = new ArrayList(keywords.length); + ArrayList lst = new ArrayList<>(keywords.length); for (String keyword : keywords) { if(keyword.length() == 0) { logger.debug("Keyword empty in structure {}", structure.getIdentifier().toString()); @@ -3317,7 +3317,7 @@ private void linkSitesToGroups() { List sites = null; //check that there are chains with which to associate the groups if (structure.getChains().isEmpty()) { - sites = new ArrayList(siteMap.values()); + sites = new ArrayList<>(siteMap.values()); logger.info("No chains to link Site Groups with - Sites will not be present in the Structure"); return; } @@ -3360,7 +3360,7 @@ private void linkSitesToGroups() { //System.out.println("SITEMAP: " + siteMap); - sites = new ArrayList(siteMap.values()); + sites = new ArrayList<>(siteMap.values()); structure.setSites(sites); //System.out.println("STRUCTURE SITES: " + structure.getSites().size()); // for (Site site : structure.getSites()) { @@ -3611,7 +3611,7 @@ private String getVolume() { } private List authorBuilder(String authorString) { - ArrayList authorList = new ArrayList(); + ArrayList authorList = new ArrayList<>(); if ("".equals(authorString)) { return authorList; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java index a5854efe08..7ee21de4b4 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java @@ -453,8 +453,8 @@ public static String getFullAtomSequence(List groups, Map seqRes, List atomRes) { - Map seqresIndexPosition = new HashMap(); - Map atomIndexPosition = new HashMap(); + Map seqresIndexPosition = new HashMap<>(); + Map atomIndexPosition = new HashMap<>(); String seq1 = getFullAtomSequence(seqRes, seqresIndexPosition, true); // @@ -573,8 +573,8 @@ private Sequence getNucleotideSequence(String seq) { */ private boolean alignProteinChains(List seqRes, List atomRes) { - Map seqresIndexPosition = new HashMap(); - Map atomIndexPosition = new HashMap(); + Map seqresIndexPosition = new HashMap<>(); + Map atomIndexPosition = new HashMap<>(); String seq1 = getFullAtomSequence(seqRes, seqresIndexPosition, false); // diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java index 252c9422dc..fd06080118 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java @@ -118,7 +118,7 @@ public static ProteinSequence getProteinSequenceForStructure(Structure struct, M for(Chain chain : struct.getChains()) { List groups = chain.getAtomGroups(); - Map chainIndexPosition = new HashMap(); + Map chainIndexPosition = new HashMap<>(); int prevLen = seqStr.length(); // get the sequence for this chain @@ -162,7 +162,7 @@ public static ProteinSequence getProteinSequenceForStructure(Structure struct, M public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Structure struct) { //1. Create ProteinSequence for struct while remembering to which group each residue corresponds - Map atomIndexPosition = new HashMap(); + Map atomIndexPosition = new HashMap<>(); ProteinSequence structSeq = getProteinSequenceForStructure(struct,atomIndexPosition); @@ -171,10 +171,10 @@ public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Stru // Identity substitution matrix with +1 for match, -1 for mismatch // TODO SubstitutionMatrix matrix = - new SimpleSubstitutionMatrix( + new SimpleSubstitutionMatrix<>( AminoAcidCompoundSet.getAminoAcidCompoundSet(), (short)1, (short)-1 ); - matrix = new SimpleSubstitutionMatrix( + matrix = new SimpleSubstitutionMatrix<>( AminoAcidCompoundSet.getAminoAcidCompoundSet(), new InputStreamReader( SimpleSubstitutionMatrix.class.getResourceAsStream("/matrices/blosum100.txt")), diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java index b3be41bad0..ca3906e4b2 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java @@ -934,7 +934,7 @@ public void consumeStructConnType(StructConnType structConnType) { @Override public void consumeStructKeywords(StructKeywords structKeywords) { - ArrayList keywordsList = new ArrayList(); + ArrayList keywordsList = new ArrayList<>(); StrColumn text = structKeywords.getText(); if (text.isDefined()) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java index 622f16122f..5b9fe460c6 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java @@ -256,8 +256,8 @@ public static int getNumGroups(Structure structure) { * @return the atoms for the input Biojava Group */ public static List getAtomsForGroup(Group inputGroup) { - Set uniqueAtoms = new HashSet(); - List theseAtoms = new ArrayList(); + Set uniqueAtoms = new HashSet<>(); + List theseAtoms = new ArrayList<>(); for(Atom a: inputGroup.getAtoms()){ theseAtoms.add(a); uniqueAtoms.add(a); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java index 84cd9ae138..d4c11544ca 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java @@ -156,9 +156,9 @@ private static void download() throws IOException { } - private Map byChainId = new HashMap(); + private Map byChainId = new HashMap<>(); - private Map byUniProtId = new HashMap(); + private Map byUniProtId = new HashMap<>(); private SiftsChainToUniprotMapping() { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java index 34b2ba1bc4..20e1008859 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsEntity.java @@ -46,7 +46,7 @@ public SiftsEntity(){ public SiftsEntity(String type, String entityId) { this.type = type; this.entityId = entityId; - segments = new ArrayList(); + segments = new ArrayList<>(); } public void addSegment(SiftsSegment s) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java index 1594228a05..e582a3881a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsSegment.java @@ -49,7 +49,7 @@ public SiftsSegment(String segId, String start, String end) { this.segId = segId; this.start = start; this.end = end; - residues = new ArrayList(); + residues = new ArrayList<>(); } public String getSegId() { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java index e566550df2..6922f49366 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java @@ -51,7 +51,7 @@ public class SiftsXMLParser { static boolean debug = false; public SiftsXMLParser(){ - entities = new ArrayList(); + entities = new ArrayList<>(); } public List getEntities(){ @@ -60,7 +60,7 @@ public List getEntities(){ public void parseXmlFile(InputStream is){ - entities = new ArrayList(); + entities = new ArrayList<>(); //get the factory DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); @@ -269,7 +269,7 @@ private String getTextValue(Element ele, String tagName) { } private List getTextValues(Element ele, String tagName) { - Listvalues = new ArrayList(); + Listvalues = new ArrayList<>(); NodeList nl = ele.getElementsByTagName(tagName); if(nl != null && nl.getLength() > 0) { for ( int i = 0 ;i < nl.getLength() ; i ++) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java index 124b44d1c2..d4e7d19d93 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SparseVector.java @@ -54,7 +54,7 @@ public class SparseVector implements Serializable{ */ public SparseVector(int N) { this.N = N; - this.symbolTable = new SymbolTable(); + this.symbolTable = new SymbolTable<>(); } /** Setter method (should it be renamed to set?) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java index 39d7926d9f..0f9066b323 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java @@ -69,7 +69,7 @@ public class SymbolTable, Value> implements Iterable * Create an empty symbol table. */ public SymbolTable() { - st = new TreeMap(); + st = new TreeMap<>(); } /** diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java index 92bdc89ead..95bcf1b402 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java @@ -76,7 +76,7 @@ private static List parseSubExpression(String expression) { } // expand ranges if present, i.e. 1-60 -> 1, 2, 3, ..., 60 - List operators = new ArrayList(); + List operators = new ArrayList<>(); for (String component : components) { if (component.contains("-")) { operators.addAll(expandRange(component)); @@ -104,7 +104,7 @@ private static List expandRange(String expression) { throw new IllegalArgumentException("Invalid range specification in oper_expression: " + expression); } - List expandedExpression = new ArrayList(last-first+1); + List expandedExpression = new ArrayList<>(last-first+1); for (int i = first; i <= last; i++) { expandedExpression.add(String.valueOf(i)); } @@ -127,7 +127,7 @@ public static List> parseBinaryOperatorExpression(String exp List rightSide = parseSubExpression(subExpressions[1]); // form the cartesian product of the two lists - CartesianProduct product = new CartesianProduct(leftSide, rightSide); + CartesianProduct product = new CartesianProduct<>(leftSide, rightSide); return product.getOrderedPairs(); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java index 083633c28f..f9597bbb7d 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java @@ -184,7 +184,7 @@ public int compare(BiologicalAssemblyTransformation t1, BiologicalAssemblyTransf * @return */ private List getChainIds(Structure asymUnit) { - List chainIds = new ArrayList(); + List chainIds = new ArrayList<>(); for ( Chain c : asymUnit.getChains()){ String intChainID = c.getId(); chainIds.add(intChainID); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java index 2fa6258cf5..36bccd7b39 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java @@ -236,7 +236,7 @@ public static BiologicalAssemblyTransformation fromXML(String xml) public static List fromMultiXML(String xml) throws ParserConfigurationException, SAXException, IOException{ - List transformations = new ArrayList(); + List transformations = new ArrayList<>(); // read the XML of a string and returns a ModelTransformationmatrix DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java index da6853a6fb..7aa4690b5c 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/CartesianProduct.java @@ -60,7 +60,7 @@ public CartesianProduct(List list1, List list2) { * @return the list of ordered pairs */ public List> getOrderedPairs() { - List> pairs = new ArrayList>(list1.size()*list2.size()); + List> pairs = new ArrayList<>(list1.size()*list2.size()); for (T element1: list1) { for (T element2: list2) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java index da1f82221f..9d30e42248 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java @@ -101,7 +101,7 @@ public String toString() { } } - private static Map> instances = new HashMap>(); + private static Map> instances = new HashMap<>(); private static final Logger logger = LoggerFactory.getLogger(Astral.class); @@ -203,8 +203,8 @@ public LinkedHashMap getFailedLines() { * Parses the FASTA file opened by reader. */ private void init(Reader reader) { - names = new TreeSet(); - failedLines = new LinkedHashMap(); + names = new TreeSet<>(); + failedLines = new LinkedHashMap<>(); BufferedReader br = null; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java index f0aab86b95..d688beadac 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.java @@ -45,7 +45,7 @@ public class BerkeleyScopInstallation extends ScopInstallation { * A map from SCOP version names which the Berkeley server offers as a * download to an array of equivalent deprecated SCOP version names. */ - public static final Map EQUIVALENT_VERSIONS = new HashMap(); + public static final Map EQUIVALENT_VERSIONS = new HashMap<>(); static { EQUIVALENT_VERSIONS.put("2.01", new String[] {"1.75A"}); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java index 34e7702e23..b6783316c8 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java @@ -243,7 +243,7 @@ protected Object clone() throws CloneNotSupportedException { * Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain. */ public Set