Releases: biojava/biojava
BioJava 5.0.1
This release contains 13 commits from 2 contributors.
Requires Java 8 or newer.
Bug fixes
Manual Download
BioJava 5.0.0
This release contains 1,170 commits from 19 contributors.
Requires Java 8 or newer.
New features
biojava-alignment
- New utlity methods for sequence alignment objects (gap, similarity and coverage).
biojava-structure
- The data structures to represent 3D macromolecules now follow the mmCIF data model.
- MMTF format support.
- Symmetry detection algorithms overhaul: better symmetry detection for tertiary and quaternary structure levels.
- New method and data structures for the clustering of protein subunits at the sequence and structure levels.
- New method to align biological assemblies, see
org.biojava.nbio.structure.align.quaternary.QsAlign. - New algorithms for base-pair geometry in nucleic acids.
- New SuperPosition interface for different 3D-structure superposition algorithms, see
org.biojava.nbio.structure.geometry.SuperPosition. - Geometry-related API now more consistently based on vecmath interfaces.
Changed
- For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included
- Symmetry expansion for bioassembly creation is now by default happening via adding new chains instead of new models.
- Make objects serializable for compatibility with big data frameworks (e.g. Spark).
Breaking API changes
- module biojava-phylo merged into biojava-alignment. The package namespace stays the same (
org.biojava.nbio.phylo). - module biojava-sequencing merged into biojava-genome. Package
org.biojava.nbio.sequencing.io.fastqis noworg.biojava.nbio.genome.io.fastq org.biojava.nbio.structure.Compound->org.biojava.nbio.structure.EntityInfoorg.biojava.nbio.structure.io.util.FileDownloadUtils->org.biojava.nbio.core.util.FileDownloadUtilsorg.biojava.nbio.structure.symmetry.core.AxisAligner->org.biojava.nbio.structure.symmetry.axis.AxisAlignerorg.biojava.nbio.structure.symmetry.core.Subunits-> refactored into several classes inorg.biojava.nbio.structure.cluster: Subunit, SubunitCluster, SubunitClustererorg.biojava.nbio.structure.align.helper.AlignTools->org.biojava.nbio.structure.align.helper.AlignUtils- All deprecations introduced in 4.0.0 or before were removed.
General
- Javadocs improvements across the board.
- All tests are now Junit4.
- Updated dependency versions (guava, slf4j, and log4j).
Bug fixes
A very long list.
Manual Download
BioJava 4.2.11
BioJava 4.2.11 is compatible with Java 7 and 8.
About
BioJava 4.2.11 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 4.2.9 release.
This release contains 3 commits from 1 contributor.
Bug fixes
- Updated hmmer scan web service URL to https.
Maven Download
BioJava 4.2.11 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>4.2.11</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
BioJava 4.2.10
BioJava 4.2.10 is compatible with Java 7 and 8.
About
BioJava 4.2.10 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 4.2.9 release.
This release contains 7 commits from 2 contributors.
Bug fixes
Maven Download
BioJava 4.2.10 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>4.2.10</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
BioJava 4.2.9
BioJava 4.2.9 is compatible with Java 7 and 8.
About
BioJava 4.2.9 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 4.2.8 release.
This release contains 15 commits from 2 contributors.
Bug fixes
- Some fixes to PDB file parsing CONECT/LINK records
- Updated URLs for external resources
Maven Download
BioJava 4.2.9 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>4.2.9</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
Release Date
BioJava 4.2.9 has been released on October 19th, 2017
BioJava 4.2.8
BioJava 4.2.8 is compatible with Java 7 and 8.
About
BioJava 4.2.8 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 4.2.7 release.
This release contains 15 commits from 3 contributors.
Bug fixes
- Small additions to AlignedSequence in core module to better support pipelines that use 4.2.x
- URLs adapted to latest RCSB PDB convention #682
Maven Download
BioJava 4.2.8 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>4.2.8</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
Release Date
BioJava 4.2.8 has been released on July 6th, 2017
BioJava 4.2.7
BioJava 4.2.7 is compatible with Java 7 and 8.
About
BioJava 4.2.7 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 4.2.6 release.
This release contains 8 commits from 4 contributors.
Bug fixes
Maven Download
BioJava 4.2.7 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>4.2.7</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
Release Date
BioJava 4.2.7 has been released on March 7th, 2017
BioJava 4.2.6
BioJava 4.2.6 is compatible with Java 7 and 8.
About
BioJava 4.2.6 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 4.2.5 release.
This release contains 12 commits from 4 contributors.
Bug fixes
- Fix for problem in chain cloning, #631
- Several bug fixes and better error check in quaternary symmetry detection code
Maven Download
BioJava 4.2.6 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>4.2.6</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
Release Date
BioJava 4.2.6 has been released on February 17th, 2017
BioJava 4.2.5
BioJava 4.2.5 is compatible with Java 7 and 8.
About
BioJava 4.2.5 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 4.2.4 release.
This release contains 30 commits from 7 contributors.
Bug fixes
- Fix for new phosphositeplus.org format, #610
- org.biojava.nbio.genome.parsers.gff.Location union() and intersect() now work correctly, #355
- Minor addition of crystallographic metadata fields to handle legacy PDB entries
- Jmol interchange format is now mmCIF, allowing for multiletter chain ids
- Update to latest jmol 14.6.2_2016.08.28
- A few minor bug fixes
Maven Download
BioJava 4.2.5 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>4.2.5</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
Release Date
BioJava 4.2.5 has been released on December 7th, 2016
BioJava 4.2.4
BioJava 4.2.4 is compatible with Java 7 and 8.
About
BioJava 4.2.4 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 4.2.3 release.
This release contains over 17 commits from 4 contributors.
Bug fixes
- NCBI links now using https (see NCBI's announcement )
- CATH links redirected to new server http://release.cathdb.info/
- SCOP default location now points to the Berkeley server after demise of Scop at MRC LMB
- Fixed important bug in mmCIF writing where structures with multiple models were written with identical coordinates
- Fixed bug in Group cloning where chemical components weren't cloned
- Added utility class for Chromosome mapping
Maven Download
BioJava 4.2.4 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>4.2.4</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies> Manual Download
Release Date
BioJava 4.2.4 has been released on July 29th, 2016