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Fix sonar issue S2293 Replace the type specification in this construc…
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…tor call with the diamond operator ('<>')
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@jlerbsc
jlerbsc committed Apr 18, 2024
1 parent 266d835 commit b182121
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Showing 324 changed files with 1,102 additions and 1,102 deletions.
12 changes: 6 additions & 6 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
View file
Expand Up @@ -95,8 +95,8 @@ public static void run(String[] args) throws Exception{
/*
* Parse input arguments
*/
List<Character> propertyList = new ArrayList<Character>();
List<Character> specificList = new ArrayList<Character>();
List<Character> propertyList = new ArrayList<>();
List<Character> specificList = new ArrayList<>();
String inputLocation = null;
String outputLocation = null;
String aminoAcidCompositionLocation = null;
Expand Down Expand Up @@ -179,14 +179,14 @@ private static LinkedHashMap<String, ProteinSequence> readInputFile(String input
}
LinkedHashMap<String, ProteinSequence> ret;
if ( inputLocation.toLowerCase().contains(".gb")) {
GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<>(
inStream, new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(set));
ret = genbankReader.process();


} else {
FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(set));
ret = fastaReader.process();
Expand Down Expand Up @@ -214,7 +214,7 @@ private static void printHeader(PrintStream output, List<Character> propertyList
* 9 Composition of the 20 standard amino acid
* 0 Composition of the specific amino acid
*/
List<String> sList = new ArrayList<String>();
List<String> sList = new ArrayList<>();
sList.add("SequenceName");
for(Character c:propertyList){
switch(c){
Expand Down Expand Up @@ -277,7 +277,7 @@ private static void compute(PrintStream output, String header, String sequence,
IPeptideProperties pp = new PeptidePropertiesImpl();

int specificCount = 0;
List<Double> dList = new ArrayList<Double>();
List<Double> dList = new ArrayList<>();
for(Character c:propertyList){
switch(c){
case '1':
Expand Down
14 changes: 7 additions & 7 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
View file
Expand Up @@ -64,14 +64,14 @@ public class Constraints {
public static AminoAcidCompound Y = aaSet.getCompoundForString("Y");
public static AminoAcidCompound V = aaSet.getCompoundForString("V");

public static Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<AminoAcidCompound, Double>();
public static Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<AminoAcidCompound, Double>();
public static Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<AminoAcidCompound, Double>();
public static Map<AminoAcidCompound, Double> aa2PKa = new HashMap<AminoAcidCompound, Double>();
public static Map<String, Double> diAA2Instability = new HashMap<String, Double>();
public static Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<>();
public static Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<>();
public static Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<>();
public static Map<AminoAcidCompound, Double> aa2PKa = new HashMap<>();
public static Map<String, Double> diAA2Instability = new HashMap<>();

public static Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<AminoAcidCompound, Double>();
public static Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<AminoAcidCompound, Double>();
public static Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<>();
public static Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<>();

