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Releases: biojava/biojava

BioJava 4.2.3

28 Jun 18:44
@josemduarte josemduarte
biojava-4.2.3
c7f77f8
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BioJava 4.2.3

BioJava 4.2.3 is compatible with Java 7 and 8.

About

BioJava 4.2.3 has been released and is available using Maven from Maven Central as well as manual download (see below). This is purely a bug fix release correcting issues found since the 4.2.2 release.

This release contains over 13 commits from 2 contributors.

Bug fixes

  • mmCIF file writing: special fields (e.g. containing hyphens) are now correctly written
  • General improvements in mmCIF file read and write

Maven Download

BioJava 4.2.3 requires Maven for the build process. All BioJava jar files are available via Maven Central as of this release.

You can create a BioJava dependency by adding the following XML to your project pom.xml file:

            <dependencies>
                    <dependency>
                            <groupId>org.biojava</groupId>
                            <artifactId>biojava-core</artifactId>
                            <version>4.2.3</version>
                    </dependency>
                    <!-- other biojava jars as needed -->
            </dependencies>

Manual Download

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.2.3.jar biojava-core-4.2.3-sources.jar biojava-core-4.2.3-javadoc.jar
biojava-alignment biojava-alignment-4.2.3.jar biojava-alignment-4.2.3-sources.jar biojava-alignment-4.2.3-javadoc.jar
biojava-genome biojava-genome-4.2.3.jar biojava-genome-4.2.3-sources.jar biojava-genome-4.2.3-javadoc.jar
biojava-structure biojava-structure-4.2.3.jar biojava-structure-4.2.3-sources.jar biojava-structure-4.2.3-javadoc.jar
biojava-structure-gui biojava-structure-gui-4.2.3.jar biojava-structure-gui-4.2.3-sources.jar biojava-structure-gui-4.2.3-javadoc.jar
biojava-phylo biojava-phylo-4.2.3.jar biojava-phylo-4.2.3-sources.jar biojava-phylo-4.2.3-javadoc.jar
biojava-modfinder biojava-modfinder-4.2.3.jar biojava-modfinder-4.2.3-sources.jar biojava-modfinder-4.2.3-javadoc.jar
biojava-ws biojava-ws-4.2.3.jar biojava-ws-4.2.3-sources.jar biojava-ws-4.2.3-javadoc.jar
biojava-aa-prop biojava-aa-prop-4.2.3.jar biojava-aa-prop-4.2.3-sources.jar biojava-aa-prop-4.2.3-javadoc.jar
biojava-ontology biojava-ontology-4.2.3.jar biojava-ontology-4.2.3-sources.jar biojava-ontology-4.2.3-javadoc.jar
biojava-survival biojava-survival-4.2.3.jar biojava-survival-4.2.3-sources.jar biojava-survival-4.2.3-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-4.2.3.jar biojava-protein-disorder-4.2.3-sources.jar biojava-protein-disorder-4.2.3-javadoc.jar
biojava-sequencing biojava-sequencing-4.2.3.jar biojava-sequencing-4.2.3-sources.jar biojava-sequencing-4.2.3-javadoc.jar

Release Date

BioJava 4.2.3 has been released on June 28th, 2016

Assets 2

BioJava 4.2.2

15 Jun 18:59
@andreasprlic andreasprlic
biojava-4.2.2
a74758c
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BioJava 4.2.2

BioJava 4.2.2 is compatible with Java 7 and 8.

About

BioJava 4.2.2 has been released and is available using Maven from Maven Central as well as manual download (see below). This is purely a bug fix release correcting issues found since the 4.2.0 release.

This release contains over 31 commits from 5 contributors.

Bug fixes

This is a bug-fix release

  • CE-Symm features and bug fixes
    • Better data structures for symmetry axes (particularly for hierarchical symmetry)
    • Fix bug with symmetry axis positioning
    • Optimization includes all symmetry repeats for hierarchical symmetry
  • Update of protein modifications to latest version,
    • including new glycans and chromophores
    • Updating naming definitions to latest conventions

Maven Download

BioJava 4.2.2 requires Maven for the build process. All BioJava jar files are available via Maven Central as of this release.

You can create a BioJava dependency by adding the following XML to your project pom.xml file:

            <dependencies>
                    <dependency>
                            <groupId>org.biojava</groupId>
                            <artifactId>biojava-core</artifactId>
                            <version>4.2.2</version>
                    </dependency>
                    <!-- other biojava jars as needed -->
            </dependencies>

