Releases | Open Source Science

Fixed

mmCIF parsing: entity type should be case insensitive #1109
Upgraded to latest version of ciftools-java, fixes mmCIF parsing performance issues in some edge cases https://github.com/rcsb/ciftools-java/issues/13
Added safeguards for Structure.get*Chain*() methods #1111

- Java
Published by josemduarte about 1 year ago

Fixed

More lenient mmCIF parsing to be able to parse PDB-IHM entries, some more edge cases #1108

- Java
Published by josemduarte over 1 year ago

Fixed

More lenient mmCIF parsing to be able to parse PDB-IHM entries #1106
Now AsaCalculator main constructor will use first model only instead of all #1107

Added

New constructor for AsaCalculator to provide Structure and model #1107

- Java
Published by josemduarte over 1 year ago

Fixed

More lenient mmCIF parsing, now can read files produced by Gemmi #1103
Javadocs: all javadoc lint errors fixed
Plugin updates and fixed issues in maven release process

- Java
Published by josemduarte over 1 year ago

Fixed

Bug in symmetry detection #1101 and rcsb/symmetry#118

- Java
Published by josemduarte almost 2 years ago

Fixed

Brought back a command line argument for protein comparison tool #1096
Upgraded the log facade framework to slf4j2 #1094
Code smell fixes (Sonar issues S2293, S1319) #1095 #1091
Various small fixes ### Removed
Removed capability of automatic download/caching of PDB archive files in MMTF format, following deprecation by RCSB PDB. Code to encode/decode in MMTF format is still in place #1099

- Java
Published by josemduarte almost 2 years ago

Fixed

Now mmCIF files that have no author fields in atom_site can be read (e.g. from PyMol or ESMAtlas) #775 #1083
No evaluations of arguments in debug level log statements #1086 #789

Removed

Minor removal from biojava-core: FileDownloadUtils::copy, replaced by Files::copy

- Java
Published by josemduarte over 2 years ago

Added

Class FastaStreamer to read FASTA-formatted files using Java streams

Fixed

Various minor fixes for code smells
Some dependency upgrades
Now using Jakarta as the JAXB implementation #1076
Fixed SCOP URL #1077

- Java
Published by josemduarte over 2 years ago

Added

Some more categories related to entity are now written in mmCIF writer #1063

Fixed

Not declaring anymore unchecked exceptions in signatures #1062

- Java
Published by josemduarte about 3 years ago

Fixed

The jar packages now contain pom.properties files #1057
Some minor improvements in a few biojava-structure methods #1058

- Java
Published by josemduarte about 3 years ago

Breaking

BioJava is now compiled at JDK 11 compatibility level. It will not work anymore under older JREs (e.g. JRE 8). This is the main reason for the major version bump.

Added

Better handling of downloads: file download validation #1024

Fixed

Upgrade to latest ciftools-java, fixes non-US locale issue #1049
Issue with some edge cases in CIF parsing #1054
Minor security issue #1046

- Java
Published by josemduarte over 3 years ago

Added

GenBankWriterHelper - method that uses the original locus line rather than creating a new one, preventing loss of information
GenBankReader - the ability to successfully parse GenBank files with a LOCUS ID containing white space
GenBankReader - the ability to successfully parse GenBank files missing a LOCUS ID
Aromaticity calculation in biojava-aa-prop module

Fixed

GenBankWriter - String Formatter error when key or value of Qualifier has character "%", #886
GenBankWriter - outputting db_xref feature qualifiers
GenBankWriter - outputting the accession version and GI ID
GenBankWriter - outputting feature locations containing joins and partial locations
GenBankReader - reading locations split over multiple lines
GenBankReader - set if feature qualifier values require quotes
Local alignment with linear gap penalty was producing an NPE, #1036
New default server for PDB files. Note that from Aug 2023 older versions of BioJava will not be able to fetch PDB files unless PDB.FILE.SERVER system property is used to override the default server
Dependency upgrades
Some bug and security fixes

- Java
Published by josemduarte over 3 years ago

Fixed

Null handling in a few places related to loading PDB, CIF, mmtf files (issue introduced in 6.0.0). #1019

- Java
Published by josemduarte over 4 years ago

Fixed

Log4j dependency upgraded to 2.17.1 to avoid new vulnerabilities
Some new tests
Fixes in tests and docs
Bugfix in LocalProteinDomainParser #1009