getChains() { - Set chains = new HashSet(); + Set chains = new HashSet<>(); List rrs = ResidueRange.parseMultiple(getRanges()); for (ResidueRange rr : rrs) chains.add(rr.getChainName()); return chains; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java index 07d848c942..d092d5485e 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java @@ -123,12 +123,12 @@ public ScopInstallation(String cacheLocation){ installedCom.set(false); scopVersion = DEFAULT_VERSION; - mirrors = new ArrayList(1); + mirrors = new ArrayList<>(1); - domainMap = new HashMap>(); + domainMap = new HashMap<>(); - sunidMap = new HashMap(); - scopTree = new TreeMap(); + sunidMap = new HashMap<>(); + scopTree = new TreeMap<>(); } @@ -189,7 +189,7 @@ public List getByCategory(ScopCategory category){ throw new ScopIOException(e); } - List matches = new ArrayList(); + List matches = new ArrayList<>(); for (Integer i : sunidMap.keySet()){ ScopDescription sc = sunidMap.get(i); if ( sc.getCategory().equals(category)) @@ -216,7 +216,7 @@ public List filterByClassificationId(String query){ throw new ScopIOException(e); } - List matches = new ArrayList(); + List matches = new ArrayList<>(); for (Integer i : sunidMap.keySet()){ ScopDescription sc = sunidMap.get(i); @@ -238,7 +238,7 @@ public List getTree(ScopDomain domain){ ScopNode node = getScopNode(domain.getSunid()); - List tree = new ArrayList(); + List tree = new ArrayList<>(); while (node != null){ //System.out.println("This node: sunid:" + node.getSunid() ); @@ -257,7 +257,7 @@ public List getTree(ScopDomain domain){ @Override public List filterByDomainName(String query) { - List domains = new ArrayList(); + List domains = new ArrayList<>(); if (query.length() <5){ return domains; } @@ -292,7 +292,7 @@ public List filterByDescription(String query) { } query = query.toLowerCase(); - List matches = new ArrayList(); + List matches = new ArrayList<>(); for (Integer i : sunidMap.keySet()){ ScopDescription sc = sunidMap.get(i); @@ -332,7 +332,7 @@ public List getDomainsForPDB(String pdbId) { List doms = domainMap.get(pdbId.toLowerCase()); - List retdoms = new ArrayList(); + List retdoms = new ArrayList<>(); if ( doms == null) return retdoms; @@ -439,7 +439,7 @@ private void parseHierarchy(BufferedReader buffer) throws IOException { String children = spl[2]; String[] childIds = children.split(","); - List chis = new ArrayList(); + List chis = new ArrayList<>(); for ( String id : childIds){ if ( "-".equals(id)) @@ -483,7 +483,7 @@ private void parseComments() throws IOException{ private void parseComments(BufferedReader buffer) throws IOException { - commentsMap = new HashMap>(); + commentsMap = new HashMap<>(); int counter = 0; String line; @@ -495,7 +495,7 @@ private void parseComments(BufferedReader buffer) throws IOException { commentsMap.put(sunId, new ArrayList(1)); continue; } - List comments = new ArrayList(parts.length - 1); + List comments = new ArrayList<>(parts.length - 1); for (int i = 1; i < parts.length; i++) { String trimmed = parts[i].trim(); if( !trimmed.isEmpty() ) { @@ -611,7 +611,7 @@ private void parseClassification(BufferedReader buffer) throws IOException { if ( domainMap.containsKey(pdbId)){ domainList = domainMap.get(pdbId); } else { - domainList = new ArrayList(); + domainList = new ArrayList<>(); domainMap.put(pdbId,domainList); } @@ -862,7 +862,7 @@ public List getScopDomainsBySunid(Integer sunid) throw new ScopIOException(e); } - List domains = new ArrayList(); + List domains = new ArrayList<>(); for (String pdbId: domainMap.keySet()){ for (ScopDomain d : domainMap.get(pdbId)){ @@ -900,7 +900,7 @@ public List getComments(int sunid) { } catch (IOException e) { throw new ScopIOException(e); } - if (!commentsMap.containsKey(sunid)) return new ArrayList(1); + if (!commentsMap.containsKey(sunid)) return new ArrayList<>(1); return commentsMap.get(sunid); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java index 3aa4417f13..f6fb7bff42 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java @@ -124,7 +124,7 @@ private static List generalParse(BufferedReader reader, String startLine = " # RESIDUE AA STRUCTURE BP1 BP2 ACC"; String line; - List secstruc = new ArrayList(); + List secstruc = new ArrayList<>(); //Find the first line of the DSSP output while((line = reader.readLine()) != null) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java index c63f3d1684..c4d308e366 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java @@ -104,8 +104,8 @@ public class SecStrucCalc { private AtomContactSet contactSet; private Map indResMap; public SecStrucCalc(){ - ladders = new ArrayList(); - bridges = new ArrayList(); + ladders = new ArrayList<>(); + bridges = new ArrayList<>(); } @@ -120,11 +120,11 @@ public SecStrucCalc(){ public List calculate(Structure s, boolean assign) throws StructureException { - List secstruc = new ArrayList(); + List secstruc = new ArrayList<>(); for(int i=0; i(); - bridges = new ArrayList(); + ladders = new ArrayList<>(); + bridges = new ArrayList<>(); groups = initGroupArray(s, i); // Initialise the contact set for this structure initContactSet(); @@ -424,7 +424,7 @@ private boolean shouldExtendLadder(Ladder ladder, BetaBridge b) { private void findBridges() { // Get the interator of contacts Iterator myIter = contactSet.iterator(); - List> outList = new ArrayList>(); + List> outList = new ArrayList<>(); // Now iterate through this while(myIter.hasNext()){ @@ -461,7 +461,7 @@ private void findBridges() { continue; } - Pair thisPair = new Pair(i,j); + Pair thisPair = new Pair<>(i,j); outList.add(thisPair); } // @@ -705,7 +705,7 @@ public boolean equals(Object o){ } private static SecStrucGroup[] initGroupArray(Structure s, int modelId) { - List groupList = new ArrayList(); + List groupList = new ArrayList<>(); // for ( Chain c : s.getChains(modelId)){ diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java index d90c5ba263..7732c04b80 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java @@ -99,7 +99,7 @@ public static List getSecStrucElements(Structure s) { int count = 0; // counts the number of residues in SSE // Create a map for the IDs of the SSE in the structure - Map ids = new TreeMap(); + Map ids = new TreeMap<>(); for (SecStrucType t : SecStrucType.values()) ids.put(t, 1); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java index b76e844965..10d9144db4 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java @@ -356,7 +356,7 @@ private Matrix4d reorientHelix(int index) { * @return list of orbits ordered by z-depth */ private void calcAlignedOrbits() { - Map> depthMap = new TreeMap>(); + Map> depthMap = new TreeMap<>(); double[] depth = getSubunitZDepth(); alignedOrbits = calcOrbits(); @@ -585,7 +585,7 @@ private double[] getSubunitZDepth() { private List> calcOrbits() { int n = subunits.getSubunitCount(); - List> orbits = new ArrayList>(); + List> orbits = new ArrayList<>(); for (int i = 0; i < n; i++) { orbits.add(Collections.singletonList(i)); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java index bb24492389..65621135d1 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java @@ -236,7 +236,7 @@ private void run () { * @return list of orbits ordered by z-depth */ private void calcAlignedOrbits() { - Map> depthMap = new TreeMap>(); + Map> depthMap = new TreeMap<>(); double[] depth = getSubunitZDepth(); alignedOrbits = calcOrbits(); @@ -539,7 +539,7 @@ private void calcZDirection() { * */ private List> getOrbitsByXYWidth() { - Map> widthMap = new TreeMap>(); + Map> widthMap = new TreeMap<>(); double[] width = getSubunitXYWidth(); List> orbits = calcOrbits(); @@ -608,14 +608,14 @@ private List> calcOrbits() { int n = subunits.getSubunitCount(); int fold = rotationGroup.getRotation(0).getFold(); - List> orbits = new ArrayList>(); + List> orbits = new ArrayList<>(); boolean[] used = new boolean[n]; Arrays.fill(used, false); for (int i = 0; i < n; i++) { if (! used[i]) { // determine the equivalent subunits - List orbit = new ArrayList(fold); + List orbit = new ArrayList<>(fold); for (int j = 0; j < fold; j++) { List permutation = rotationGroup.getRotation(j).getPermutation(); orbit.add(permutation.get(i)); @@ -637,7 +637,7 @@ private List deconvolute(List orbit) { // System.out.println("Permutation0: " + p0); // System.out.println("Permutation1: " + p1); - List inRotationOrder = new ArrayList(orbit.size()); + List inRotationOrder = new ArrayList<>(orbit.size()); inRotationOrder.add(orbit.get(0)); for (int i = 1; i < orbit.size(); i++) { int current = inRotationOrder.get(i-1); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java index f62208aadf..ff9c77cf13 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java @@ -30,7 +30,7 @@ public class HelicalRepeatUnit { private QuatSymmetrySubunits subunits = null; private List repeatUnitCenters = new ArrayList(); private List repeatUnits = new ArrayList(); - private List> repeatUnitIndices = new ArrayList>(); + private List> repeatUnitIndices = new ArrayList<>(); private Map interactingNeighbors = Collections.emptyMap(); public HelicalRepeatUnit(QuatSymmetrySubunits subunits) { @@ -74,10 +74,10 @@ private void run() { private List calcRepeatUnitCenters() { // TODO why do we use models here? it should not matter. Setting to 0 all - List models = new ArrayList(subunits.getSubunitCount()); + List models = new ArrayList<>(subunits.getSubunitCount()); for (int s = 0; s uniqueModels = new HashSet(Arrays.asList(1)); + Set uniqueModels = new HashSet<>(Arrays.asList(1)); int modelCount = uniqueModels.size(); List folds = this.subunits.getFolds(); @@ -90,7 +90,7 @@ private List calcRepeatUnitCenters() { if (maxFold%modelCount == 0 && modelCount > 1 && subunits.getSubunitCount() > 3) { // System.out.println("calcRepeatUnitCenters case 1"); for (int i = 0; i < modelCount; i++) { - List subunitIndices = new ArrayList(); + List subunitIndices = new ArrayList<>(); Point3d p = new Point3d(); int count = 0; // System.out.println("Models: " + models.size()); @@ -113,7 +113,7 @@ private List calcRepeatUnitCenters() { // Case of 3B5U: A14, but seems to form (A2)*7 and symmetry related subunits don't have direct contact List sequenceClusterIds = subunits.getClusterIds(); for (int i = 0; i < subunits.getSubunitCount(); i++) { - List subunitIndices = new ArrayList(1); + List subunitIndices = new ArrayList<>(1); if (sequenceClusterIds.get(i) == 0) { repeatCenters.add(new Point3d(centers.get(i))); // System.out.println("Orig Repeat unit: " + centers.get(i)); @@ -135,11 +135,11 @@ private List calcRepeatUnitCenters() { private List calcRepeatUnits() { // TODO why do we use models here? it should not matter. Setting to 0 all - List models = new ArrayList( + List models = new ArrayList<>( subunits.getSubunitCount()); for (int s = 0; s < subunits.getSubunitCount(); s++) models.add(0); - Set uniqueModels = new HashSet(Arrays.asList(1)); + Set uniqueModels = new HashSet<>(Arrays.asList(1)); int modelCount = uniqueModels.size(); List folds = this.subunits.getFolds(); @@ -180,7 +180,7 @@ private List calcRepeatUnits() { } private Map findInteractingNeigbors() { - Map contactMap = new HashMap(); + Map contactMap = new HashMap<>(); Map> distanceMap = findClosestPairs(8); for (List pairs: distanceMap.values()) @@ -196,9 +196,9 @@ private Map findInteractingNeigbors() { } private Map> findClosestPairs(int maxNeighbors) { - Map> reducedMap = new TreeMap>(); + Map> reducedMap = new TreeMap<>(); - Map> distanceMap = new TreeMap>(); + Map> distanceMap = new TreeMap<>(); int nCenters = repeatUnitCenters.size(); // System.out.println("repeatUnitCenters: " + repeatUnitCenters); @@ -212,7 +212,7 @@ private Map> findClosestPairs(int maxNeighbors) { List pairs = distanceMap.get(intDist); // save only one representative pair for each distance if (pairs == null) { - pairs = new ArrayList(); + pairs = new ArrayList<>(); } Integer[] pair = new Integer[2]; pair[0] = i; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java index d25f14ec34..4dabe0c0ac 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java @@ -161,7 +161,7 @@ public String toString() { } public List> getLayerLines() { - List> layerLines = new ArrayList>(); + List> layerLines = new ArrayList<>(); createLineSegments(permutation, layerLines); @@ -192,7 +192,7 @@ private static void createLineSegments(List permutation, List> layerLines) { for (int i = 0; i < permutation.size(); i++) { if (permutation.get(i) != -1 ) { - List lineSegment = new ArrayList(); + List lineSegment = new ArrayList<>(); lineSegment.add(i); lineSegment.add(permutation.get(i)); layerLines.add(lineSegment); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java index 30d799b6f3..f99a998131 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java @@ -40,7 +40,7 @@ public Point3d[] extendHelix(int steps) { List> layerLines = helix.getLayerLines(); // get list of subunit indices to be used for helix extension - List indices = new ArrayList(); + List indices = new ArrayList<>(); for (List line: layerLines) { if (steps < 0) { indices.add(line.get(0)); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java index a42958d062..bbcce99df0 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java @@ -29,7 +29,7 @@ * @author Peter */ public class HelixLayers { - private List helices = new ArrayList(); + private List helices = new ArrayList<>(); private double symmetryDeviation = 0; public int size() { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java index a2d002280c..ff76812152 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java @@ -73,7 +73,7 @@ private void solve() { HelicalRepeatUnit unit = new HelicalRepeatUnit(subunits); List repeatUnitCenters = unit.getRepeatUnitCenters(); List repeatUnits = unit.getRepeatUnits(); - Set> permutations = new HashSet>(); + Set> permutations = new HashSet<>(); double minRise = parameters.getMinimumHelixRise() * fold; // for n-start // helix, @@ -129,7 +129,7 @@ private void solve() { // keep track of which subunits are permuted - Set permSet = new HashSet(); + Set permSet = new HashSet<>(); int count = 0; boolean valid = true; for (int i = 0; i < permutation.size(); i++) { @@ -355,7 +355,7 @@ private List getPermutation(Matrix4d transformation) { List centers = subunits.getOriginalCenters(); List seqClusterId = subunits.getClusterIds(); - List permutations = new ArrayList(centers.size()); + List permutations = new ArrayList<>(centers.size()); double[] dSqs = new double[centers.size()]; boolean[] used = new boolean[centers.size()]; Arrays.fill(used, false); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java index 8bbcb5a650..e1f4792410 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java @@ -32,7 +32,7 @@ * @author Peter */ public class PermutationGroup implements Iterable> { - List> permutations = new ArrayList>(); + List> permutations = new ArrayList<>(); public void addPermutation(List permutation) { if (!permutations.contains(permutation)) { @@ -60,13 +60,13 @@ public int getOrder() { */ public void completeGroup() { // Copy initial set to allow permutations to grow - List> gens = new ArrayList>(permutations); + List> gens = new ArrayList<>(permutations); // Keep HashSet version of permutations for fast lookup. - Set> known = new HashSet>(permutations); + Set> known = new HashSet<>(permutations); //breadth-first search through the map of all members - List> currentLevel = new ArrayList>(permutations); + List> currentLevel = new ArrayList<>(permutations); while( currentLevel.size() > 0) { - List> nextLevel = new ArrayList>(); + List> nextLevel = new ArrayList<>(); for( List p : currentLevel) { for(List gen : gens) { List y = combine(p,gen); @@ -93,7 +93,7 @@ public String toString() { } public static List combine(List permutation1, List permutation2) { - List intermediate = new ArrayList(permutation1.size()); + List intermediate = new ArrayList<>(permutation1.size()); for (int i = 0, n = permutation1.size(); i < n; i++) { intermediate.add(permutation2.get(permutation1.get(i))); } @@ -101,7 +101,7 @@ public static List combine(List permutation1, List pe } public static int getOrder(List permutation) { - List copy = new ArrayList(permutation); + List copy = new ArrayList<>(permutation); for (int i = 0, n = permutation.size(); i < n; i++) { copy = combine(copy, permutation); if (copy.equals(permutation)) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java index cdc7341c4b..db5cb229a2 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java @@ -72,7 +72,7 @@ public QuatSymmetryResults(Stoichiometry stoichiometry, this.stoichiometry = stoichiometry; this.clusters = stoichiometry.getClusters(); - subunits = new ArrayList(); + subunits = new ArrayList<>(); for (SubunitCluster c : clusters) { subunits.addAll(c.getSubunits()); } @@ -95,7 +95,7 @@ public QuatSymmetryResults(Stoichiometry stoichiometry, this.stoichiometry = stoichiometry; this.clusters = stoichiometry.getClusters(); - subunits = new ArrayList(); + subunits = new ArrayList<>(); for (SubunitCluster c : clusters) { subunits.addAll(c.getSubunits()); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java index 27d16cd6fe..98eb315855 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java @@ -105,7 +105,7 @@ public List getClusterIds() { */ public List getChainIds() { - List chains = new ArrayList(getSubunitCount()); + List chains = new ArrayList<>(getSubunitCount()); // Loop through all subunits in the clusters and fill Lists for (int c = 0; c < clusters.size(); c++) { @@ -125,7 +125,7 @@ public List getChainIds() { */ public List getModelNumbers() { - List models = new ArrayList(getSubunitCount()); + List models = new ArrayList<>(getSubunitCount()); // Loop through all subunits in the clusters and fill Lists for (int c = 0; c < clusters.size(); c++) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java index 9a13d35813..9d25a7acbc 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java @@ -35,7 +35,7 @@ * @author Peter */ public class RotationGroup implements Iterable { - private List rotations = new ArrayList(); + private List rotations = new ArrayList<>(); private int principalAxisIndex = 0; private int higherOrderRotationAxis = 0; private int twoFoldsPerpendicular = 0; @@ -61,7 +61,7 @@ public void addRotation(Rotation rotation) { public void setC1(int n) { Rotation r = new Rotation(); - List permutation = new ArrayList(n); + List permutation = new ArrayList<>(n); for (int i = 0; i < n; i++) { permutation.add(i); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java index 95c73cb540..37a44be7ac 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java @@ -282,7 +282,7 @@ private List getAngles() { n = 60; } List folds = subunits.getFolds(); - List angles = new ArrayList(folds.size()-1); + List angles = new ArrayList<>(folds.size()-1); // note this loop starts at 1, we do ignore 1-fold symmetry, which is the first entry for (int fold: folds) { @@ -370,7 +370,7 @@ private static Rotation createSymmetryOperation(List permutation, Matri private void setupDistanceBox() { distanceThreshold = calcDistanceThreshold(); - box = new DistanceBox(distanceThreshold); + box = new DistanceBox<>(distanceThreshold); for (int i = 0; i < originalCoords.length; i++) { box.addPoint(originalCoords[i], i); @@ -402,7 +402,7 @@ private double calcDistanceThreshold() { * @return A list mapping each subunit to the closest transformed subunit */ private List getPermutation() { - List permutation = new ArrayList(transformedCoords.length); + List permutation = new ArrayList<>(transformedCoords.length); double sum = 0.0f; for (Point3d t: transformedCoords) { @@ -432,7 +432,7 @@ private List getPermutation() { } // check uniqueness of indices - Set set = new HashSet(permutation); + Set set = new HashSet<>(permutation); // if size mismatch, clear permutation (its invalid) if (set.size() != originalCoords.length) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java index 4ad0494c28..d13fa4db16 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java @@ -50,7 +50,7 @@ public class SystematicSolver implements QuatSymmetrySolver { private RotationGroup rotations = new RotationGroup(); private Vector3d centroid = new Vector3d(); private Matrix4d centroidInverse = new Matrix4d(); - private Set> hashCodes = new HashSet>(); + private Set> hashCodes = new HashSet<>(); public SystematicSolver(QuatSymmetrySubunits subunits, QuatSymmetryParameters parameters) { if (subunits.getSubunitCount()== 2) { @@ -77,7 +77,7 @@ private void solve() { // loop over all permutations while (g.hasMore()) { int[] perm = g.getNext(); - List permutation = new ArrayList(perm.length); + List permutation = new ArrayList<>(perm.length); for (int j = 0; j < n; j++) { permutation.add(perm[j]); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java index 37430260ca..2d9b1d6dca 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java @@ -63,12 +63,12 @@ public class DistanceBox { 1 + ( 1 * 10000) + ( 1 * 1000000000L) }; - private List tempBox = new ArrayList(offset.length); + private List tempBox = new ArrayList<>(offset.length); /** Creates a new instance of DistanceBox */ public DistanceBox(double binWidth) { - map = new HashMap>(); - layerMap = new HashMap>(); + map = new HashMap<>(); + layerMap = new HashMap<>(); this.inverseBinWidth = 1.0f/binWidth; this.modified = true; } @@ -82,7 +82,7 @@ public void addPoint(Point3d point, T object) { List box = map.get(location); if (box == null) { - box = new ArrayList(); + box = new ArrayList<>(); map.put(location, box); } @@ -127,8 +127,8 @@ public List getNeighbors(Point3d point) { } public List getIntersection(DistanceBox distanceBox) { - List intersection = new ArrayList(); - HashSet checkedLocations = new HashSet(); + List intersection = new ArrayList<>(); + HashSet checkedLocations = new HashSet<>(); for (Iterator iter = map.keySet().iterator(); iter.hasNext();) { long location = iter.next(); @@ -171,7 +171,7 @@ private List getBoxTwo(long location) { } else if (tempBox.size() == 1) { boxTwo = Collections.singletonList(tempBox.get(0)); } else { - boxTwo = new ArrayList(tempBox); + boxTwo = new ArrayList<>(tempBox); } return boxTwo; } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java index 6b5d7edacf..770126b601 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java @@ -119,7 +119,7 @@ public Point3d[] getVertices() { @Override public List getLineLoops() { - List list = new ArrayList(); + List list = new ArrayList<>(); int[] l1 = new int[2*n+2]; for (int i = 0; i < n; i++) { l1[i] = i; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java index 66626ef3f0..43ee89c234 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java @@ -189,7 +189,7 @@ protected static CeSymmResult align(Atom[] atoms, CESymmParameters params) CECalculator calculator = new CECalculator(params); Matrix lastMatrix = null; - List selfAlignments = new ArrayList(); + List selfAlignments = new ArrayList<>(); AFPChain optimalAFP = null; // STEP 2: perform the self-alignments of the structure diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java index f1e50b756d..4527a7fa49 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java @@ -89,7 +89,7 @@ public class CeSymmIterative { public CeSymmIterative(CESymmParameters param) { params = param; alignGraph = new SimpleGraph(DefaultEdge.class); - levels = new ArrayList(); + levels = new ArrayList<>(); } /** @@ -231,7 +231,7 @@ private CeSymmResult reconstructSymmResult(Atom[] atoms) ConnectivityInspector inspector = new ConnectivityInspector( alignGraph); List> comps = inspector.connectedSets(); - List groups = new ArrayList(comps.size()); + List groups = new ArrayList<>(comps.size()); for (Set comp : comps) groups.add(new ResidueGroup(comp)); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java index 441bcda2ce..67d91362bd 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java @@ -106,7 +106,7 @@ public List getRepeatsID() throws StructureException { if (!isRefined()) return null; - List repeats = new ArrayList( + List repeats = new ArrayList<>( numRepeats); PdbId pdbId = structureId.toCanonical().getPdbId(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java index 822e62a8c2..db1dbb8939 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java @@ -59,7 +59,7 @@ public int calculateOrder(AFPChain selfAlignment, Atom[] ca) List> components = inspector.connectedSets(); // The order maximizes the residues aligned - Map counts = new HashMap(); + Map counts = new HashMap<>(); for (Set c : components) { if (counts.containsKey(c.size())) counts.put(c.size(), counts.get(c.size()) + c.size()); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java index 6c7d44f6a7..efcd4c34b0 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java @@ -68,7 +68,7 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order) List> components = inspector.connectedSets(); // Filter components with size != order, and transform to ResidueGroups - List groups = new ArrayList(); + List groups = new ArrayList<>(); for (Set comp : components) { if (comp.size() == order) { ResidueGroup group = new ResidueGroup(comp); @@ -103,7 +103,7 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order) } // The compatibility score is the sum of rows of the matrix - List rowScores = new ArrayList(size); + List rowScores = new ArrayList<>(size); for (int i = 0; i < size; i++) { GVector row = new GVector(size); matrix.getRow(i, row); @@ -113,7 +113,7 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order) } // Refined multiple alignment Block as a result - List> alignRes = new ArrayList>(order); + List> alignRes = new ArrayList<>(order); for (int i = 0; i < order; i++) alignRes.add(new ArrayList()); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java index 2fb0b0e64e..a9e1bcdeb5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java @@ -48,7 +48,7 @@ public class ResidueGroup { */ public ResidueGroup(Set component) { // Transform component into sorted List of residues - residues = new ArrayList(component); + residues = new ArrayList<>(component); Collections.sort(residues); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java index 9635debb05..beeba62df2 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java @@ -117,8 +117,8 @@ public static Map refineSymmetry(Map alignme // 2. f^K-1(x) is defined // 3. score(f^K-1(x))>0 - TreeSet forwardLoops = new TreeSet(); - TreeSet backwardLoops = new TreeSet(); + TreeSet forwardLoops = new TreeSet<>(); + TreeSet backwardLoops = new TreeSet<>(); List eligible = null; @@ -240,7 +240,7 @@ private static List initializeEligible(Map alignment, // Assume all residues are eligible to start if(eligible == null) { - eligible = new LinkedList(alignment.keySet()); + eligible = new LinkedList<>(alignment.keySet()); } // Precalculate f^K-1(x) @@ -334,8 +334,8 @@ private static List initializeEligible(Map alignment, private static Map applyAlignmentAndCheckCycles(Map alignmentMap, int k, List eligible) { // Convert to lists to establish a fixed order (avoid concurrent modification) - List preimage = new ArrayList(alignmentMap.keySet()); // currently unmodified - List image = new ArrayList(preimage); + List preimage = new ArrayList<>(alignmentMap.keySet()); // currently unmodified + List image = new ArrayList<>(preimage); for (int n = 1; n <= k; n++) { // apply alignment @@ -351,7 +351,7 @@ private static Map applyAlignmentAndCheckCycles(Map imageMap = new HashMap(alignmentMap.size()); + Map imageMap = new HashMap<>(alignmentMap.size()); // now populate with actual values for (int i = 0; i < preimage.size(); i++) { @@ -372,7 +372,7 @@ private static Map applyAlignmentAndCheckCycles(Map initializeScores(Map alignment, Map scores, int k) { if(scores == null) { - scores = new HashMap(alignment.size()); + scores = new HashMap<>(alignment.size()); } else { scores.clear(); } @@ -444,7 +444,7 @@ private static AFPChain partitionAFPchain(AFPChain afpChain, int repeatLen = afpChain.getOptLength()/order; //Extract all the residues considered in the first chain of the alignment - List alignedRes = new ArrayList(); + List alignedRes = new ArrayList<>(); for (int su=0; su(); - lengthHistory = new ArrayList(); - rmsdHistory = new ArrayList(); - mcScoreHistory = new ArrayList(); - tmScoreHistory = new ArrayList(); + timeHistory = new ArrayList<>(); + lengthHistory = new ArrayList<>(); + rmsdHistory = new ArrayList<>(); + mcScoreHistory = new ArrayList<>(); + tmScoreHistory = new ArrayList<>(); C = 20 * order; // Initialize alignment variables block = msa.getBlock(0).getAlignRes(); - freePool = new ArrayList(); + freePool = new ArrayList<>(); length = block.get(0).size(); // Store the residues aligned in the block - List aligned = new ArrayList(); + List aligned = new ArrayList<>(); for (int su = 0; su < order; su++) aligned.addAll(block.get(su)); @@ -196,11 +196,11 @@ public MultipleAlignment optimize() throws StructureException, initialize(); // Save the optimal alignment - List> optBlock = new ArrayList>(); - List optFreePool = new ArrayList(); + List> optBlock = new ArrayList<>(); + List optFreePool = new ArrayList<>(); optFreePool.addAll(freePool); for (int k = 0; k < order; k++) { - List b = new ArrayList(); + List b = new ArrayList<>(); b.addAll(block.get(k)); optBlock.add(b); } @@ -214,11 +214,11 @@ public MultipleAlignment optimize() throws StructureException, while (i < maxIter && conv < stepsToConverge) { // Save the state of the system - List> lastBlock = new ArrayList>(); - List lastFreePool = new ArrayList(); + List> lastBlock = new ArrayList<>(); + List lastFreePool = new ArrayList<>(); lastFreePool.addAll(freePool); for (int k = 0; k < order; k++) { - List b = new ArrayList(); + List b = new ArrayList<>(); b.addAll(block.get(k)); lastBlock.add(b); } @@ -281,11 +281,11 @@ public MultipleAlignment optimize() throws StructureException, // Store as the optimal alignment if better if (mcScore > optScore) { - optBlock = new ArrayList>(); - optFreePool = new ArrayList(); + optBlock = new ArrayList<>(); + optFreePool = new ArrayList<>(); optFreePool.addAll(freePool); for (int k = 0; k < order; k++) { - List b = new ArrayList(); + List b = new ArrayList<>(); b.addAll(block.get(k)); optBlock.add(b); } @@ -366,7 +366,7 @@ private void updateMultipleAlignment() throws StructureException, */ private boolean checkGaps() { - List shrinkColumns = new ArrayList(); + List shrinkColumns = new ArrayList<>(); // Loop for each column for (int res = 0; res < length; res++) { int gapCount = 0; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java index fcf9ff29d0..5eb2584401 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java @@ -541,7 +541,7 @@ private int getNumRepeats(int level) { * @return List of first Repeats of each index, sorted in ascending order */ public List getFirstRepeats(int level) { - List firstRepeats = new ArrayList(); + List firstRepeats = new ArrayList<>(); int m = getNumRepeats(level+1); //size of the level int d = axes.get(level).getOrder(); //degree of this level int n = m*d; // number of repeats included in each axis diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java index 492e1485e1..892e326fb5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.java @@ -29,7 +29,7 @@ public class ProteinComplexSignature { private BlastClustReader blastClust = null; private String pdbId = ""; private List chainIds = null; - private List chainSignatures = new ArrayList(); + private List chainSignatures = new ArrayList<>(); public ProteinComplexSignature(String pdbId, List chainIds, BlastClustReader blastClust) { @@ -75,15 +75,15 @@ public int getSubunitTypeCount() { private List getChainSignatures() { String alpha = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"; - Map mapCounts = new TreeMap(); - Map> mapChainIds = new TreeMap>(); + Map mapCounts = new TreeMap<>(); + Map> mapChainIds = new TreeMap<>(); for (String chainId: chainIds) { String rep = blastClust.getRepresentativeChain(pdbId, chainId); Integer value = mapCounts.get(rep); if (value == null) { mapCounts.put(rep, 1); - List list = new ArrayList(); + List list = new ArrayList<>(); list.add(chainId); mapChainIds.put(rep, list); } else { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java index a0653c2055..b2b3298157 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java @@ -102,7 +102,7 @@ public List> getPdbChainIdClusters(String pdbId) { loadClusters(sequenceIdentity); String pdbIdUpper = pdbId.toUpperCase(); - List> matches = new ArrayList>(); + List> matches = new ArrayList<>(); for (List cluster: clusters) { for (String chainId: cluster) { if (chainId.startsWith(pdbIdUpper)) { @@ -117,14 +117,14 @@ public List> getPdbChainIdClusters(String pdbId) { public List> getChainIdsInEntry(String pdbId) { loadClusters(sequenceIdentity); - List> matches = new ArrayList>(); + List> matches = new ArrayList<>(); List match = null; for (List cluster: clusters) { for (String chainId: cluster) { if (chainId.startsWith(pdbId)) { if (match == null) { - match = new ArrayList(); + match = new ArrayList<>(); } match.add(chainId.substring(5)); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java index 10b5652ea1..bfaa0e375e 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/PowerSet.java @@ -52,16 +52,16 @@ public PowerSet() { * @return the set of power Sets of the original Set */ public Set> powerSet(Set originalSet) { - Set> sets = new LinkedHashSet>(); + Set> sets = new LinkedHashSet<>(); if (originalSet.isEmpty()) { sets.add(new LinkedHashSet()); return sets; } - List list = new ArrayList(originalSet); + List list = new ArrayList<>(originalSet); T head = list.get(0); - Set rest = new LinkedHashSet(list.subList(1, list.size())); + Set rest = new LinkedHashSet<>(list.subList(1, list.size())); for (Set set : powerSet(rest)) { - Set newSet = new LinkedHashSet(); + Set newSet = new LinkedHashSet<>(); newSet.add(head); newSet.addAll(set); sets.add(newSet); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java index 3cac9be3f1..431babdd5f 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java @@ -443,7 +443,7 @@ public static double getAngle(AFPChain afpChain, Atom[] ca1, Atom[] ca2) { public static List> buildSymmetryGraph(List afps, Atom[] atoms, boolean undirected) { - List> graph = new ArrayList>(); + List> graph = new ArrayList<>(); for (int n = 0; n < atoms.length; n++) { graph.add(new ArrayList()); @@ -512,7 +512,7 @@ public static List divideStructure(CeSymmResult symmetry) Atom[] atoms = symmetry.getAtoms(); Set allGroups = StructureTools.getAllGroupsFromSubset(atoms, GroupType.HETATM); List repeatsId = symmetry.getRepeatsID(); - List repeats = new ArrayList(order); + List repeats = new ArrayList<>(order); // Create new structure containing