static{
initMolecularWeight();
Expand Down
4 changes: 2 additions & 2 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
View file
Expand Up @@ -532,7 +532,7 @@ public static final Map<AminoAcidCompound, Double> getAAComposition(String seque
*/
public static final Map<String, Double> getAACompositionString(String sequence){
Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
Map<String, Double> aaString2Composition = new HashMap<String, Double>();
Map<String, Double> aaString2Composition = new HashMap<>();
aaString2Composition = aa2Composition.keySet().stream() .collect(Collectors.toMap(aaCompound -> aaCompound.getShortName(),aaCompound ->aa2Composition.get(aaCompound)));
return aaString2Composition;
}
Expand All @@ -550,7 +550,7 @@ public static final Map<String, Double> getAACompositionString(String sequence){
*/
public static final Map<Character, Double> getAACompositionChar(String sequence){
Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
Map<Character, Double> aaChar2Composition = new HashMap<Character, Double>();
Map<Character, Double> aaChar2Composition = new HashMap<>();
for(AminoAcidCompound aaCompound:aa2Composition.keySet()){
aaChar2Composition.put(aaCompound.getShortName().charAt(0), aa2Composition.get(aaCompound));
}
Expand Down
6 changes: 3 additions & 3 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
View file
Expand Up @@ -210,7 +210,7 @@ private Map<AminoAcidCompound, Integer> getExtinctAACount(ProteinSequence sequen
}
}
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
Map<AminoAcidCompound, Integer> extinctAA2Count = new HashMap<AminoAcidCompound, Integer>();
Map<AminoAcidCompound, Integer> extinctAA2Count = new HashMap<>();
//Ignore Case is always true
extinctAA2Count.put(aaSet.getCompoundForString("W"), numW + smallW);
extinctAA2Count.put(aaSet.getCompoundForString("C"), (int) (numC + smallC));
Expand Down Expand Up @@ -532,7 +532,7 @@ private Map<AminoAcidCompound, Integer> getChargedAACount(ProteinSequence sequen
}
}
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
Map<AminoAcidCompound, Integer> chargedAA2Count = new HashMap<AminoAcidCompound, Integer>();
Map<AminoAcidCompound, Integer> chargedAA2Count = new HashMap<>();
chargedAA2Count.put(aaSet.getCompoundForString("K"), numK);
chargedAA2Count.put(aaSet.getCompoundForString("R"), numR);
chargedAA2Count.put(aaSet.getCompoundForString("H"), numH);
Expand All @@ -558,7 +558,7 @@ public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAci
@Override
public Map<AminoAcidCompound, Double> getAAComposition(ProteinSequence sequence) {
int validLength = 0;
Map<AminoAcidCompound, Double> aa2Composition = new HashMap<AminoAcidCompound, Double>();
Map<AminoAcidCompound, Double> aa2Composition = new HashMap<>();
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
for(AminoAcidCompound aa:aaSet.getAllCompounds()){
aa2Composition.put(aa, 0.0);
Expand Down
2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
View file
Expand Up @@ -106,7 +106,7 @@ public final static int getNumberOfInvalidChar(String sequence, Set<Character>
* a new sequence with all invalid characters being replaced by '-'.
*/
public final static String cleanSequence(String sequence, Set<Character> cSet){
Set<Character> invalidCharSet = new HashSet<Character>();
Set<Character> invalidCharSet = new HashSet<>();
StringBuilder cleanSeq = new StringBuilder();
if(cSet == null) cSet = PeptideProperties.standardAASet;
for(char c:sequence.toCharArray()){
Expand Down
14 changes: 7 additions & 7 deletions ...va-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
View file
Expand Up @@ -125,43 +125,43 @@ private Convertor getConvertor(ATTRIBUTE attribute) throws Exception{

@Override
public Map<GROUPING, Double> getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
Map<GROUPING, Double> grouping2Composition = new HashMap<GROUPING, Double>();
Map<GROUPING, Double> grouping2Composition = new HashMap<>();
for(GROUPING group:GROUPING.values()) grouping2Composition.put(group, getComposition(sequence, attribute, group));
return grouping2Composition;
}

@Override
public Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(ProteinSequence sequence) throws Exception {
Map<ATTRIBUTE, Map<GROUPING, Double>> attribute2Grouping2Composition = new HashMap<ATTRIBUTE, Map<GROUPING, Double>>();
Map<ATTRIBUTE, Map<GROUPING, Double>> attribute2Grouping2Composition = new HashMap<>();
for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Grouping2Composition.put(attribute, getComposition(sequence, attribute));
return attribute2Grouping2Composition;
}

@Override
public Map<TRANSITION, Double> getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
Map<TRANSITION, Double> transition2Double = new HashMap<TRANSITION, Double>();
Map<TRANSITION, Double> transition2Double = new HashMap<>();
for(TRANSITION transition:TRANSITION.values()) transition2Double.put(transition, getTransition(sequence, attribute, transition));
return transition2Double;
}