- Java
Published by josemduarte over 4 years ago

Fixed

Log4j dependency upgraded to 2.16.0, to avoid log4hshell vulnerability

- Java
Published by josemduarte over 4 years ago

Fixed

Log4j dependency upgraded to 2.15.0, to avoid log4hshell vulnerability
PDB and mmCIF resolution parsing fixes. #1000

- Java
Published by josemduarte over 4 years ago

Fixed

Now actually runnable in a java-8 JRE. Previous release 6.0.0 had a java-11 dependency that made it incompatible. #996
Switch JAXB to glassfish implementation for better java 15+ support. Now biojava should run under a java-15 JRE. #996

- Java
Published by josemduarte over 4 years ago

Removed

All code related to All-vs-All structural alignments db calculation and access
JFatCatClient and all code depending on it
PDP domain providers (depended on JFatCatClient)
Support for retrieving structure data with prefix "PDP:" (AtomCache, StructureIO)
RemoteScopInstallation consuming data provided by source.rcsb.org
The whole org.biojava.nbio.structure.rcsb package, a client for the legacy RCSB PDB APIs (disappearing in Nov 2020)
The whole org.biojava.nbio.structure.validation package
The org.biojava.nbio.structure.domain.PDBDomainProvider class to pull domain definitions from legacy RCSB PDB APIs
Support for automatically fetching dssp files from RCSB (org.biojava.nbio.structure.secstruc.DSSPParser.fetch())
org.biojava.nbio.structure.PDBStatus: simplified Status enum to 3 states, with OBSOLETE now called REMOVED
org.biojava.nbio.structure.PDBStatus: removed getReplacement and getReplaces
Removed org.biojava.nbio.structure.io.mmcif package
Removed functionality to write isolated CIF headers from FileConvert
Removed org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()
Removed from org.biojava.nbio.structure.Chain interface: getParent(), setParent(), getAtomLigands(), getSwissprotId(), setSwissprotId(), getInternalChainID(), setInternalChainID(), getChainID(), setChainID()
Removed from org.biojava.nbio.structure.Structure interface: findChain(), getId(), setId(), getChainByPDB(), getCompoundById(), getResidueRanges(), getRanges()
Removed from org.biojava.nbio.structure.StructureTools : isNucleicAcid(), isProtein(), getPredominantGroupType(), isChainWaterOnly(), isChainPureNonPolymer(), getReducedStructure()
Removed org.biojava.nbio.structure.io.SandboxStyleStructureProvider
In org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser made all methods private except parseXMLfile

Breaking API changes

Extracted StructureIO.StructureFiletype enum to org.biojava.nbio.structure.io.StructureFiletype (supports PDB, MMTF, CIF, and BCIF)
org.biojava.nbio.structure.align.util.AtomCache: removed setUseMmCif, setUseMmtf, isUseMmCif, and isUseMmtf - replaced by setFiletype and getFiletype that controls parsed content via the StructureFiletype
org.biojava.nbio.structure.io.MMCIFFileReader is now effectively org.biojava.nbio.structure.io.CifFileReader
Moved org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord to org.biojava.nbio.structure.DatabasePDBRevRecord.java
Moved all chem-comp model classes from org.biojava.nbio.structure.io.mmcif.chem to org.biojava.nbio.structure.chem
Moved all chem-comp parsing classes from org.biojava.nbio.structure.io.mmcif.chem to org.biojava.nbio.structure.io.cif
Moved classes in org.biojava.nbio.structure.io.mmcif to org.biojava.nbio.structure.chem
Fixed CRC64Checksum#public void update(byte[] b, int offset, int length) to use the length argument correctly as specified in java.util.zip.Checksum interface.
In SubstructureIdentifier, StructureName, EcodDomain, ScopDomain : getPdbId() returns PdbId object instead of String.
Removed DownloadChemCompProvider.useDefaultUrlLayout with a more flexible system to provide templated URLs DownloadChemCompProvider.setChemCompPathUrlTemplate() and DownloadChemCompProvider.setServerBaseUrl()
In Structure (and StructureImple), the accessor methods String getPdbId() and setPdbId(String) were previously depricated. They were revived in BioJava 6.0.0 but as PdbId getPdbId() and setPdbId(PdbId) instead.n