the repeat atoms for (int i = 0; i < order; i++) { @@ -613,7 +613,7 @@ public static MultipleAlignment toRepeatsAlignment(CeSymmResult result) MultipleAlignment repeats = newEnsemble.getMultipleAlignment(0); Block block = repeats.getBlock(0); - List atomArrays = new ArrayList(); + List atomArrays = new ArrayList<>(); for (Structure s : repSt) atomArrays.add(StructureTools.getRepresentativeAtomArray(s)); @@ -737,7 +737,7 @@ public static QuatSymmetryResults getQuaternarySymmetry(CeSymmResult result) */ public static List getGroups(Atom[] rAtoms) { - List groups = new ArrayList(rAtoms.length); + List groups = new ArrayList<>(rAtoms.length); for (Atom a : rAtoms) { Group g = a.getGroup(); @@ -774,8 +774,8 @@ public static void updateSymmetryTransformation(SymmetryAxes axes, for (int level = 0; level < axes.getNumLevels(); level++) { // Calculate the aligned atom arrays to superimpose - List list1 = new ArrayList(); - List list2 = new ArrayList(); + List list1 = new ArrayList<>(); + List list2 = new ArrayList<>(); for (int firstRepeat : axes.getFirstRepeats(level)) { @@ -866,7 +866,7 @@ public static Atom[] getRepresentativeAtoms(Structure structure) { else { // Get Atoms of all models - List atomList = new ArrayList(); + List atomList = new ArrayList<>(); for (int m = 0; m < structure.nrModels(); m++) { for (Chain c : structure.getModel(m)) atomList.addAll(Arrays.asList(StructureTools @@ -888,7 +888,7 @@ public static Atom[] getRepresentativeAtoms(Structure structure) { */ public static List getValidFolds(List stoichiometry) { - List denominators = new ArrayList(); + List denominators = new ArrayList<>(); if (stoichiometry.isEmpty()) return denominators; @@ -896,7 +896,7 @@ public static List getValidFolds(List stoichiometry) { int nChains = Collections.max(stoichiometry); // Remove duplicate stoichiometries - Set nominators = new TreeSet(stoichiometry); + Set nominators = new TreeSet<>(stoichiometry); // find common denominators for (int d = 1; d <= nChains; d++) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java index 02efe5be5a..69eca10550 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/BravaisLattice.java @@ -62,7 +62,7 @@ public CrystalCell getExampleUnitCell() { } private static HashMap initname2bl(){ - HashMap name2bl = new HashMap(); + HashMap name2bl = new HashMap<>(); for (BravaisLattice bl:BravaisLattice.values()) { name2bl.put(bl.getName(), bl); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java index b1449475f0..d8fa098458 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java @@ -489,7 +489,7 @@ public double getMaxDimension() { Point3d vert7 = new Point3d(1,1,1); transfToOrthonormal(vert7); - ArrayList vertDists = new ArrayList(); + ArrayList vertDists = new ArrayList<>(); vertDists.add(vert0.distance(vert7)); vertDists.add(vert3.distance(vert4)); vertDists.add(vert1.distance(vert6)); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java index 768724eac7..cff84c70f8 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java @@ -105,7 +105,7 @@ public SpaceGroup(int id, int multiplicity, int primitiveMultiplicity, String sh this.shortSymbol = shortSymbol; this.altShortSymbol = altShortSymbol; transformations = new ArrayList(multiplicity); - transfAlgebraic = new ArrayList(multiplicity); + transfAlgebraic = new ArrayList<>(multiplicity); cellTranslations = new Vector3d[multiplicity/primitiveMultiplicity]; this.bravLattice = bravLattice; } @@ -649,7 +649,7 @@ public void setTransfAlgebraic(List transfAlgebraic) { transformations = new ArrayList(transfAlgebraic.size()); if ( this.transfAlgebraic == null || this.transfAlgebraic.size() == 0) - this.transfAlgebraic = new ArrayList(transfAlgebraic.size()); + this.transfAlgebraic = new ArrayList<>(transfAlgebraic.size()); for ( String transf : transfAlgebraic){ addTransformation(transf); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java index 4024c6e811..5d58e019eb 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java @@ -98,7 +98,7 @@ private static TreeMap parseSpaceGroupsXML() { System.exit(1); } - TreeMap map = new TreeMap(); + TreeMap map = new TreeMap<>(); try { map = parseSpaceGroupsXML(spaceGroupIS); @@ -110,7 +110,7 @@ private static TreeMap parseSpaceGroupsXML() { System.exit(1); } - name2sgs = new HashMap(); + name2sgs = new HashMap<>(); for (SpaceGroup sg:map.values()) { @@ -193,8 +193,8 @@ public static TreeMap getAllSpaceGroups() { * @return */ public static TreeMap parseSymopLib(InputStream symoplibIS) { - TreeMap map = new TreeMap(); - name2sgs = new HashMap(); + TreeMap map = new TreeMap<>(); + name2sgs = new HashMap<>(); try { BufferedReader br = new BufferedReader(new InputStreamReader(symoplibIS)); String line; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java index aab18d3ff0..2116b94471 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapAdapter.java @@ -42,7 +42,7 @@ public SpaceGroupMapElements[] marshal(Map arg0) throws Exc @Override public Map unmarshal(SpaceGroupMapElements[] arg0) throws Exception { - Map r = new TreeMap(); + Map r = new TreeMap<>(); for (SpaceGroupMapElements mapelement : arg0) r.put(mapelement.key, mapelement.value); return r; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java index eaf23f6d6e..b711e3179b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.java @@ -43,7 +43,7 @@ public class SpaceGroupMapRoot { private TreeMap mapProperty; public SpaceGroupMapRoot() { - mapProperty = new TreeMap(); + mapProperty = new TreeMap<>(); } @XmlJavaTypeAdapter(SpaceGroupMapAdapter.class) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java index c1416b7fad..e4d4847597 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.java @@ -41,7 +41,7 @@ public String[] marshal(List arg0) throws Exception { @Override public List unmarshal(String[] arg0) throws Exception { - List l = new ArrayList(); + List l = new ArrayList<>(); for (String s : arg0) l.add(s); return l; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java index 5a438b55d7..2a5f760f2b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.java @@ -52,7 +52,7 @@ public class TreeMapSpaceGroupWrapper implements Serializable{ public TreeMapSpaceGroupWrapper(){ - data = new TreeMap(); + data = new TreeMap<>(); } public TreeMap getData() { diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java index 728e6e925c..a6e4779a44 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java @@ -42,9 +42,9 @@ public class CoxCC { static public void process(CoxInfo ci) throws Exception { ArrayList survivalInfoList = ci.survivalInfoList; //r - ArrayList variables = new ArrayList(ci.getCoefficientsList().keySet()); + ArrayList variables = new ArrayList<>(ci.getCoefficientsList().keySet()); - ArrayList strataClass = new ArrayList(survivalInfoList.size()); + ArrayList strataClass = new ArrayList<>(survivalInfoList.size()); double[] wt = new double[survivalInfoList.size()]; for (int i = 0; i < survivalInfoList.size(); i++) { SurvivalInfo si = survivalInfoList.get(i); @@ -75,7 +75,7 @@ static public void process(CoxInfo ci) throws Exception { rvar = ci.getVariance(); } //nj - LinkedHashMap nj = new LinkedHashMap(); + LinkedHashMap nj = new LinkedHashMap<>(); Collections.sort(strataClass); for (Integer value : strataClass) { Double count = nj.get(value); @@ -86,7 +86,7 @@ static public void process(CoxInfo ci) throws Exception { nj.put(value, count); } //Nj - LinkedHashMap Nj = new LinkedHashMap(); + LinkedHashMap Nj = new LinkedHashMap<>(); //N = N + Nj[key]; double N = 0; for (int i = 0; i < survivalInfoList.size(); i++) { @@ -106,7 +106,7 @@ static public void process(CoxInfo ci) throws Exception { N = N + value; } - LinkedHashMap k1j = new LinkedHashMap(); + LinkedHashMap k1j = new LinkedHashMap<>(); for (Integer key : nj.keySet()) { double _nj = (nj.get(key)); //trying to copy what R is doing on precision double _Nj = (Nj.get(key)); @@ -119,7 +119,7 @@ static public void process(CoxInfo ci) throws Exception { for (Integer i : k1j.keySet()) { // System.out.println("Strata=" + i + " " + k1j.get(i) + " " + Nj.get(i) + " " + nj.get(i)); if (nj.get(i) > 1) { - LinkedHashMap variableStatsMap = new LinkedHashMap(); + LinkedHashMap variableStatsMap = new LinkedHashMap<>(); for (int p = 0; p < survivalInfoList.size(); p++) { SurvivalInfo si = survivalInfoList.get(p); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java index 920fd3cc33..dfc149c54e 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java @@ -71,7 +71,7 @@ public static CoxInfo process(String datafile, String timeColumn, String statusC public static CoxInfo process(WorkSheet worksheet, String timeColumn, String statusColumn, String weightColumn, String strataColumn, String clusterColumn, ArrayList variables, boolean useStrata, boolean useWeights) { try { - ArrayList survivalInfoList = new ArrayList(); + ArrayList survivalInfoList = new ArrayList<>(); int i = 1; for (String row : worksheet.getRows()) { @@ -152,7 +152,7 @@ public static void main(String[] args) { try { if (true) { String datafile = "/Users/Scooter/scripps/ngs/DataSets/E2197/misc/ecoglabtransfer/500790/2013.05.10.12.28.58.313/clindasl0228.txt"; - ArrayList variables = new ArrayList(); + ArrayList variables = new ArrayList<>(); variables.add("nndpos"); variables.add("meno"); // variables.add("er1"); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java index d60d8a316e..7bfafba710 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java @@ -59,9 +59,9 @@ public class CoxInfo { int numSamples = 0; int numEvents = 0; private LinkedHashMap metaDataFilter = null; - private LinkedHashMap coefficientsList = new LinkedHashMap(); - LinkedHashMap baselineSurvivorFunction = new LinkedHashMap(); - ArrayList survivalInfoList = new ArrayList(); + private LinkedHashMap coefficientsList = new LinkedHashMap<>(); + LinkedHashMap baselineSurvivorFunction = new LinkedHashMap<>(); + ArrayList survivalInfoList = new ArrayList<>(); /** * */ @@ -184,7 +184,7 @@ public double[] getWeighted() { * @return */ public double[][] getVariableResiduals() { - ArrayList variables = new ArrayList(coefficientsList.keySet()); + ArrayList variables = new ArrayList<>(coefficientsList.keySet()); double[][] rr = new double[survivalInfoList.size()][variables.size()]; int p = 0; for (SurvivalInfo si : this.survivalInfoList) { @@ -204,7 +204,7 @@ public double[][] getVariableResiduals() { * @param rr */ public void setVariableResiduals(double[][] rr) { - ArrayList variables = new ArrayList(coefficientsList.keySet()); + ArrayList variables = new ArrayList<>(coefficientsList.keySet()); int p = 0; for (SurvivalInfo si : this.survivalInfoList) { @@ -320,7 +320,7 @@ private void calcSummaryValues() { //beta - ArrayList variables = new ArrayList(coefficientsList.keySet()); + ArrayList variables = new ArrayList<>(coefficientsList.keySet()); for (int i = 0; i < variables.size(); i++) { String variable = variables.get(i); CoxCoefficient coe = coefficientsList.get(variable); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java index 6a3002f492..943dde980d 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java @@ -273,7 +273,7 @@ public CoxInfo process(ArrayList variables, ArrayList data ArrayList clusterList = null; if(cluster){ - clusterList = new ArrayList(); + clusterList = new ArrayList<>(); } //copy data over to local arrays to minimuze changing code for (person = 0; person < nused; person++) { @@ -797,7 +797,7 @@ public void coxphfitSCleanup(CoxInfo ci, boolean useWeighted,boolean robust, Arr double[] infs = Matrix.abs(Matrix.multiply(ci.u, ci.getVariance())); // StdArrayIO.print(infs); - ArrayList