@josemduarte josemduarte released this Mar 24, 2018 · 96 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