Added

New keywords field in PDBHeader class, populated by PDB and mmCIF parsers #946
OBO parsing now supports multiple altids, #960
New class PdbId that wrapps a PDB Identifier and handles conversion between current short PDBID format and upcoming extended PDBID format #930

Fixed

Correct chain assignment to entities when parsing PDB/mmCIF without entity information (in cases with more than 3 chains per entity) #931
Dealing with chain ids correctly when parsing bonds in PDB-format files #943 #929

- Java
Published by josemduarte over 4 years ago

New features

Minimal read support for mmCIF files with branched entities (upcoming PDB release July 2020). The new entity type is understood now but branched entities are still treated as non-polymers within BioJava. #868
InterfaceFinder class to find interfaces of a given PDB assembly #867
New switch in Subunit clusterer useEntityIdForSeqIdentityDetermination #857 #859

Changed

Now genbank parser will allow 5'<3' for circular DNA #855

Bug fixes

Issue in bonds between atoms of different alt locs (https://github.com/rcsb/mmtf/issues/44) #854
Upgrade ciftools-java dependency to latest java-8 compatible release 0.7.1

- Java
Published by josemduarte almost 6 years ago

New features

Support for reading structures from binary cif format in structure module, thanks to CIFTools-java library. Thanks @JonStargaryen
Reading structures from mmCIF via new parser from CIFTools-java library. Much better read performance than existing parser. Both parsers still live alongside in BioJava 5.3.0, with default still being the BioJava native one.

Bug fixes

8x performance increase in reading (non-gzipped) MMTF files thanks to mmtf-java dependency upgrade to 1.0.9
Bug fixes in MMTF file reading, #671 #850
Bug fix in OBO reading, where only one synonym was saved, #836
Bug fix in Genbank LOCUS line parsing #833
Bug fix in PDB file reading of MTRIX records #845
Bug fix in GenbankReader #800 #829
Dependencies and maven plugin upgrades

- Java
Published by josemduarte almost 7 years ago

Bug fixes

2 bugfixes in ASA calculation introduced in 5.2.0: calculation would fail when an atom had no neighbors or when supplying a 0-length atom array, #824
Fixes in bioassembly creation, where EntityInfo objects weren't correctly cloned and wired #825
More efficient interface ASA calculation in NCS cases #823
Add EntityInfo to reduced structure #822

- Java
Published by josemduarte over 7 years ago

New Feature

improved algorithm for ASA computation. It is much faster on large molecules. #820

Bug fixes

Fix broken tests #809 & ed7fb66
Add tests for new GenBank formats (confirmed that the parser worked) #811
Fix exceptions displaying CE-Symm results #816 #817
Merge in bug fixes from the 4.2.x series (4.2.6 through 4.2.12)

- Java
Published by sbliven over 7 years ago

org.biojava - BioJava 5.1.1

This release contains 22 commits from 3 contributors.

Note this is the first version of BioJava that will run under 9, 10 or 11 JREs. It is still fully compatible with Java 8.

Bug fixes

#801 - Chain identifiers for generated bioassemblies now more explicit
#804 - Adapted BioJava to run under 9, 10 and 111 JREs

Manual Download

- Java
Published by josemduarte over 7 years ago

org.biojava - BioJava 5.1.0

This release contains 55 commits from 7 contributors.

New feature

ABI tracer ported from legacy biojava, #769, thanks @MaxGreil

Bug fixes

Performance improvement for secondary structure calculation, #789
#731
Improved alt locs docs and some fixes, #778
Jmol dep updated to 14.29.17
#712
#791
#797
#784

Manual Download

- Java
Published by josemduarte almost 8 years ago

org.biojava - BioJava 4.2.12

This is a bugfix release in the 4.2 branch. This branch is being maintained for use with Java 7. Applications using more recent versions of Java are encouraged to migrate to BioJava 5.

Changes:

Fix #703: Recover from empty structure files in PDBCACHEDIR
Reflect changes in external resources (#780, 0c10a2e)
CE-Symm bug fixes (#92)

This release is associated with CE-Symm 2.0.0.

- Java
Published by sbliven almost 8 years ago

org.biojava - BioJava 5.0.2

This release contains 5 commits from 2 contributors.

Requires Java 8 or newer.

Bug fixes

Fixed issue #770
Upgraded to latest mmtf-java 1.0.8

Manual Download

- Java
Published by josemduarte about 8 years ago

org.biojava - BioJava 5.0.1

This release contains 13 commits from 2 contributors.

