@josemduarte josemduarte released this Sep 28, 2018 · 9 commits to master since this release

Assets 2

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.1.1.jar biojava-core-5.1.1-sources.jar biojava-core-5.1.1-javadoc.jar
biojava-alignment biojava-alignment-5.1.1.jar biojava-alignment-5.1.1-sources.jar biojava-alignment-5.1.1-javadoc.jar
biojava-genome biojava-genome-5.1.1.jar biojava-genome-5.1.1-sources.jar biojava-genome-5.1.1-javadoc.jar
biojava-structure biojava-structure-5.1.1.jar biojava-structure-5.1.1-sources.jar biojava-structure-5.1.1-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.1.1.jar biojava-structure-gui-5.1.1-sources.jar biojava-structure-gui-5.1.1-javadoc.jar
biojava-phylo biojava-phylo-5.1.1.jar biojava-phylo-5.1.1-sources.jar biojava-phylo-5.1.1-javadoc.jar
biojava-modfinder biojava-modfinder-5.1.1.jar biojava-modfinder-5.1.1-sources.jar biojava-modfinder-5.1.1-javadoc.jar
biojava-ws biojava-ws-5.1.1.jar biojava-ws-5.1.1-sources.jar biojava-ws-5.1.1-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.1.1.jar biojava-aa-prop-5.1.1-sources.jar biojava-aa-prop-5.1.1-javadoc.jar
biojava-ontology biojava-ontology-5.1.1.jar biojava-ontology-5.1.1-sources.jar biojava-ontology-5.1.1-javadoc.jar
biojava-survival biojava-survival-5.1.1.jar biojava-survival-5.1.1-sources.jar biojava-survival-5.1.1-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.1.1.jar biojava-protein-disorder-5.1.1-sources.jar biojava-protein-disorder-5.1.1-javadoc.jar
biojava-sequencing biojava-sequencing-5.1.1.jar biojava-sequencing-5.1.1-sources.jar biojava-sequencing-5.1.1-javadoc.jar

@josemduarte josemduarte released this Aug 30, 2018 · 31 commits to master since this release

Assets 2

This release contains 55 commits from 7 contributors.

New feature

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.1.0.jar biojava-core-5.1.0-sources.jar biojava-core-5.1.0-javadoc.jar
biojava-alignment biojava-alignment-5.1.0.jar biojava-alignment-5.1.0-sources.jar biojava-alignment-5.1.0-javadoc.jar
biojava-genome biojava-genome-5.1.0.jar biojava-genome-5.1.0-sources.jar biojava-genome-5.1.0-javadoc.jar
biojava-structure biojava-structure-5.1.0.jar biojava-structure-5.1.0-sources.jar biojava-structure-5.1.0-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.1.0.jar biojava-structure-gui-5.1.0-sources.jar biojava-structure-gui-5.1.0-javadoc.jar
biojava-phylo biojava-phylo-5.1.0.jar biojava-phylo-5.1.0-sources.jar biojava-phylo-5.1.0-javadoc.jar
biojava-modfinder biojava-modfinder-5.1.0.jar biojava-modfinder-5.1.0-sources.jar biojava-modfinder-5.1.0-javadoc.jar
biojava-ws biojava-ws-5.1.0.jar biojava-ws-5.1.0-sources.jar biojava-ws-5.1.0-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.1.0.jar biojava-aa-prop-5.1.0-sources.jar biojava-aa-prop-5.1.0-javadoc.jar
biojava-ontology biojava-ontology-5.1.0.jar biojava-ontology-5.1.0-sources.jar biojava-ontology-5.1.0-javadoc.jar
biojava-survival biojava-survival-5.1.0.jar biojava-survival-5.1.0-sources.jar biojava-survival-5.1.0-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.1.0.jar biojava-protein-disorder-5.1.0-sources.jar biojava-protein-disorder-5.1.0-javadoc.jar
biojava-sequencing biojava-sequencing-5.1.0.jar biojava-sequencing-5.1.0-sources.jar biojava-sequencing-5.1.0-javadoc.jar

@sbliven sbliven released this Jul 2, 2018 · 1279 commits to master since this release

Assets 2

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 PDB_CACHE_DIR
  • Reflect changes in external resources (#780, 0c10a2e)
  • CE-Symm bug fixes (#92)

This release is associated with CE-Symm 2.0.0.

