BioJava 5.0.0
josemduarte
released this
24 Mar 00:27
·
1117 commits
to master
since this release
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 noworg.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 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.