Manual Download

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.2.2.jar biojava-core-4.2.2-sources.jar biojava-core-4.2.2-javadoc.jar
biojava-alignment biojava-alignment-4.2.2.jar biojava-alignment-4.2.2-sources.jar biojava-alignment-4.2.2-javadoc.jar
biojava-genome biojava-genome-4.2.2.jar biojava-genome-4.2.2-sources.jar biojava-genome-4.2.2-javadoc.jar
biojava-structure biojava-structure-4.2.2.jar biojava-structure-4.2.2-sources.jar biojava-structure-4.2.2-javadoc.jar
biojava-structure-gui biojava-structure-gui-4.2.2.jar biojava-structure-gui-4.2.2-sources.jar biojava-structure-gui-4.2.2-javadoc.jar
biojava-phylo biojava-phylo-4.2.2.jar biojava-phylo-4.2.2-sources.jar biojava-phylo-4.2.2-javadoc.jar
biojava-modfinder biojava-modfinder-4.2.2.jar biojava-modfinder-4.2.2-sources.jar biojava-modfinder-4.2.2-javadoc.jar
biojava-ws biojava-ws-4.2.2.jar biojava-ws-4.2.2-sources.jar biojava-ws-4.2.2-javadoc.jar
biojava-aa-prop biojava-aa-prop-4.2.2.jar biojava-aa-prop-4.2.2-sources.jar biojava-aa-prop-4.2.2-javadoc.jar
biojava-ontology biojava-ontology-4.2.2.jar biojava-ontology-4.2.2-sources.jar biojava-ontology-4.2.2-javadoc.jar
biojava-survival biojava-survival-4.2.2.jar biojava-survival-4.2.2-sources.jar biojava-survival-4.2.2-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-4.2.2.jar biojava-protein-disorder-4.2.2-sources.jar biojava-protein-disorder-4.2.2-javadoc.jar
biojava-sequencing biojava-sequencing-4.2.2.jar biojava-sequencing-4.2.2-sources.jar biojava-sequencing-4.2.2-javadoc.jar

Release Date

BioJava 4.2.2 has been released on June 14th, 2016

Assets 2

BioJava 4.2.1

03 May 23:13
@josemduarte josemduarte
biojava-4.2.1
8504664
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BioJava 4.2.1

BioJava 4.2.1 is compatible with Java 7 and 8.

About

BioJava 4.2.1 has been released and is available using Maven from Maven Central as well as manual download (see below). This is purely a bug fix release correcting issues found since the 4.2.0 release.

This release contains over 31 commits from 7 contributors.

Bug fixes

Biojava-structure

  • Nucleotide bonds are now generated
  • BIO: identifiers are now correctly handled
  • Several fixes for CE-Symm
  • Substructures now contain seqres groups (isse #449)
  • Structures containing insertion codes are now written correctly to mmCIF
  • AtomCache now uses the correct default parsing parameters (issue #455)
  • Fixed problem with some atom charges that weren't being added
  • CATH updated to 4.0.0
  • Better ECOD javadocs (issue #452)

Biojava-structure-gui

  • Removed javaws dependency (issue #459)

Maven Download

BioJava 4.2.1 requires Maven for the build process. All BioJava jar files are available via Maven Central as of this release.

You can create a BioJava dependency by adding the following XML to your project pom.xml file:

            <dependencies>
                    <dependency>
                            <groupId>org.biojava</groupId>
                            <artifactId>biojava-core</artifactId>
                            <version>4.2.1</version>
                    </dependency>
                    <!-- other biojava jars as needed -->
            </dependencies>

Manual Download

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.2.1.jar biojava-core-4.2.1-sources.jar biojava-core-4.2.1-javadoc.jar
biojava-alignment biojava-alignment-4.2.1.jar biojava-alignment-4.2.1-sources.jar biojava-alignment-4.2.1-javadoc.jar
biojava-genome biojava-genome-4.2.1.jar biojava-genome-4.2.1-sources.jar biojava-genome-4.2.1-javadoc.jar
biojava-structure biojava-structure-4.2.1.jar biojava-structure-4.2.1-sources.jar biojava-structure-4.2.1-javadoc.jar
biojava-structure-gui biojava-structure-gui-4.2.1.jar biojava-structure-gui-4.2.1-sources.jar biojava-structure-gui-4.2.1-javadoc.jar
biojava-phylo biojava-phylo-4.2.1.jar biojava-phylo-4.2.1-sources.jar biojava-phylo-4.2.1-javadoc.jar
biojava-modfinder biojava-modfinder-4.2.1.jar biojava-modfinder-4.2.1-sources.jar biojava-modfinder-4.2.1-javadoc.jar
biojava-ws biojava-ws-4.2.1.jar biojava-ws-4.2.1-sources.jar biojava-ws-4.2.1-javadoc.jar
biojava-aa-prop biojava-aa-prop-4.2.1.jar biojava-aa-prop-4.2.1-sources.jar biojava-aa-prop-4.2.1-javadoc.jar
biojava-ontology biojava-ontology-4.2.1.jar biojava-ontology-4.2.1-sources.jar biojava-ontology-4.2.1-javadoc.jar
biojava-survival biojava-survival-4.2.1.jar biojava-survival-4.2.1-sources.jar biojava-survival-4.2.1-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-4.2.1.jar biojava-protein-disorder-4.2.1-sources.jar biojava-protein-disorder-4.2.1-javadoc.jar
biojava-sequencing biojava-sequencing-4.2.1.jar biojava-sequencing-4.2.1-sources.jar biojava-sequencing-4.2.1-javadoc.jar

Browse API docs

You can also browse the documentation at BioJava 4.2.1 api

Release Date

BioJava 4.2.1 has been released on May 3rd, 2016

Assets 2

BioJava 4.2.0

19 Apr 09:16
@sbliven sbliven
biojava-4.2.0
e248837
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BioJava 4.2.0

BioJava 4.2.0 is compatible with Java 7 and 8.

