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MikkelVestergaardMikkelVestergaard
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Merge pull request #1 from biojava/master
Implement all changes from biojava/biojava into DK-MV/biojava
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‎.gitattributes‎

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# Set the default behavior, in case people don't have core.autocrlf set.
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* text=auto
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# Explicitly declare text files you want to always be normalized and converted
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# to native line endings on checkout.
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*.MF text
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*.blasttxt text
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*.blastxml text
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*.cif text
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*.dssp text
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*.faa text
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*.fasta text
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*.fastq text
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*.fatcat text
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*.fna text
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*.gb text
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*.gff3 text
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*.html text
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*.in text
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*.java text
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*.list text
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*.lst text
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*.mat text
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*.md text
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*.obo text
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*.onto text
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*.out text
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*.pairs text
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*.pdb text
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*.properties text
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*.py text
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*.rec text
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*.selex text
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*.sh text
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*.sto text
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*.sto text
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*.tsv text
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*.txt text
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*.xml text
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*.xsd text
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*.yml text
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# Declare files that will always have CRLF line endings on checkout.
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#*.sln text eol=crlf
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# Denote all files that are truly binary and should not be modified.
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*.png binary
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*.jpg binary
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*.gz
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*.mmtf

‎.travis.yml‎

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language: java
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jdk:
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- oraclejdk8
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sudo: false
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#after_success:
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# - mvn clean cobertura:cobertura coveralls:report
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- oraclejdk8
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sudo: required
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cache:
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directories:
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- "$HOME/.m2"
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before_install:
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- if [ ! -z "$GPG_SECRET_KEYS" ]; then echo $GPG_SECRET_KEYS | base64 --decode | $GPG_EXECUTABLE --import; fi
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- if [ ! -z "$GPG_OWNERTRUST" ]; then echo $GPG_OWNERTRUST | base64 --decode | $GPG_EXECUTABLE --import-ownertrust; fi
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after_success:
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- '[[ $TRAVIS_BRANCH == "master" ]] && { mvn deploy --settings travis-settings.xml -DskipTests=true -B ; };'
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env:
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global:
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- secure: MkIoyU3GmlgDRhO0n1lDKvZ/k0myVY3IsFTRNUFjaBBpohLyOBrs5L8gYmfnHYHB/LvJsP6EWA6i0wCchy8hU/2pn66T12K1+WZHyqCe7RRz2kgcvVgMXTsHgvVyZ3dERcBfEDeZENzEYCYADaysT+A73ofWdJemOqfa7IFEb80=
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- secure: it5av1icAvJn/6UI0aWS23m+En0ij1hCiPKw1QIbDLCE3oJOE4nHR8qINcnontH4XUQYTkmekStDkXj0WVVgp08zArj9o018XBtadYY+15h2QZBBAIpYb3UdlJoQfkcAx8yCv59BMd/u6DhMtcKSTHptVWvsLAS7YGW5hR6ZNYA=