Requires Java 8 or newer.

Bug fixes

Fixed issue #767
Fixed issue #761
Pom fixes for mvn site
Some logging fixes

Manual Download

- Java
Published by josemduarte about 8 years ago

org.biojava - 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.fastq is now org.biojava.nbio.genome.io.fastq
org.biojava.nbio.structure.Compound -> org.biojava.nbio.structure.EntityInfo
org.biojava.nbio.structure.io.util.FileDownloadUtils -> org.biojava.nbio.core.util.FileDownloadUtils
org.biojava.nbio.structure.symmetry.core.AxisAligner -> org.biojava.nbio.structure.symmetry.axis.AxisAligner
org.biojava.nbio.structure.symmetry.core.Subunits -> refactored into several classes in org.biojava.nbio.structure.cluster: Subunit, SubunitCluster, SubunitClusterer
org.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

- Java
Published by josemduarte about 8 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.11</version> </dependency>  </dependencies>

Manual Download

- Java
Published by josemduarte over 8 years ago

org.biojava - 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

Fixed issue #659
Fixed issue #715

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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.10</version> </dependency>  </dependencies>

Manual Download

- Java
Published by josemduarte over 8 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.9</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.9 has been released on October 19th, 2017

- Java
Published by josemduarte over 8 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.8</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.8 has been released on July 6th, 2017

- Java
Published by josemduarte almost 9 years ago

org.biojava - 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

Fix for hmmer web service in biojava-ws #640
Fix in chromosome mapping tool #636

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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.7</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.7 has been released on March 7th, 2017

- Java
Published by josemduarte over 9 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.6</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.6 has been released on February 17th, 2017

- Java
Published by josemduarte over 9 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.5</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.5 has been released on December 7th, 2016

- Java
Published by josemduarte over 9 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.4</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.4 has been released on July 29th, 2016

- Java
Published by josemduarte almost 10 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.3</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.3 has been released on June 28th, 2016

- Java
Published by josemduarte almost 10 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.2</version> </dependency>  </dependencies>

Manual Download

Release Date

BioJava 4.2.2 has been released on June 14th, 2016

- Java
Published by andreasprlic about 10 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.1</version> </dependency>  </dependencies>

Manual Download

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

- Java
Published by josemduarte about 10 years ago

org.biojava - 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:

xml <dependencies> <dependency> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId> <version>4.2.0</version> </dependency>  </dependencies>

Manual Download

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

- Java
Published by sbliven about 10 years ago

Recent Releases of org.biojava

org.biojava - BioJava 7.2.2

Fixed

org.biojava - BioJava 7.2.1

Fixed

org.biojava - BioJava 7.2.0

Fixed

Added

org.biojava - BioJava 7.1.4

Fixed

org.biojava - BioJava 7.1.3

Fixed

org.biojava - BioJava 7.1.2

Fixed

org.biojava - BioJava 7.1.1

Fixed

Removed

org.biojava - BioJava 7.1.0

Added

Fixed

org.biojava - BioJava 7.0.2

Added

Fixed

org.biojava - BioJava 7.0.1

Fixed

org.biojava - BioJava 7.0.0

Breaking

Added

Fixed

org.biojava - BioJava 6.1.0

Added

Fixed

org.biojava - BioJava 6.0.5

Fixed

org.biojava - BioJava 6.0.4

Fixed

org.biojava - BioJava 6.0.3

Fixed

org.biojava - BioJava 6.0.2

Fixed

org.biojava - BioJava 6.0.1

Fixed

org.biojava - BioJava 6.0.0

Removed

Breaking API changes

Added

Fixed

org.biojava - BioJava 5.4.0

New features

Changed

Bug fixes

org.biojava - BioJava 5.3.0

New features

Bug fixes

org.biojava - BioJava 5.2.1

Bug fixes

org.biojava - BioJava 5.2.0

New Feature

Bug fixes

org.biojava - BioJava 5.1.1

Bug fixes

Manual Download

org.biojava - BioJava 5.1.0

New feature

Bug fixes

Manual Download

org.biojava - BioJava 4.2.12

org.biojava - BioJava 5.0.2

Bug fixes

Manual Download

org.biojava - BioJava 5.0.1

Bug fixes

Manual Download

org.biojava - BioJava 5.0.0

New features

biojava-alignment

biojava-structure

Changed

Breaking API changes

General