coxCoefficients = new ArrayList(ci.getCoefficientsList().values()); + ArrayList coxCoefficients = new ArrayList<>(ci.getCoefficientsList().values()); for (int i = 0; i < infs.length; i++) { double inf = infs[i]; @@ -958,7 +958,7 @@ public static void main(String[] args) { WorkSheet worksheet = WorkSheet.readCSV(is, '\t'); - ArrayList survivalInfoList = new ArrayList(); + ArrayList survivalInfoList = new ArrayList<>(); int i = 0; for (String row : worksheet.getRows()) { double time = worksheet.getCellDouble(row, "TIME"); @@ -977,7 +977,7 @@ public static void main(String[] args) { } CoxR cox = new CoxR(); - ArrayList variables = new ArrayList(); + ArrayList variables = new ArrayList<>(); // variables.add("AGE"); variables.add("AGE"); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java index dd8e73822e..cc51ec4d3f 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java @@ -41,7 +41,7 @@ public static double[][] process(CoxMethod method, ArrayList survi double temp; int n = survivalInfoList.size(); - ArrayList variables = new ArrayList(coxInfo.getCoefficientsList().keySet()); + ArrayList variables = new ArrayList<>(coxInfo.getCoefficientsList().keySet()); int nvar = variables.size(); double deaths; diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java index bfcaa5bd97..7a99f4db02 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java @@ -55,7 +55,7 @@ public int getUniqueID() { String link = geneSet + "_" + cohortName; return link.hashCode(); } - private LinkedHashMap coxInfoHashMap = new LinkedHashMap(); + private LinkedHashMap coxInfoHashMap = new LinkedHashMap<>(); /** * diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java index 819ad24e0b..94baf9dce8 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java @@ -124,7 +124,7 @@ public static double[][] process(CoxInfo ci, Type type, boolean useWeighted, Arr * @return */ private static double[][] rowsum(double[][] rr, ArrayList sets) throws Exception { - LinkedHashMap sumMap = new LinkedHashMap(); + LinkedHashMap sumMap = new LinkedHashMap<>(); if (rr.length != sets.size()) { throw new Exception("Cluster value for each sample are not of equal length n=" + rr.length + " cluster length=" + sets.size()); } @@ -144,7 +144,7 @@ private static double[][] rowsum(double[][] rr, ArrayList sets) throws E sum = new double[sumMap.size()][rr[0].length]; } - ArrayList index = new ArrayList(sumMap.keySet()); + ArrayList index = new ArrayList<>(sumMap.keySet()); //sorting does seem to make a difference in test cases at the .0000000001 // ArrayList in = new ArrayList(); // for (String s : index) { diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java index 11b01cf41c..5cf88613ab 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java @@ -31,19 +31,19 @@ */ public class StrataInfo { - private ArrayList time = new ArrayList(); - private ArrayList status = new ArrayList(); - private ArrayList nevent = new ArrayList(); - private ArrayList ncens = new ArrayList(); - private ArrayList nrisk = new ArrayList(); - private ArrayList weight = new ArrayList(); - private ArrayList surv = new ArrayList(); - private ArrayList varhaz = new ArrayList(); - private ArrayList stderr = new ArrayList(); - private ArrayList stdlow = new ArrayList(); - private ArrayList upper = new ArrayList(); - private ArrayList lower = new ArrayList(); - private LinkedHashMap ndead = new LinkedHashMap(); + private ArrayList time = new ArrayList<>(); + private ArrayList status = new ArrayList<>(); + private ArrayList nevent = new ArrayList<>(); + private ArrayList ncens = new ArrayList<>(); + private ArrayList nrisk = new ArrayList<>(); + private ArrayList weight = new ArrayList<>(); + private ArrayList surv = new ArrayList<>(); + private ArrayList varhaz = new ArrayList<>(); + private ArrayList stderr = new ArrayList<>(); + private ArrayList stdlow = new ArrayList<>(); + private ArrayList upper = new ArrayList<>(); + private ArrayList lower = new ArrayList<>(); + private LinkedHashMap ndead = new LinkedHashMap<>(); DecimalFormat df = new DecimalFormat("#.######"); DecimalFormat dfe = new DecimalFormat("0.000000E0"); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java index 0d2567a78b..c22e6fb9b5 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java @@ -29,8 +29,8 @@ */ public class SurvFitInfo { - private LinkedHashMap strataInfoHashMap = new LinkedHashMap(); - private LinkedHashMap unweightedStrataInfoHashMap = new LinkedHashMap(); + private LinkedHashMap strataInfoHashMap = new LinkedHashMap<>(); + private LinkedHashMap unweightedStrataInfoHashMap = new LinkedHashMap<>(); private boolean weighted = false; diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java index 6d4455193e..c1ed799293 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java @@ -45,12 +45,12 @@ public class SurvivalInfo implements Comparable { private double residual = 0.0; private String clusterValue = ""; - LinkedHashMap residualVariableMap = new LinkedHashMap(); + LinkedHashMap residualVariableMap = new LinkedHashMap<>(); - LinkedHashMap data = new LinkedHashMap(); + LinkedHashMap data = new LinkedHashMap<>(); // LinkedHashMap discreteData = new LinkedHashMap(); - LinkedHashMap unknownDataType = new LinkedHashMap(); - LinkedHashMap originalMetaData = new LinkedHashMap(); + LinkedHashMap unknownDataType = new LinkedHashMap<>(); + LinkedHashMap originalMetaData = new LinkedHashMap<>(); /** * @@ -177,7 +177,7 @@ public Double getContinuousVariable(String variable) { * @return */ public ArrayList getGroupCategories(String groupName) { - ArrayList groupNameList = new ArrayList(); + ArrayList groupNameList = new ArrayList<>(); for (String key : data.keySet()) { if (key.startsWith(groupName + "_")) { groupNameList.add(key); @@ -199,7 +199,7 @@ public ArrayList getGroupCategories(String groupName) { * @return */ public ArrayList getDataVariables(){ - ArrayList v = new ArrayList(); + ArrayList v = new ArrayList<>(); v.addAll(data.keySet()); v.addAll(unknownDataType.keySet()); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java index 4e5c0981c0..6e292d1633 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java @@ -86,13 +86,13 @@ private static boolean isCategorical(LinkedHashMap values) { public static void categorizeData(ArrayList DataT) { //Go through and get all variable value pairs - LinkedHashMap> valueMap = new LinkedHashMap>(); + LinkedHashMap> valueMap = new LinkedHashMap<>(); for (SurvivalInfo si : DataT) { for (String key : si.unknownDataType.keySet()) { LinkedHashMap map = valueMap.get(key); if (map == null) { - map = new LinkedHashMap(); + map = new LinkedHashMap<>(); valueMap.put(key, map); } map.put(si.unknownDataType.get(key), null); @@ -102,7 +102,7 @@ public static void categorizeData(ArrayList DataT) { for (String variable : valueMap.keySet()) { LinkedHashMap values = valueMap.get(variable); if (isCategorical(values)) { - ArrayList categories = new ArrayList(values.keySet()); + ArrayList categories = new ArrayList<>(values.keySet()); Collections.sort(categories); //go ahead and put in alphabetical order if (categories.size() == 2) { for (String value : values.keySet()) { @@ -147,7 +147,7 @@ public static void categorizeData(ArrayList DataT) { * @return */ public static ArrayList addInteraction(String variable1, String variable2, ArrayList survivalInfoList) { - ArrayList variables = new ArrayList(); + ArrayList variables = new ArrayList<>(); variables.add(variable1); variables.add(variable2); variables.add(variable1 + ":" + variable2); @@ -170,7 +170,7 @@ public static ArrayList addInteraction(String variable1, String variable * @throws Exception */ public static void groupByRange(double[] range, String variable, String groupName, ArrayList survivalInfoList) throws Exception { - ArrayList labels = new ArrayList(); + ArrayList labels = new ArrayList<>(); for (int i = 0; i < range.length; i++) { String label = ""; if (i == 0) { @@ -184,7 +184,7 @@ public static void groupByRange(double[] range, String variable, String groupNam } labels.add(label); } - ArrayList validLabels = new ArrayList(); + ArrayList validLabels = new ArrayList<>(); //need to find the categories so we can set 1 and 0 and not include ranges with no values for (SurvivalInfo si : survivalInfoList) { diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java index ba85c9084b..7760cbe23d 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java @@ -45,7 +45,7 @@ public static double[][] process(CoxMethod method, ArrayList survi //double temp; int n = survivalInfoList.size(); - ArrayList variables = new ArrayList(coxInfo.getCoefficientsList().keySet()); + ArrayList variables = new ArrayList<>(coxInfo.getCoefficientsList().keySet()); int nvar = variables.size(); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java index ca98b8d9d9..9e4de21fcc 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java @@ -31,10 +31,10 @@ */ public class WorkSheet { - private LinkedHashMap columnLookup = new LinkedHashMap(); - private LinkedHashMap rowLookup = new LinkedHashMap(); + private LinkedHashMap columnLookup = new LinkedHashMap<>(); + private LinkedHashMap rowLookup = new LinkedHashMap<>(); private CompactCharSequence[][] data = new CompactCharSequence[1][1]; - HashMap dataGrid = new HashMap(); + HashMap dataGrid = new HashMap<>(); private String indexColumnName = ""; /** @@ -233,14 +233,14 @@ public WorkSheet(CompactCharSequence[][] values) { data = values; } - private LinkedHashMap metaDataColumnsHashMap = new LinkedHashMap(); + private LinkedHashMap metaDataColumnsHashMap = new LinkedHashMap<>(); /** * * @return */ public ArrayList getMetaDataColumns() { - ArrayList metaColumns = new ArrayList(); + ArrayList metaColumns = new ArrayList<>(); for (String key : metaDataColumnsHashMap.keySet()) { HeaderInfo hi = columnLookup.get(key); if (!hi.isHide()) { @@ -255,7 +255,7 @@ public ArrayList getMetaDataColumns() { * @return */ public ArrayList getMetaDataRows() { - ArrayList metaRows = new ArrayList(); + ArrayList metaRows = new ArrayList<>(); for (String key : metaDataRowsHashMap.keySet()) { HeaderInfo hi = rowLookup.get(key); if (!hi.isHide()) { @@ -270,7 +270,7 @@ public ArrayList getMetaDataRows() { * @return */ public ArrayList getDataColumns() { - ArrayList dataColumns = new ArrayList(); + ArrayList dataColumns = new ArrayList<>(); ArrayList columns = this.getColumns(); for (String column : columns) { if (!metaDataColumnsHashMap.containsKey(column)) { @@ -292,7 +292,7 @@ public void shuffleColumnsAndThenRows(ArrayList columns, ArrayList rowIndex = new ArrayList(); + ArrayList rowIndex = new ArrayList<>(); for (int i = 0; i < rows.size(); i++) { rowIndex.add(i); } @@ -311,7 +311,7 @@ public void shuffleColumnsAndThenRows(ArrayList columns, ArrayList columnIndex = new ArrayList(); + ArrayList columnIndex = new ArrayList<>(); for (int i = 0; i < columns.size(); i++) { columnIndex.add(i); } @@ -344,7 +344,7 @@ public void shuffleColumnValues(ArrayList columns) throws Exception { doubleValues.clear(); ArrayList rows = this.getDataRows(); for (String column : columns) { //shuffle all values in the column - ArrayList rowIndex = new ArrayList(); + ArrayList rowIndex = new ArrayList<>(); for (int i = 0; i < rows.size(); i++) { rowIndex.add(i); } @@ -375,7 +375,7 @@ public void shuffleRowValues(ArrayList rows) throws Exception { doubleValues.clear(); ArrayList columns = this.getColumns(); for (String row : rows) { - ArrayList columnIndex = new ArrayList(); + ArrayList columnIndex = new ArrayList<>(); for (int i = 