@Override
public Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(ProteinSequence sequence) throws Exception {
Map<ATTRIBUTE, Map<TRANSITION, Double>> attribute2Transition2Double = new HashMap<ATTRIBUTE, Map<TRANSITION, Double>>();
Map<ATTRIBUTE, Map<TRANSITION, Double>> attribute2Transition2Double = new HashMap<>();
for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Transition2Double.put(attribute, getTransition(sequence, attribute));
return attribute2Transition2Double;
}

@Override
public Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception {
Map<DISTRIBUTION, Double> distribution2Double = new HashMap<DISTRIBUTION, Double>();
Map<DISTRIBUTION, Double> distribution2Double = new HashMap<>();
for(DISTRIBUTION distribution:DISTRIBUTION.values())
distribution2Double.put(distribution, getDistributionPosition(sequence, attribute, group, distribution));
return distribution2Double;
}

@Override
public Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
Map<GROUPING, Map<DISTRIBUTION, Double>> grouping2Distribution2Double = new HashMap<GROUPING, Map<DISTRIBUTION, Double>>();
Map<GROUPING, Map<DISTRIBUTION, Double>> grouping2Distribution2Double = new HashMap<>();
for(GROUPING group:GROUPING.values())
grouping2Distribution2Double.put(group, getDistributionPosition(sequence, attribute, group));
return grouping2Distribution2Double;
Expand All @@ -170,7 +170,7 @@ public Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinS
@Override
public Map<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception {
Map<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>> attribute2Grouping2Distribution2Double =
new HashMap<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>>();
new HashMap<>();
for(ATTRIBUTE attribute:ATTRIBUTE.values())
attribute2Grouping2Distribution2Double.put(attribute, getDistributionPosition(sequence, attribute));
return attribute2Grouping2Distribution2Double;
Expand Down
2 changes: 1 addition & 1 deletion ...va-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
View file
Expand Up @@ -83,7 +83,7 @@ private void generatesAminoAcidCompoundSet(){
* Stores the mass of elements and isotopes
*/
public void computeMolecularWeight(ElementTable eTable){
this.aaSymbol2MolecularWeight = new HashMap<Character, Double>();
this.aaSymbol2MolecularWeight = new HashMap<>();
for(AminoAcidComposition a:aminoacid){
//Check to ensure that the symbol is of single character
if(a.getSymbol().length() != 1){
Expand Down
16 changes: 8 additions & 8 deletions ...aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
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Expand Up @@ -39,9 +39,9 @@
*/
public class CaseFreeAminoAcidCompoundSet implements CompoundSet<AminoAcidCompound> {

private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();
private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<>();
private final Map<AminoAcidCompound, Set<AminoAcidCompound>> equivalentsCache =
new HashMap<AminoAcidCompound, Set<AminoAcidCompound>>();
new HashMap<>();

public CaseFreeAminoAcidCompoundSet() {
aminoAcidCompoundCache.put("A", new AminoAcidCompound(null, "A", "Ala", "Alanine", 71.0788f));
Expand Down Expand Up @@ -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<String, AminoAcidCompound> lowerCaseSet = new HashMap<String, AminoAcidCompound>();
Map<String, AminoAcidCompound> lowerCaseSet = new HashMap<>();
for(String s:this.aminoAcidCompoundCache.keySet()){
lowerCaseSet.put(s.toLowerCase(), this.aminoAcidCompoundCache.get(s));
}
Expand Down Expand Up @@ -144,7 +144,7 @@ public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
addAmbiguousEquivalents("I", "L", "J");
// ambiguous gaps
AminoAcidCompound gap1, gap2, gap3;
Set<AminoAcidCompound> gaps = new HashSet<AminoAcidCompound>();
Set<AminoAcidCompound> gaps = new HashSet<>();
gaps.add(gap1 = aminoAcidCompoundCache.get("-"));
gaps.add(gap2 = aminoAcidCompoundCache.get("."));
gaps.add(gap3 = aminoAcidCompoundCache.get("_"));
Expand All @@ -162,18 +162,18 @@ private void addAmbiguousEquivalents(String one, String two, String either) {
Set<AminoAcidCompound> equivalents;
AminoAcidCompound cOne, cTwo, cEither;