‎CHANGELOG.md‎

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BioJava 5.0.0
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=============
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This release contains [1,170 commits](https://github.com/biojava/biojava/compare/biojava-4.2.11...biojava-5.0.0) from 19 contributors.
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Requires Java 8 or newer.
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### New features
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#### biojava-alignment
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* New utlity methods for sequence alignment objects (gap, similarity and coverage).
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#### biojava-structure
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* The data structures to represent 3D macromolecules now follow the mmCIF data model.
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* [MMTF format](http://mmtf.rcsb.org/) support.
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* Symmetry detection algorithms overhaul: better symmetry detection for tertiary and quaternary structure levels.
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* New method and data structures for the clustering of protein subunits at the sequence and structure levels.
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* New method to align biological assemblies, see `org.biojava.nbio.structure.align.quaternary.QsAlign`.
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* New algorithms for base-pair geometry in nucleic acids.
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* New SuperPosition interface for different 3D-structure superposition algorithms, see `org.biojava.nbio.structure.geometry.SuperPosition`.
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* Geometry-related API now more consistently based on vecmath interfaces.
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### Changed
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* For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included
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* Symmetry expansion for bioassembly creation is now by default happening via adding new chains instead of new models.
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* Make objects serializable for compatibility with big data frameworks (e.g. Spark).
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### Breaking API changes
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* module biojava-phylo merged into biojava-alignment. The package namespace stays the same (`org.biojava.nbio.phylo`).
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* module biojava-sequencing merged into biojava-genome. Package `org.biojava.nbio.sequencing.io.fastq` is now `org.biojava.nbio.genome.io.fastq`
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* `org.biojava.nbio.structure.Compound` -> `org.biojava.nbio.structure.EntityInfo`
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* `org.biojava.nbio.structure.io.util.FileDownloadUtils` -> `org.biojava.nbio.core.util.FileDownloadUtils`
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* `org.biojava.nbio.structure.symmetry.core.AxisAligner` -> `org.biojava.nbio.structure.symmetry.axis.AxisAligner`
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* `org.biojava.nbio.structure.symmetry.core.Subunits` -> refactored into several classes in `org.biojava.nbio.structure.cluster`: Subunit, SubunitCluster, SubunitClusterer
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* `org.biojava.nbio.structure.align.helper.AlignTools` -> `org.biojava.nbio.structure.align.helper.AlignUtils`
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* All deprecations introduced in 4.0.0 or before were removed.
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### General
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* Javadocs improvements across the board.
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* All tests are now Junit4.
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* Updated dependency versions (guava, slf4j, and log4j).
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### Bug fixes
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A very long list.
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BioJava 4.2.11
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==============
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release date: January 11th 2018
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This release contains [3](https://github.com/biojava/biojava/compare/biojava-4.2.10...biojava-4.2.11) commits from 1 contributor.
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### Bug fixes
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- Updated hmmer scan web service URL to https.
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BioJava 4.2.10
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==============
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release date: December 11th 2017
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This release contains [7](https://github.com/biojava/biojava/compare/biojava-4.2.9...biojava-4.2.10) commits from 2 contributors.
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### Bug fixes
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- Fixed issue #659
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- Fixed issue #715
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BioJava 4.2.9
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=============
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release date: October 19th 2017
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This release contains [15](https://github.com/biojava/biojava/compare/biojava-4.2.8...biojava-4.2.9) commits from 2 contributors.
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### Bug fixes
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- Some fixes to PDB file parsing CONECT/LINK records
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- Updated URLs for external resources
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BioJava 4.2.8
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=============
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release date: July 6th 2017
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This release contains [15](https://github.com/biojava/biojava/compare/biojava-4.2.7...biojava-4.2.8) commits from 3 contributors.
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### Bug fixes
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- Small additions to AlignedSequence in core module to better support pipelines that use 4.2.x
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- URLs adapted to latest RCSB PDB convention #682
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BioJava 4.2.7
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=============
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release date: March 7th 2017
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This release contains [8](https://github.com/biojava/biojava/compare/biojava-4.2.6...biojava-4.2.7) commits from 4 contributors.
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### Bug fixes
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- Fix for hmmer web service in biojava-ws #640
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- Fix in chromosome mapping tool #636
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BioJava 4.2.6
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=============
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release date: February 17th 2017
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This release contains [12](https://github.com/biojava/biojava/compare/biojava-4.2.5...biojava-4.2.6) commits from 4 contributors.
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### Bug fixes
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* Fix for problem in chain cloning, #631
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* Several bug fixes and better error check in quaternary symmetry detection code
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BioJava 4.2.5
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=============
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release date: December 7th 2016
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This release contains [30](https://github.com/biojava/biojava/compare/biojava-4.2.4...biojava-4.2.5) commits from 7 contributors.
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### Bug fixes
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* Fix for new phosphositeplus.org format, #610
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* org.biojava.nbio.genome.parsers.gff.Location union() and intersect() now work correctly, #355
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* Minor addition of crystallographic metadata fields to handle legacy PDB entries
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* Jmol interchange format is now mmCIF, allowing for multiletter chain ids
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* Update to latest jmol 14.6.2_2016.08.28
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* A few minor bug fixes
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BioJava 4.2.4
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=============
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release date: July 29th 2016
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This release contains over [17](https://github.com/biojava/biojava/compare/biojava-4.2.3...biojava-4.2.4) commits from 4 contributors.
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### Bug fixes
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* NCBI links now using https (see [NCBI's announcement](http://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/) )
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* CATH links redirected to new server http://release.cathdb.info/
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* SCOP default location now points to the Berkeley server after demise of Scop at MRC LMB
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* Fixed important bug in mmCIF writing where structures with multiple models were written with identical coordinates
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* Fixed bug in Group cloning where chemical components weren't cloned
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* Added utility class for Chromosome mapping
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BioJava 4.2.3
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=============
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release date: July 28th 2016
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This release contains over [13](https://github.com/biojava/biojava/compare/biojava-4.2.2...biojava-4.2.3) commits from 2 contributors.
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### Bug fixes
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* mmCIF file writing: special fields (e.g. containing hyphens) are now correctly written
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* General improvements in mmCIF file read and write
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BioJava 4.2.2
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=============
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release date: June 14th 2016
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This release contains over [31](https://github.com/biojava/biojava/compare/biojava-4.2.1...biojava-4.2.2) commits from 5 contributors.
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### Bug fixes
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This is a bug-fix release
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* CE-Symm features and bug fixes
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- Better data structures for symmetry axes (particularly for hierarchical symmetry)
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- Fix bug with symmetry axis positioning
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- Optimization includes all symmetry repeats for hierarchical symmetry
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* Update of protein modifications to latest version,
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- including new glycans and chromophores
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- Updating naming definitions to latest conventions
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BioJava 4.2.1
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=============
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release date: May 3rd 2016
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This release contains over [31](https://github.com/biojava/biojava/compare/biojava-4.2.0...biojava-4.2.1) commits from 7 contributors.
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### Bug fixes
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Biojava-structure
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- Nucleotide bonds are now generated
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- BIO: identifiers are now correctly handled
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- Several fixes for CE-Symm
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- Substructures now contain seqres groups (isse #449)
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- Structures containing insertion codes are now written correctly to mmCIF
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- AtomCache now uses the correct default parsing parameters (issue #455)
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- Fixed problem with some atom charges that weren't being added
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- CATH updated to 4.0.0
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- Better ECOD javadocs (issue #452)
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Biojava-structure-gui
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- Removed javaws dependency (issue #459)
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BioJava 4.2.0
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=============
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release date: March 10th 2016
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This release contains over [750](https://github.com/biojava/biojava/compare/6f8d796fee92edbbcd001c33cdae4f15c5480741...biojava-4.2.0) commits from 16 contributors.
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BioJava 4.2.0 offers many new features, as well several bug-fixes.
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- Requires Java 7
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- Better logging with SLF4J
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### New Features
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#### biojava-core
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- New SearchIO framework including blast xml parser
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#### biojava-structure
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- Secondary structure assignment (DSSP compatible)
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- Multiple Structure Alignments
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- New MultipleStructureAlignment datastructure supporting flexible and order-independent alignments
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- MultipleMC algorithm
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- Can use any pairwise StructureAlignment implementation
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- serialize and parse multiple structure alignments as XML files, output as Text, FatCat, FASTA, Rotation Matrices, etc.
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- More complete mmCIF and cif parsing
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- Parse bonds, sites, charges
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- Better support for non-deposited pdb and mmcif files
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- Include CE-Symm algorithm for finding internal symmetry (Myers-Turnbull, 2014)
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- Replaced internal graph datastructures with Jgraph
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- Unified StructureIdentifier framework
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- Improved chemical component framework, now by default providing full chemical description by using DownloadChemCompProvider
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- Optimised memory usage of Residue/Atoms
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#### biojava-structure-gui
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- MultipleAlignmentGUI for visualizing Multiple Structure Alignments with Jmol
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- SymmetryDisplay for visualizing internal symmetry
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#### biojava-phylo
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- Use `Forester 1.038`
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- Significant bug fixes
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- use `SubstitutionMatrices` in the core module (instead of imported Jalview matrices)
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- use `Sequence` and `Compound` classes from the alignment module
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- provide some Wrapper methods to communicate with forester
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- decouple distance matrix calculation from tree constructor
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- provide methods for common distance matrix calculations and framework for user-defined distances
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- update the forester version to have the correct NJ tree constructor
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- correct some of the tree evaluator statistics.