0; i < columns.size(); i++) { columnIndex.add(i); } @@ -521,7 +521,7 @@ public boolean isMetaDataRow(String row) { return true; } } - private LinkedHashMap metaDataRowsHashMap = new LinkedHashMap(); + private LinkedHashMap metaDataRowsHashMap = new LinkedHashMap<>(); /** * @@ -646,7 +646,7 @@ public void applyColumnFilter(String column, ChangeValue changeValue) throws Exc * @param defaultValue */ public void addColumn(String column, String defaultValue) { - ArrayList columns = new ArrayList(); + ArrayList columns = new ArrayList<>(); columns.add(column); addColumns(columns, defaultValue); } @@ -694,7 +694,7 @@ public void addColumns(ArrayList columns, String defaultValue) { * @param defaultValue */ public void addRow(String row, String defaultValue) { - ArrayList rows = new ArrayList(); + ArrayList rows = new ArrayList<>(); rows.add(row); addRows(rows, defaultValue); } @@ -808,7 +808,7 @@ public boolean isValidColumn(String col) { } } //When we do gene signatures we ask for the same data value often. This method took up 50% of the time. - HashMap doubleValues = new HashMap(); + HashMap doubleValues = new HashMap<>(); boolean cacheDoubleValues = false; /** @@ -909,7 +909,7 @@ public String getCell(String row, String col) throws Exception { * @param changeValue */ public void changeRowHeader(ChangeValue changeValue) { - ArrayList rows = new ArrayList(rowLookup.keySet()); + ArrayList rows = new ArrayList<>(rowLookup.keySet()); for (String row : rows) { String newRow = changeValue.change(row); HeaderInfo value = rowLookup.get(row); @@ -923,7 +923,7 @@ public void changeRowHeader(ChangeValue changeValue) { * @param changeValue */ public void changeColumnHeader(ChangeValue changeValue) { - ArrayList columns = new ArrayList(columnLookup.keySet()); + ArrayList columns = new ArrayList<>(columnLookup.keySet()); for (String col : columns) { String newCol = changeValue.change(col); HeaderInfo value = columnLookup.get(col); @@ -1030,8 +1030,8 @@ public ArrayList getRandomDataColumns(int number) { * @return */ public ArrayList getRandomDataColumns(int number, ArrayList columns) { - ArrayList randomColumns = new ArrayList(); - HashMap picked = new HashMap(); + ArrayList randomColumns = new ArrayList<>(); + HashMap picked = new HashMap<>(); while (picked.size() < number) { double v = Math.random(); int index = (int) (v * columns.size()); @@ -1051,7 +1051,7 @@ public ArrayList getRandomDataColumns(int number, ArrayList colu * @return */ public ArrayList getAllColumns() { - ArrayList columns = new ArrayList(); + ArrayList columns = new ArrayList<>(); for (String col : columnLookup.keySet()) { columns.add(col); } @@ -1064,7 +1064,7 @@ public ArrayList getAllColumns() { * @return */ public ArrayList getColumns() { - ArrayList columns = new ArrayList(); + ArrayList columns = new ArrayList<>(); for (String col : columnLookup.keySet()) { HeaderInfo hi = columnLookup.get(col); if (!hi.isHide()) { @@ -1082,8 +1082,8 @@ public ArrayList getColumns() { * @throws Exception */ public ArrayList getDiscreteColumnValues(String column) throws Exception { - HashMap hashMapValues = new HashMap(); - ArrayList values = new ArrayList(); + HashMap hashMapValues = new HashMap<>(); + ArrayList values = new ArrayList<>(); ArrayList rows = getDataRows(); for (String row : rows) { String value = getCell(row, column); @@ -1103,8 +1103,8 @@ public ArrayList getDiscreteColumnValues(String column) throws Exception * @throws Exception */ public ArrayList getDiscreteRowValues(String row) throws Exception { - HashMap hashMapValues = new HashMap(); - ArrayList values = new ArrayList(); + HashMap hashMapValues = new HashMap<>(); + ArrayList values = new ArrayList<>(); for (String column : getColumns()) { String value = getCell(row, column); if (!hashMapValues.containsKey(value)) { @@ -1121,7 +1121,7 @@ public ArrayList getDiscreteRowValues(String row) throws Exception { * @return */ public ArrayList getAllRows() { - ArrayList rows = new ArrayList(); + ArrayList rows = new ArrayList<>(); for (String row : rowLookup.keySet()) { rows.add(row); } @@ -1135,7 +1135,7 @@ public ArrayList getAllRows() { * @return */ public ArrayList getRows() { - ArrayList rows = new ArrayList(); + ArrayList rows = new ArrayList<>(); for (String row : rowLookup.keySet()) { HeaderInfo hi = rowLookup.get(row); if (!hi.isHide()) { @@ -1151,7 +1151,7 @@ public ArrayList getRows() { * @return */ public ArrayList getDataRows() { - ArrayList rows = new ArrayList(); + ArrayList rows = new ArrayList<>(); for (String row : rowLookup.keySet()) { if (this.isMetaDataRow(row)) { continue; @@ -1262,7 +1262,7 @@ static CompactCharSequence[][] getAllValuesCompactCharSequence(InputStream is, c BufferedReader br = new BufferedReader(new InputStreamReader(is)); - ArrayList rows = new ArrayList(); + ArrayList rows = new ArrayList<>(); String line = br.readLine(); int numcolumns = -1; @@ -1309,7 +1309,7 @@ static CompactCharSequence[][] getAllValuesCompactCharSequence(InputStream is, c static String[][] getAllValues(String fileName, char delimiter) throws Exception { FileReader reader = new FileReader(fileName); BufferedReader br = new BufferedReader(reader); - ArrayList rows = new ArrayList(); + ArrayList rows = new ArrayList<>(); String line = br.readLine(); int numcolumns = -1; @@ -1388,7 +1388,7 @@ static public WorkSheet unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boole } } - ArrayList joinedColumns = new ArrayList(); + ArrayList joinedColumns = new ArrayList<>(); joinedColumns.addAll(w1DataColumns); joinedColumns.addAll(w2DataColumns); if (!joinedColumns.contains("META_DATA") && (w1MetaDataColumns.size() > 0 || w2MetaDataColumns.size() > 0)) { @@ -1406,9 +1406,9 @@ static public WorkSheet unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boole } ArrayList w1Rows = w1.getRows(); ArrayList w2Rows = w2.getRows(); - ArrayList rows = new ArrayList(); + ArrayList rows = new ArrayList<>(); - HashSet w1Key = new HashSet(w1Rows); + HashSet w1Key = new HashSet<>(w1Rows); for (String key : w2Rows) { if (w1Key.contains(key)) { rows.add(key); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java index a6fda3f095..d8d120aee7 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java @@ -41,7 +41,7 @@ public class ExpressionFigure extends JPanel { private static final long serialVersionUID = 1L; - ArrayList title = new ArrayList(); + ArrayList title = new ArrayList<>(); /** * */ @@ -70,8 +70,8 @@ public class ExpressionFigure extends JPanel { FontMetrics fm; KMFigureInfo kmfi = new KMFigureInfo(); // LinkedHashMap> survivalData = new LinkedHashMap>(); - ArrayList lineInfoList = new ArrayList(); - ArrayList siList = new ArrayList(); + ArrayList lineInfoList = new ArrayList<>(); + ArrayList siList = new ArrayList<>(); String variable = ""; private String fileName = ""; @@ -120,7 +120,7 @@ public void setFigureLineInfo(ArrayList lineInfoList) { * @param variable */ public void setSurvivalInfo(ArrayList title, ArrayList _siList, String variable) { - this.siList = new ArrayList(); + this.siList = new ArrayList<>(); this.title = title; this.variable = variable; @@ -372,13 +372,13 @@ public static void main(String[] args) { application.setSize(500, 400); // window is 500 pixels wide, 400 high application.setVisible(true); - ArrayList titles = new ArrayList(); + ArrayList titles = new ArrayList<>(); titles.add("Line 1"); titles.add("line 2"); - ArrayList figureInfo = new ArrayList(); + ArrayList figureInfo = new ArrayList<>(); - ArrayList survivalInfoList = new ArrayList(); + ArrayList survivalInfoList = new ArrayList<>(); for (int i = 0; i < 600; i++) { double r = Math.random(); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java index 24f053d592..d17d6afa51 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java @@ -87,7 +87,7 @@ public class KMFigureInfo { * */ public Color[] legendColor = {Color.RED, Color.BLUE, Color.GREEN, Color.CYAN, Color.ORANGE, Color.YELLOW, Color.MAGENTA, Color.PINK}; - public ArrayList xAxisLabels = new ArrayList();//new ArrayList(Arrays.asList(0.0, 5.0, 10.0, 15.0, 20.0)); + public ArrayList xAxisLabels = new ArrayList<>();//new ArrayList(Arrays.asList(0.0, 5.0, 10.0, 15.0, 20.0)); public String xAxisLegend = ""; public String yAxisLegend = ""; public Color getColor(int index) { diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java index c5d358cbeb..f1e8877f97 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java @@ -42,7 +42,7 @@ public class KaplanMeierFigure extends JPanel { private static final long serialVersionUID = 1L; - ArrayList title = new ArrayList(); + ArrayList title = new ArrayList<>(); /** * */ @@ -69,12 +69,12 @@ public class KaplanMeierFigure extends JPanel { double maxPercentage = 1.0; FontMetrics fm; KMFigureInfo kmfi = new KMFigureInfo(); - LinkedHashMap> survivalData = new LinkedHashMap>(); - ArrayList lineInfoList = new ArrayList(); + LinkedHashMap> survivalData = new LinkedHashMap<>(); + ArrayList lineInfoList = new ArrayList<>(); SurvFitInfo sfi = new SurvFitInfo(); private String fileName = ""; - private ArrayList xAxisTimeValues = new ArrayList(); - private ArrayList xAxisTimeCoordinates = new ArrayList(); + private ArrayList xAxisTimeValues = new ArrayList<>(); + private ArrayList xAxisTimeCoordinates = new ArrayList<>(); /** * @@ -91,7 +91,7 @@ public KaplanMeierFigure() { * @return */ public ArrayList getGroups() { - return new ArrayList(survivalData.keySet()); + return new ArrayList<>(survivalData.keySet()); } /** @@ -160,7 +160,7 @@ public void setFigureLineInfo(ArrayList lineInfoList) { * @throws Exception */ public void setCoxInfo(ArrayList title, CoxInfo ci, String strataVariable, LinkedHashMap legendMap, Boolean useWeighted) throws Exception { - LinkedHashMap> survivalData = new LinkedHashMap>(); + LinkedHashMap> survivalData = new LinkedHashMap<>(); ArrayList siList = ci.getSurvivalInfoList(); int n = 0; int event = 0; @@ -173,7 +173,7 @@ public void setCoxInfo(ArrayList title, CoxInfo ci, String strataVariabl } ArrayList censorStatusList = survivalData.get(legend); if (censorStatusList == null) { - censorStatusList = new ArrayList(); + censorStatusList = new ArrayList<>(); survivalData.put(legend, censorStatusList); } CensorStatus cs = new CensorStatus(strata, si.getTime(), si.getStatus() + ""); @@ -195,7 +195,7 @@ public void setCoxInfo(ArrayList title, CoxInfo ci, String strataVariabl // System.out.println("setCoxInfo=" + cc.pvalue + " " + title); - ArrayList lines = new ArrayList(); + ArrayList lines = new ArrayList<>(); lines.add(line1); lines.add(line2); lines.add(line3); @@ -303,7 +303,7 @@ public void setSurvivalData(ArrayList title, LinkedHashMap labels = new ArrayList(survivalData.keySet()); + ArrayList labels = new ArrayList<>(survivalData.keySet()); Collections.sort(labels); for (String legend : labels) { ArrayList censorStatusList = survivalData.get(legend); @@ -394,7 +394,7 @@ private void drawSurvivalCurves(Graphics g) { int colorIndex = 0; - ArrayList labels = new ArrayList(sfi.getStrataInfoHashMap().keySet()); + ArrayList labels = new ArrayList<>(sfi.getStrataInfoHashMap().keySet()); Collections.sort(labels); LinkedHashMap strataInfoHashMap = sfi.getStrataInfoHashMap(); @@ -763,7 +763,7 @@ public static void main(String[] args) { try { KaplanMeierFigure kaplanMeierFigure = new KaplanMeierFigure(); - LinkedHashMap> survivalDataHashMap = new LinkedHashMap>(); + LinkedHashMap> survivalDataHashMap = new LinkedHashMap<>(); // if (false) { //http://sph.bu.edu/otlt/MPH-Modules/BS/BS704_Survival/ // ArrayList graph1 = new ArrayList(); @@ -801,7 +801,7 @@ public static void main(String[] args) { - ArrayList graph1 = new ArrayList(); + ArrayList graph1 = new ArrayList<>(); graph1.add(new CensorStatus("A", 1.0, "1")); graph1.add(new CensorStatus("A", 1.0, "1")); graph1.add(new CensorStatus("A", 1.0, "1")); @@ -841,7 +841,7 @@ public static void main(String[] args) { survivalDataHashMap.put("Label 1", graph1); - ArrayList graph2 = new ArrayList(); + ArrayList graph2 = new ArrayList<>(); graph2.add(new CensorStatus("A", 1.0, "1")); graph2.add(new CensorStatus("A", 1.0, "1")); graph2.add(new CensorStatus("A", 1.0, "0")); @@ -882,7 +882,7 @@ public static void main(String[] args) { survivalDataHashMap.put("Label 2", graph2); } - ArrayList figureInfo = new ArrayList(); + ArrayList figureInfo = new ArrayList<>(); //DecimalFormat dfe = new DecimalFormat("0.00E0"); //DecimalFormat df = new DecimalFormat("0.00"); @@ -896,7 +896,7 @@ public static void main(String[] args) { application.setSize(500, 400); // window is 500 pixels wide, 400 high application.setVisible(true); - ArrayList titles = new ArrayList(); + ArrayList titles = new ArrayList<>(); titles.add("Line 1"); titles.add("Line 2"); kaplanMeierFigure.setSurvivalData(titles, survivalDataHashMap, true); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java index b1278b838c..dc3e57994e 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java @@ -69,7 +69,7 @@ private void paintTable(Graphics g) { g2.setStroke(kmfi.kmStroke); SurvFitInfo sfi = kmf.getSurvivalFitInfo(); - LinkedHashMap sfiHashMap = new LinkedHashMap(); + LinkedHashMap sfiHashMap = new LinkedHashMap<>(); if(sfi.isWeighted()){ sfiHashMap = sfi.getUnweightedStrataInfoHashMap(); }else{ @@ -94,7 +94,7 @@ private void paintTable(Graphics g) { ArrayList xaxisTimeValues = kmf.getxAxisTimeValues(); ArrayList xAxisTimeCoordinates = kmf.getxAxisTimeCoordinates(); - ArrayList labels = new ArrayList(sfiHashMap.keySet()); + ArrayList labels = new ArrayList<>(sfiHashMap.keySet()); Collections.sort(labels); for (String group : labels) { diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java index f315eaaf0a..764c8af76f 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java @@ -122,7 +122,7 @@ public enum ConfLower { * @throws Exception */ public SurvFitInfo process(LinkedHashMap> survivalData, boolean useWeights) throws Exception { - ArrayList survivalInfoList = new ArrayList(); + ArrayList survivalInfoList = new ArrayList<>(); int i = 0; for (String strata : survivalData.keySet()) { ArrayList csList = survivalData.get(strata); @@ -154,7 +154,7 @@ public SurvFitInfo process(LinkedHashMap> surviv */ public SurvFitInfo process(String datafile, String timeColumn, String statusColumn, String weightColumn, String variableColumn, boolean useWeights) throws Exception { WorkSheet worksheet = WorkSheet.readCSV(datafile, '\t'); - ArrayList survivalInfoList = new ArrayList(); + ArrayList survivalInfoList = new ArrayList<>(); int i = 1; for (String row : worksheet.getRows()) { @@ -223,8 +223,8 @@ public LinkedHashMap processStrataInfo(String variable, Arr int n = dataT.size(); - LinkedHashMap levels = new LinkedHashMap(); - LinkedHashMap> strataHashMap = new LinkedHashMap>(); + LinkedHashMap levels = new LinkedHashMap<>(); + LinkedHashMap> strataHashMap = new LinkedHashMap<>(); for (int i = 0; i < n; i++) { SurvivalInfo si = dataT.get(i); @@ -237,7 +237,7 @@ public LinkedHashMap processStrataInfo(String variable, Arr levels.put(value, count); ArrayList strataList = strataHashMap.get(value); if (strataList == null) { - strataList = new ArrayList(); + strataList = new ArrayList<>(); strataHashMap.put(value, strataList); } strataList.add(si); @@ -246,7 +246,7 @@ public LinkedHashMap processStrataInfo(String variable, Arr //int nstrat = levels.size(); - LinkedHashMap strataInfoHashMap = new LinkedHashMap(); + LinkedHashMap strataInfoHashMap = new LinkedHashMap<>(); for (String strata : strataHashMap.keySet()) { @@ -379,8 +379,8 @@ public LinkedHashMap processStrataInfo(String variable, Arr } - ArrayList events = new ArrayList(); - ArrayList nrisk = new ArrayList(); + ArrayList events = new ArrayList<>(); + ArrayList nrisk = new ArrayList<>(); for (StrataInfo strataInfo : strataInfoHashMap.values()) { boolean firsttime = true; for (int j = 0; j < strataInfo.getNevent().size(); j++) { @@ -395,19 +395,19 @@ public LinkedHashMap processStrataInfo(String variable, Arr } } - ArrayList zz = new ArrayList(); + ArrayList zz = new ArrayList<>(); for (int i = 0; i < events.size(); i++) { if (events.get(i)) { zz.add(i + 1); } } zz.add(events.size() + 1); - ArrayList diffzz = new ArrayList(); + ArrayList diffzz = new ArrayList<>(); for (int i = 0; i < zz.size() - 1; i++) { diffzz.add(zz.get(i + 1) - zz.get(i)); } //System.out.println(diffzz); - ArrayList nlag = new ArrayList(); + ArrayList nlag = new ArrayList<>(); for (int j = 0; j < nrisk.size(); j++) { int count = diffzz.get(j); for (int c = 0; c < count; c++) { @@ -542,12 +542,12 @@ public static void main(String[] args) { application.setSize(500, 400); // window is 500 pixels wide, 400 high application.setVisible(true); - ArrayList titles = new ArrayList(); + ArrayList titles = new ArrayList<>(); titles.add("Line 1"); titles.add("line 2"); kaplanMeierFigure.setSurvivalData(titles, si, null); - ArrayList figureInfo = new ArrayList(); + ArrayList figureInfo = new ArrayList<>(); // figureInfo.add("HR=2.1 95% CI(1.8-2.5)"); // figureInfo.add("p-value=.001"); kaplanMeierFigure.setFigureLineInfo(figureInfo); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java index b75cc2d3ad..3b1ca8fe15 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java @@ -66,7 +66,7 @@ static public void process(WorkSheet worksheet, String sensorMapColumn, LinkedHa public static void main(String[] args) { try { - LinkedHashMap censorMap = new LinkedHashMap(); + LinkedHashMap censorMap = new LinkedHashMap<>(); censorMap.put("a", "0"); censorMap.put("d", "1"); censorMap.put("d-d.s.", "1"); @@ -74,7 +74,7 @@ public static void main(String[] args) { String timeColumn = "TIME"; String sensorMapColumn = "last_follow_up_status"; // "survstat3"; double timeScale = 1.0; - ArrayList metaDataInfoList = new ArrayList(); + ArrayList metaDataInfoList = new ArrayList<>(); metaDataInfoList.add(new MetaDataInfo("age_at_diagnosis", true, new MeanQuantizer())); metaDataInfoList.add(new MetaDataInfo("size", true, new MeanQuantizer())); metaDataInfoList.add(new MetaDataInfo("lymph_nodes_positive", true, new MeanQuantizer())); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java index 26bcef3081..bad051b590 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java @@ -42,7 +42,7 @@ public class MetaDataInfo { * */ public DiscreteQuantizerInterface discreteQuantizer = null; - ArrayList discreteValues = new ArrayList(); + ArrayList discreteValues = new ArrayList<>(); /** * diff --git a/biojava-ws/src/main/java/demo/HmmerDemo.java b/biojava-ws/src/main/java/demo/HmmerDemo.java index 689d62ec92..3c6f3ff1f2 100644 --- a/biojava-ws/src/main/java/demo/HmmerDemo.java +++ b/biojava-ws/src/main/java/demo/HmmerDemo.java @@ -86,7 +86,7 @@ public static void main(String[] args) throws Exception { private static ProteinSequence getUniprot(String uniProtID) throws Exception { AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet(); - UniprotProxySequenceReader uniprotSequence = new UniprotProxySequenceReader(uniProtID,set); + UniprotProxySequenceReader uniprotSequence = new UniprotProxySequenceReader<>(uniProtID,set); ProteinSequence seq = new ProteinSequence(uniprotSequence); diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java index db184a9a53..196dc30c90 100644 --- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java +++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java @@ -45,7 +45,7 @@ public class NCBIQBlastAlignmentProperties implements RemotePairwiseAlignmentProperties { private static final long serialVersionUID = 7158270364392309841L; - private Map param = new HashMap(); + private Map param = new HashMap<>(); /** * This method forwards to {@link #getAlignmentOption(BlastAlignmentParameterEnum)}. Consider using it instead. @@ -69,7 +69,7 @@ public void setAlignementOption(String key, String val) { */ @Override public Set getAlignmentOptions() { - Set result = new HashSet(); + Set result = new HashSet<>(); for (BlastAlignmentParameterEnum parameter : param.keySet()) { result.add(parameter.name()); } diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java index 8efc91908b..3c38328ae6 100644 --- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java +++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java @@ -41,7 +41,7 @@ public class NCBIQBlastOutputProperties implements RemotePairwiseAlignmentOutputProperties { private static final long serialVersionUID = -9202060390925345163L; - private Map param = new HashMap(); + private Map param = new HashMap<>(); /** * This constructor builds the parameters for the output of the GET command sent to the QBlast service with default @@ -96,7 +96,7 @@ public void setOutputOption(BlastOutputParameterEnum key, String value) { */ @Override public Set getOutputOptions() { - Set result = new HashSet(); + Set result = new HashSet<>(); for (BlastOutputParameterEnum parameter : param.keySet()) { result.add(parameter.name()); } diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java index c63a4b7eb9..42fafb0155 100644 --- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java +++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java @@ -72,7 +72,7 @@ public class NCBIQBlastService implements RemotePairwiseAlignmentService { private String email = DEFAULT_EMAIL; private String tool = DEFAULT_TOOL; - private Map jobs = new HashMap(); + private Map jobs = new HashMap<>(); /** Constructs a service object that targets the public NCBI BLAST network * service. @@ -164,7 +164,7 @@ public String sendAlignmentRequest(int gid, RemotePairwiseAlignmentProperties rp */ @Override public String sendAlignmentRequest(String query, RemotePairwiseAlignmentProperties alignmentProperties) throws Exception { - Map params = new HashMap(); + Map params = new HashMap<>(); for (String key : alignmentProperties.getAlignmentOptions()) { params.put(key, alignmentProperties.getAlignmentOption(key)); } @@ -318,7 +318,7 @@ public boolean isReady(String id, long present) throws Exception { */ @Override public InputStream getAlignmentResults(String id, RemotePairwiseAlignmentOutputProperties outputProperties) throws Exception { - Map params = new HashMap(); + Map params = new HashMap<>(); for (String key : outputProperties.getOutputOptions()) { params.put(key, outputProperties.getOutputOption(key)); } diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java index 2083db63aa..2c8e494971 100644 --- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java +++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java @@ -134,7 +134,7 @@ public SortedSet scan(ProteinSequence sequence, URL serviceLocation // process the response and build up a container for the data. - SortedSet results = new TreeSet(); + SortedSet results = new TreeSet<>(); try { JSONObject json = JSONObject.fromObject(result.toString()); @@ -170,7 +170,7 @@ public SortedSet scan(ProteinSequence sequence, URL serviceLocation JSONArray hmmdomains = hit.getJSONArray("domains"); - SortedSet domains = new TreeSet(); + SortedSet domains = new TreeSet<>(); for ( int j= 0 ; j < hmmdomains.size() ; j++){ JSONObject d = hmmdomains.getJSONObject(j); Integer is_included = getInteger(d.get("is_included"));