equivalents = new HashSet<AminoAcidCompound>();
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<AminoAcidCompound>();
equivalents = new HashSet<>();
equivalents.add(cOne);
equivalents.add(cEither);
equivalentsCache.put(cOne, equivalents);

equivalents = new HashSet<AminoAcidCompound>();
equivalents = new HashSet<>();
equivalents.add(cTwo);
equivalents.add(cEither);
equivalentsCache.put(cTwo, equivalents);
Expand All @@ -186,7 +186,7 @@ public boolean hasCompound(AminoAcidCompound compound) {

@Override
public List<AminoAcidCompound> getAllCompounds() {
return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
return new ArrayList<>(aminoAcidCompoundCache.values());
}


Expand Down
2 changes: 1 addition & 1 deletion biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
View file
Expand Up @@ -120,7 +120,7 @@ public List<Isotope> getIsotopes() {

public void setIsotopes(List<Isotope> isotopes) {
this.isotope = isotopes;
this.name2Isotope = new HashMap<String, Isotope>();
this.name2Isotope = new HashMap<>();
if(isotopes != null){
for(Isotope i:isotopes){
name2Isotope.put(i.getName(), i);
Expand Down
4 changes: 2 additions & 2 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
View file
Expand Up @@ -58,8 +58,8 @@ public void setElement(List<Element> eList){
* Populate the Maps for quick retrieval
*/
public void populateMaps(){
this.elementName2Element = new HashMap<String, Element>();
this.isotopeName2Isotope = new HashMap<String, Isotope>();
this.elementName2Element = new HashMap<>();
this.isotopeName2Isotope = new HashMap<>();
if(this.element != null){
for(Element e:this.element){
this.elementName2Element.put(e.getName(), e);
Expand Down
4 changes: 2 additions & 2 deletions ...aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
View file
Expand Up @@ -28,7 +28,7 @@

public class ModifiedAminoAcidCompoundSet implements CompoundSet<AminoAcidCompound> {

private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();
private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<>();

public ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character, Double> aaSymbol2MolecularWeight) {
this.aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "", "", 0.0f));
Expand Down Expand Up @@ -84,7 +84,7 @@ public boolean hasCompound(AminoAcidCompound compound) {

@Override
public List<AminoAcidCompound> getAllCompounds() {
return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
return new ArrayList<>(aminoAcidCompoundCache.values());
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion biojava-alignment/src/main/java/demo/CookbookMSA.java
View file
Expand Up @@ -43,7 +43,7 @@ public static void main(String[] args) throws Exception {
}

private static void multipleSequenceAlignment(String[] ids) throws Exception {
List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
List<ProteinSequence> lst = new ArrayList<>();
for (String id : ids) {
lst.add(getSequenceForId(id));
}
Expand Down
4 changes: 2 additions & 2 deletions biojava-alignment/src/main/java/demo/DemoDistanceTree.java
View file
Expand Up @@ -58,7 +58,7 @@ public static void main(String[] args) throws Exception {
.getResourceAsStream("/PF00104_small.fasta");

FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
new FastaReader<ProteinSequence, AminoAcidCompound>(
new FastaReader<>(
inStream,
new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet
Expand All @@ -70,7 +70,7 @@ public static void main(String[] args) throws Exception {
inStream.close();

MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa =
new MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
new MultipleSequenceAlignment<>();

for (ProteinSequence proteinSequence : proteinSequences.values()) {
msa.addAlignedSequence(proteinSequence);
Expand Down

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