‎CONTRIBUTING.md‎

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## Modules
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BioJava is composed of several submodules, one per broad bioinformatics topic.
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[biojava-core](https://github.com/biojava/biojava/tree/master/biojava-core) contains general core methods that are shared across different modules.
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## Contributing
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- All contributions should happen through pull requests so that there is open reviewing. The master branch is protected,
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users can't push directly to it.
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- Please add javadocs following standard java conventions. Javadocs are a must for public facing API methods.
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- Add `@author` tags to class javadocs.
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- Be sure to add `@since` tags whenever adding a new public-facing API method/field/class.
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- Removed unused imports and variables or any other obvious compiler warning.
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- Please handle exceptions carefully. Follow the "Throw early, catch late" philosophy, see #111.
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- Add tutorial docs to the [biojava-tutorial repository](https://github.com/biojava/biojava-tutorial)
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## Testing
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- We use junit 4 for testing. Some older tests are in junit 3, but all new ones should be 4.
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- Unit tests should cover reasonably the code. The tests should go into the `src/test/main/` directory
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of the corresponding biojava module.
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- We store heavier and longer running tests into the [biojava-integrationtest module](https://github.com/biojava/biojava/tree/master/biojava-integrationtest)
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- Try minimising use of external resources in tests. We haven't been very good at that in the past.

biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CacheFactory.java renamed to HEADER.txt

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*
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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.structure.align.util;
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import org.biojava.nbio.core.util.SoftHashMap;
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/** provides a SoftHashMap singleton.
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*
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*
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* @Deprecated find better ways for caching or use a SoftHashMap directly
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*/
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public class CacheFactory {
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@SuppressWarnings("rawtypes")
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private static SoftHashMap cache = new SoftHashMap ();
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// no public constructor;
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private CacheFactory(){
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}
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@SuppressWarnings("rawtypes")
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public static SoftHashMap getCache(){
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return cache;
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}
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}
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*/

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