@josemduarte josemduarte released this May 22, 2018 · 86 commits to master since this release

Assets 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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.0.2.jar biojava-core-5.0.2-sources.jar biojava-core-5.0.2-javadoc.jar
biojava-alignment biojava-alignment-5.0.2.jar biojava-alignment-5.0.2-sources.jar biojava-alignment-5.0.2-javadoc.jar
biojava-genome biojava-genome-5.0.2.jar biojava-genome-5.0.2-sources.jar biojava-genome-5.0.2-javadoc.jar
biojava-structure biojava-structure-5.0.2.jar biojava-structure-5.0.2-sources.jar biojava-structure-5.0.2-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.0.2.jar biojava-structure-gui-5.0.2-sources.jar biojava-structure-gui-5.0.2-javadoc.jar
biojava-phylo biojava-phylo-5.0.2.jar biojava-phylo-5.0.2-sources.jar biojava-phylo-5.0.2-javadoc.jar
biojava-modfinder biojava-modfinder-5.0.2.jar biojava-modfinder-5.0.2-sources.jar biojava-modfinder-5.0.2-javadoc.jar
biojava-ws biojava-ws-5.0.2.jar biojava-ws-5.0.2-sources.jar biojava-ws-5.0.2-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.0.2.jar biojava-aa-prop-5.0.2-sources.jar biojava-aa-prop-5.0.2-javadoc.jar
biojava-ontology biojava-ontology-5.0.2.jar biojava-ontology-5.0.2-sources.jar biojava-ontology-5.0.2-javadoc.jar
biojava-survival biojava-survival-5.0.2.jar biojava-survival-5.0.2-sources.jar biojava-survival-5.0.2-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.0.2.jar biojava-protein-disorder-5.0.2-sources.jar biojava-protein-disorder-5.0.2-javadoc.jar
biojava-sequencing [biojava-sequencing-5.0.2.

@josemduarte josemduarte released this May 11, 2018 · 90 commits to master since this release

Assets 2

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.0.1.jar biojava-core-5.0.1-sources.jar biojava-core-5.0.1-javadoc.jar
biojava-alignment biojava-alignment-5.0.1.jar biojava-alignment-5.0.1-sources.jar biojava-alignment-5.0.1-javadoc.jar
biojava-genome biojava-genome-5.0.1.jar biojava-genome-5.0.1-sources.jar biojava-genome-5.0.1-javadoc.jar
biojava-structure biojava-structure-5.0.1.jar biojava-structure-5.0.1-sources.jar biojava-structure-5.0.1-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.0.1.jar biojava-structure-gui-5.0.1-sources.jar biojava-structure-gui-5.0.1-javadoc.jar
biojava-phylo biojava-phylo-5.0.1.jar biojava-phylo-5.0.1-sources.jar biojava-phylo-5.0.1-javadoc.jar
biojava-modfinder biojava-modfinder-5.0.1.jar biojava-modfinder-5.0.1-sources.jar biojava-modfinder-5.0.1-javadoc.jar
biojava-ws biojava-ws-5.0.1.jar biojava-ws-5.0.1-sources.jar biojava-ws-5.0.1-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.0.1.jar biojava-aa-prop-5.0.1-sources.jar biojava-aa-prop-5.0.1-javadoc.jar
biojava-ontology biojava-ontology-5.0.1.jar biojava-ontology-5.0.1-sources.jar biojava-ontology-5.0.1-javadoc.jar
biojava-survival biojava-survival-5.0.1.jar biojava-survival-5.0.1-sources.jar biojava-survival-5.0.1-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.0.1.jar biojava-protein-disorder-5.0.1-sources.jar biojava-protein-disorder-5.0.1-javadoc.jar
biojava-sequencing biojava-sequencing-5.0.1.jar biojava-sequencing-5.0.1-sources.jar biojava-sequencing-5.0.1-javadoc.jar

@josemduarte josemduarte released this Mar 24, 2018 · 103 commits to master since this release

Assets 2

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.0.0.jar biojava-core-5.0.0-sources.jar biojava-core-5.0.0-javadoc.jar
biojava-alignment biojava-alignment-5.0.0.jar biojava-alignment-5.0.0-sources.jar biojava-alignment-5.0.0-javadoc.jar
biojava-genome biojava-genome-5.0.0.jar biojava-genome-5.0.0-sources.jar biojava-genome-5.0.0-javadoc.jar
biojava-structure biojava-structure-5.0.0.jar biojava-structure-5.0.0-sources.jar biojava-structure-5.0.0-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.0.0.jar biojava-structure-gui-5.0.0-sources.jar biojava-structure-gui-5.0.0-javadoc.jar
biojava-phylo biojava-phylo-5.0.0.jar biojava-phylo-5.0.0-sources.jar biojava-phylo-5.0.0-javadoc.jar
biojava-modfinder biojava-modfinder-5.0.0.jar biojava-modfinder-5.0.0-sources.jar biojava-modfinder-5.0.0-javadoc.jar
biojava-ws biojava-ws-5.0.0.jar biojava-ws-5.0.0-sources.jar biojava-ws-5.0.0-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.0.0.jar biojava-aa-prop-5.0.0-sources.jar biojava-aa-prop-5.0.0-javadoc.jar
biojava-ontology biojava-ontology-5.0.0.jar biojava-ontology-5.0.0-sources.jar biojava-ontology-5.0.0-javadoc.jar
biojava-survival biojava-survival-5.0.0.jar biojava-survival-5.0.0-sources.jar biojava-survival-5.0.0-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.0.0.jar biojava-protein-disorder-5.0.0-sources.jar biojava-protein-disorder-5.0.0-javadoc.jar
biojava-sequencing biojava-sequencing-5.0.0.jar biojava-sequencing-5.0.0-sources.jar biojava-sequencing-5.0.0-javadoc.jar
Feb 13, 2018
[maven-release-plugin] copy for tag biojava-5.0.0-alpha15
Jan 31, 2018
[maven-release-plugin] copy for tag biojava-5.0.0-alpha14

