BioJava:Download 4.0.0

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This page offers downloads for the BioJava 4.0.0 release.

BioJava 4.0.0 is compatible with Java 6, 7, and 8.

Contents

About

BioJava 4.0.0 has been released and is available using Maven from Maven Central as well as manual download (see below).

This release contains over 500 commits from 17 authors:

@andreasprlic @benjamintboyle @christiam @dmyersturnbull @Elinow @emckee2006 @jgrzebyta @josemduarte @kevinwu1 @pibizza @heuermh @paolopavan @parit @pwrose @sbliven @sroughley @willishf

New Features

BioJava 4.0.0 is a major release, with many new features as well as core API changes. In accordance with semantic versioning nomenclature, the jump to 4.x.x indicates that existing applications may need to be modified (e.g. due to the removal of deprecated methods). In most cases there should be a clearly documented replacement method. See below for details on how to upgrade.

New Features:

  • General
    • Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations. (many contributors, including @benjamintboyle and @josemduarte)
    • Improved handling of exceptions (@dmyersturnbull and @josemduarte)
    • Removed deprecated methods
    • Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and @sbliven)
    • Updated dependencies where applicable
    • Available on Maven Central (@andreasprlic and @heuermh)
  • biojava-core
    • Improved Genbank parser, including support for feature records, qualifiers, and nested locations. (@paolopavan and @jgrzebyta)
  • biojava-structure
    • Better support for crystallographic information, including crystallographic operators, unit cells, and protein-protein interfaces. (@josemduarte)
    • Better organization of downloaded structure files (set using the PDB_DIR and PDB_CACHE_DIR environmental variables) (@sbliven)
    • Better command-line tools for structure alignment (@sbliven)
    • New algorithm for symmetry detection in biological assemblies (@pwrose)
    • New algorithm for fast contact calculation, both intra-chain and inter-chain (@josemduarte)
    • Support for Accessible Surface Area (ASA) calculation through and implementation of the Shrake & Rupley algorithm, both single-thread and parallel (memory permitting) (@josemduarte)
    • Support for large structures (memory permitting) and multi-character chain IDs.
    • Default to mmCIF file format, as recommended by the wwPDB


Bug fixes:

  • biojava-alignment
    • Fixed a bug in AbstractMatrixAligner that was causing the scores to overflow. biojava-alignment now uses ints instead of shorts. (@josemduarte)
    • Fixed a bug in SimpleSubstitutionMatrix where "A" aligned against "a" gets scored correctly, but "A" against "A" and "a" against "a" do not. (@dmyersturnbull)
  • biojava-structure
    • Fixed a bug that was causing downloading PDB and mmCIF files through AtomCache to be slow and fail often. (@josemduarte)
    • Fixed a bug that was causing the chains IDs of residue numbers in mmCIF structures to be incorrect. (@sbliven)
    • Replaced the misleading AtomPositionMap.calcLength methods with new getLength methods. The new methods return the number of residues, inclusive. (@sbliven).
    • Improved ResidueRange and fixed several bugs. Length-related code is now in the subclass ResidueRangeAndLength. (@sbliven and @dmyersturnbull)


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

How to Upgrade

Since we renamed all package names to be consistent across the whole project, there will be import errors when upgrading to this version. These can automatically get resolved using Eclipse by selecting the Optimize Import menu item. Note: IntelliJ can NOT be used for the same operation.

The changed namespaces are:

  • Package namespace: all packages have been renamed to org.biojava.nbio.modulename.*. This is for all modules including structure and structure-gui
  • Module names and maven artifacts: all prefixed with biojava-, e.g. biojava-core, biojava-alignment

Maven Download

BioJava 4.0.0 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>4.0.0</version>
                </dependency>
                <!-- other biojava jars as needed -->
        </dependencies>	

Manual Download

.tar.gz containing all jars, source and javadocs: biojava-4.0.0-all

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.0.0.jar biojava-core-4.0.0-sources.jar biojava-core-4.0.0-javadoc.jar
biojava-alignment biojava-alignment-4.0.0.jar biojava-alignment-4.0.0-sources.jar biojava-alignment-4.0.0-javadoc.jar
biojava-genome biojava-genome-4.0.0.jar biojava-genome-4.0.0-sources.jar biojava-genome-4.0.0-javadoc.jar
biojava-structure biojava-structure-4.0.0.jar biojava-structure-4.0.0-sources.jar biojava-structure-4.0.0-javadoc.jar
biojava-structure-gui biojava-structure-gui-4.0.0.jar biojava-structure-gui-4.0.0-sources.jar biojava-structure-gui-4.0.0-javadoc.jar
biojava-phylo biojava-phylo-4.0.0.jar biojava-phylo-4.0.0-sources.jar biojava-phylo-4.0.0-javadoc.jar
biojava-modfinder biojava-modfinder-4.0.0.jar biojava-modfinder-4.0.0-sources.jar biojava-modfinder-4.0.0-javadoc.jar
biojava-ws biojava-ws-4.0.0.jar biojava-ws-4.0.0-sources.jar biojava-ws-4.0.0-javadoc.jar
biojava-aa-prop biojava-aa-prop-4.0.0.jar biojava-aa-prop-4.0.0-sources.jar biojava-aa-prop-4.0.0-javadoc.jar
biojava-ontology biojava-ontology-4.0.0.jar biojava-ontology-4.0.0-sources.jar biojava-ontology-4.0.0-javadoc.jar
biojava-survival biojava-survival-4.0.0.jar biojava-survival-4.0.0-sources.jar biojava-survival-4.0.0-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-4.0.0.jar biojava-protein-disorder-4.0.0-sources.jar biojava-protein-disorder-4.0.0-javadoc.jar

Browse API docs

You can also browse the documentation at BioJava 4.0.0 api

Release Date

BioJava 4.0.0 has been released on January 30th, 2015

Getting older versions

  • The release of 3.1.0 can be found here (requires Java 1.6 or 1.7)
  • The release of 3.0.8 can be found here (requires Java 1.6+)
  • The release of 3.0.7 can be found here (requires Java 1.6+)
  • The release of 3.0.6 can be found here (requires Java 1.6+)
  • The release of 3.0.5 can be found here (requires Java 1.6+)
  • The release of 3.0.4 can be found here (requires Java 1.6+)
  • The release of 3.0.3 can be found here (requires Java 1.6+)
  • The release of 3.0.2 can be found here (requires Java 1.6+)
  • The release of 3.0.1 can be found here (requires Java 1.6+)
  • The release of 3.0 can be found here (requires Java 1.5+)
  • The legacy release of 1.9.1 can be found here (requires Java 1.5+)
  • The legacy release of 1.9.0 can be found here (requires Java 1.5+)
  • The legacy release of 1.8.5 can be found here (requires Java 1.5+)
  • The legacy release of 1.8.4 can be found here (requires Java 1.5+)
  • The legacy release of 1.8.2 can be found here (requires Java 1.5+)
  • The legacy release of 1.8.1 can be found here (requires Java 1.5+)
  • The legacy release of 1.7.1 can be found here (requires Java 1.5+)
  • The legacy release of 1.7 can be found here (requires Java 1.5+)
  • The legacy release of 1.6 can be found here (requires Java 1.5+)
  • The legacy release of 1.5 can be found here (requires Java 1.4.2+)
  • The legacy release of 1.4 can be found here
  • The legacy release 1.3 can be found here.
  • Older releases of BioJava can be found in the download area.
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