About

BioJava 4.2.0 has been released and is available using Maven from Maven Central as well as manual download (see below).

This release contains over 750 commits from 16 contributors.

New Features

BioJava 4.2.0 offers many new features, as well several bug-fixes.

General

  • Requires Java 7
  • Better logging with SLF4J

Biojava-Core

  • New SearchIO framework including blast xml parser

Biojava-structure

  • Secondary structure assignment (DSSP compatible)
  • Multiple Structure Alignments
  • New MultipleStructureAlignment datastructure supporting flexible and order-independent alignments
  • MultipleMC algorithm
    - Can use any pairwise StructureAlignment implementation
  • serialize and parse multiple structure alignments as XML files, output as Text, FatCat, FASTA, Rotation Matrices, etc.
  • More complete mmCIF and cif parsing
  • Parse bonds, sites, charges
  • Better support for non-deposited pdb and mmcif files
  • Include CE-Symm algorithm for finding internal symmetry (Myers-Turnbull, 2014)
  • Replaced internal graph datastructures with Jgraph
  • Unified StructureIdentifier framework
  • Improved chemical component framework, now by default providing full chemical description by using DownloadChemCompProvider
  • Optimised memory usage of Residue/Atoms

Biojava-structure-gui

  • MultipleAlignmentGUI for visualizing Multiple Structure Alignments with Jmol
  • SymmetryDisplay for visualizing internal symmetry

Biojava-Phylo

  • Use Forester 1.038
  • Significant bug fixes
  • use SubstitutionMatrices in the core module (instead of imported Jalview matrices),
  • use Sequence and Compound classes from the alignment module
  • provide some Wrapper methods to communicate with forester,
  • decouple distance matrix calculation from tree constructor,
  • provide methods for common distance matrix calculations and framework for user-defined distances,
  • update the forester version to have the correct NJ tree constructor
    AND
  • correct some of the tree evaluator statistics.

View the BioJava:Modules page for a list of current modules.

Maven Download

BioJava 4.2.0 requires Maven for the build process. All BioJava jar files are available via Maven Central as of this release.

You can create a BioJava dependency by adding the following XML to your project pom.xml file:

            <dependencies>
                    <dependency>
                            <groupId>org.biojava</groupId>
                            <artifactId>biojava-core</artifactId>
                            <version>4.2.0</version>
                    </dependency>
                    <!-- other biojava jars as needed -->
            </dependencies>

Manual Download

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.2.0.jar biojava-core-4.2.0-sources.jar biojava-core-4.2.0-javadoc.jar
biojava-alignment biojava-alignment-4.2.0.jar biojava-alignment-4.2.0-sources.jar biojava-alignment-4.2.0-javadoc.jar
biojava-genome biojava-genome-4.2.0.jar biojava-genome-4.2.0-sources.jar biojava-genome-4.2.0-javadoc.jar
biojava-structure biojava-structure-4.2.0.jar biojava-structure-4.2.0-sources.jar biojava-structure-4.2.0-javadoc.jar
biojava-structure-gui biojava-structure-gui-4.2.0.jar biojava-structure-gui-4.2.0-sources.jar biojava-structure-gui-4.2.0-javadoc.jar
biojava-phylo biojava-phylo-4.2.0.jar biojava-phylo-4.2.0-sources.jar biojava-phylo-4.2.0-javadoc.jar
biojava-modfinder biojava-modfinder-4.2.0.jar biojava-modfinder-4.2.0-sources.jar biojava-modfinder-4.2.0-javadoc.jar
biojava-ws biojava-ws-4.2.0.jar biojava-ws-4.2.0-sources.jar biojava-ws-4.2.0-javadoc.jar
biojava-aa-prop biojava-aa-prop-4.2.0.jar biojava-aa-prop-4.2.0-sources.jar biojava-aa-prop-4.2.0-javadoc.jar
biojava-ontology biojava-ontology-4.2.0.jar biojava-ontology-4.2.0-sources.jar biojava-ontology-4.2.0-javadoc.jar
biojava-survival biojava-survival-4.2.0.jar biojava-survival-4.2.0-sources.jar biojava-survival-4.2.0-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-4.2.0.jar biojava-protein-disorder-4.2.0-sources.jar biojava-protein-disorder-4.2.0-javadoc.jar
biojava-sequencing biojava-sequencing-4.2.0.jar biojava-sequencing-4.2.0-sources.jar biojava-sequencing-4.2.0-javadoc.jar

Browse API docs

You can also browse the documentation at BioJava 4.2.0 api

Release Date

BioJava 4.2.0 has been released on March 10th, 2016

Assets 3