@josemduarte josemduarte released this Jan 12, 2018 · 1279 commits to master since this release

Assets 2

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.2.11.jar biojava-core-4.2.11-sources.jar biojava-core-4.2.11-javadoc.jar
biojava-alignment biojava-alignment-4.2.11.jar biojava-alignment-4.2.11-sources.jar biojava-alignment-4.2.11-javadoc.jar
biojava-genome biojava-genome-4.2.11.jar biojava-genome-4.2.11-sources.jar biojava-genome-4.2.11-javadoc.jar
biojava-structure biojava-structure-4.2.11.jar biojava-structure-4.2.11-sources.jar biojava-structure-4.2.11-javadoc.jar
biojava-structure-gui biojava-structure-gui-4.2.11.jar biojava-structure-gui-4.2.11-sources.jar biojava-structure-gui-4.2.11-javadoc.jar
biojava-phylo biojava-phylo-4.2.11.jar biojava-phylo-4.2.11-sources.jar biojava-phylo-4.2.11-javadoc.jar
biojava-modfinder biojava-modfinder-4.2.11.jar biojava-modfinder-4.2.11-sources.jar biojava-modfinder-4.2.11-javadoc.jar
biojava-ws biojava-ws-4.2.11.jar biojava-ws-4.2.11-sources.jar biojava-ws-4.2.11-javadoc.jar
biojava-aa-prop biojava-aa-prop-4.2.11.jar biojava-aa-prop-4.2.11-sources.jar biojava-aa-prop-4.2.11-javadoc.jar
biojava-ontology biojava-ontology-4.2.11.jar biojava-ontology-4.2.11-sources.jar biojava-ontology-4.2.11-javadoc.jar
biojava-survival biojava-survival-4.2.11.jar biojava-survival-4.2.11-sources.jar biojava-survival-4.2.11-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-4.2.11.jar biojava-protein-disorder-4.2.11-sources.jar biojava-protein-disorder-4.2.11-javadoc.jar
biojava-sequencing biojava-sequencing-4.2.11.jar biojava-sequencing-4.2.11-sources.jar biojava-sequencing-4.2.11-javadoc.jar

@josemduarte josemduarte released this Dec 12, 2017 · 1279 commits to master since this release

Assets 2

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.2.10.jar biojava-core-4.2.10-sources.jar biojava-core-4.2.10-javadoc.jar
biojava-alignment biojava-alignment-4.2.10.jar biojava-alignment-4.2.10-sources.jar biojava-alignment-4.2.10-javadoc.jar
biojava-genome biojava-genome-4.2.10.jar biojava-genome-4.2.10-sources.jar biojava-genome-4.2.10-javadoc.jar
biojava-structure biojava-structure-4.2.10.jar biojava-structure-4.2.10-sources.jar biojava-structure-4.2.10-javadoc.jar
biojava-structure-gui biojava-structure-gui-4.2.10.jar biojava-structure-gui-4.2.10-sources.jar biojava-structure-gui-4.2.10-javadoc.jar
biojava-phylo biojava-phylo-4.2.10.jar biojava-phylo-4.2.10-sources.jar biojava-phylo-4.2.10-javadoc.jar
biojava-modfinder biojava-modfinder-4.2.10.jar biojava-modfinder-4.2.10-sources.jar biojava-modfinder-4.2.10-javadoc.jar
biojava-ws biojava-ws-4.2.10.jar biojava-ws-4.2.10-sources.jar biojava-ws-4.2.10-javadoc.jar
biojava-aa-prop biojava-aa-prop-4.2.10.jar biojava-aa-prop-4.2.10-sources.jar biojava-aa-prop-4.2.10-javadoc.jar
biojava-ontology biojava-ontology-4.2.10.jar biojava-ontology-4.2.10-sources.jar biojava-ontology-4.2.10-javadoc.jar
biojava-survival biojava-survival-4.2.10.jar biojava-survival-4.2.10-sources.jar biojava-survival-4.2.10-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-4.2.10.jar biojava-protein-disorder-4.2.10-sources.jar biojava-protein-disorder-4.2.10-javadoc.jar
biojava-sequencing biojava-sequencing-4.2.10.jar biojava-sequencing-4.2.10-sources.jar biojava-sequencing-4.2.10-javadoc.jar