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‎CHANGELOG.md‎

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BioJava 5.1.0
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=============
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### New feature
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* ABI tracer ported from legacy biojava, #769, thanks @MaxGreil
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### Bug fixes
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* Performance improvement for secondary structure calculation, #789
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* Fixed issue #731
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* Improved alt locs docs and some fixes, #778
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* Jmol dep updated to 14.29.17
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* Fixed issue #712
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* Fixed issue #791
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* Fixed issue #797
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* Fixed issue #784
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BioJava 5.0.2
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=============
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### Bug fixes
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* Fixed issue #770
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* Upgraded to latest mmtf-java 1.0.8
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BioJava 5.0.1
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=============
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### Bug fixes
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* Fixed issue #767
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* Fixed issue #761
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* Pom fixes for mvn site
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* Some logging fixes
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BioJava 5.0.0
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=============
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@@ -239,3 +268,98 @@ BioJava 4.2.0 offers many new features, as well several bug-fixes.
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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.
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BioJava 4.1.0
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=============
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release date: June 24th 2015
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### New Features:
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- New algorithm for multiple structure alignments
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- Improved visualization of structural alignments in Jmol
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- Support for the ECOD protein classification
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- Better mmCIF support: limited write support, better parsing
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BioJava 4.0.0
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=============
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release date: January 30th 2015
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### New Features:
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- General
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- Consistent error logging. SLF4J is used for logging and provides adaptors for all major
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logging implementations. (many contributors, including @benjamintboyle and @josemduarte)
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- Improved handling of exceptions (@dmyersturnbull)
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- Removed deprecated methods
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- Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and @sbliven)
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- Updated dependencies where applicable
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- Available on Maven Central (@andreasprlic and @heuermh)
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- biojava3-core
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- Improved Genbank parser, including support for feature records, qualifiers, and nested
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locations. (@paolopavan and @jgrzebyta)
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- biojava3-structure
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- Better support for crystallographic information, including crystallographic operators,
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unit cells, and protein-protein interfaces. (@josemduarte)
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- Better organization of downloaded structure files (set using the PDB_DIR and PDB_CACHE_DIR
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environmental variables) (@sbliven)
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- Better command-line tools for structure alignment (@sbliven)
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- New algorithm for symmetry detection in biological assemblies (@pwrose)
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- New algorithm for fast contact calculation, both intra-chain and inter-chain (@josemduarte)
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- Support for Accessible Surface Area (ASA) calculation through and implementation of
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the Shrake & Rupley algorithm, both single-thread and parallel (memory permitting) (@josemduarte)
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- Support for large structures (memory permitting) and multi-character chain IDs.
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- Default to mmCIF file format, as recommended by the wwPDB
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This version is compatible with Java 6, 7, and 8.
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### Upgrading
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Since we renamed all package names to be consistent across the whole project,
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there will be import errors when upgrading to this version. These can automatically get resolved
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by IDEs such as Eclipse or IntelliJ by selecting the Optimize Import menu item.
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BioJava 3.1.0
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=============
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release date: August 25th 2014
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While most development is going towards the upcoming 4.0.0 release, this release provides
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bug fixes and a few new features:
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- CE-CP version 1.4, with additional parameters
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- Update to SCOPe 2.04
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- Improvements in FASTQ parsing
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- Fix bugs in PDB parsing
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- Minor fixes in structure alignments
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This version is compatible with Java 6 and 7.
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BioJava 3.0.8
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=============
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release date: March 25th 2014
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New Features:
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- New Genbank writer
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- New parser for Karyotype file from UCSC
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- New parser for Gene locations from UCSC
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- New parser for Gene names file from genenames.org
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- New module for Cox regression code for survival analysis
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- New calculation of accessible surface area (ASA)
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- New module for parsing .OBO files (ontologies)
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- Improved representation of SCOP and Berkeley-SCOP classifications
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BioJava 3.0.7
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=============
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release date: September 23rd 2013
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New features:
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- added a basic genbank parser
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- fixed a problem when translating codons with N
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- now can infer bonds in protein structures
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- added support to parse mmcif records for organism and expression system
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- many small bug fixes and improvements

‎biojava-aa-prop/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-aa-prop</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

‎biojava-alignment/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-alignment</artifactId>
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<name>biojava-alignment</name>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestSubOptimalMSA.java‎

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Profile<DNASequence, NucleotideCompound> msa = Alignments
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.getMultipleSequenceAlignment(sequences, gapP);
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assertEquals("TTGGGGCCTCTAAACGGGGTCTT\n"
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+ "TTGGGGCCTCTAAACGGG-TCTT\n"
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+ "TTGGGGC-TCTAA-CGGG-TCTT\n",
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assertEquals("TTGGGGCCTCTAAACGGGGTCTT" + System.lineSeparator()
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+ "TTGGGGCCTCTAAACGGG-TCTT" + System.lineSeparator()
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+ "TTGGGGC-TCTAA-CGGG-TCTT" + System.lineSeparator(),
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msa.toString());
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ConcurrencyTools.shutdown();
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.getMultipleSequenceAlignment(sequences, gapP);
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// TODO test not passing (see issue 288 in github) - Aleix 03.2016
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assertEquals("TTGGGGCCTCTAAACGGGGTCTT\n"
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+ "TTGGGGCCTCTAAACGGG-TCTT\n"
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+ "TTGGGGC-TCTAA-CGGG-TCTT\n",
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assertEquals("TTGGGGCCTCTAAACGGGGTCTT" + System.lineSeparator()
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+ "TTGGGGCCTCTAAACGGG-TCTT" + System.lineSeparator()
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+ "TTGGGGC-TCTAA-CGGG-TCTT" + System.lineSeparator(),
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msa.toString());
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ConcurrencyTools.shutdown();

‎biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java‎

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String expected = "";
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for (ProteinSequence proteinSequence : proteinSequences.values()) {
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msa.addAlignedSequence(proteinSequence);
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expected += ">" + proteinSequence.getOriginalHeader() + "\n"
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+ proteinSequence.toString() + "\n";
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expected += ">" + proteinSequence.getOriginalHeader() + System.lineSeparator()
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+ proteinSequence.toString() + System.lineSeparator();
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}
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// Convert the biojava MSA to a FASTA String
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StringBuilder sb = new StringBuilder();
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for (int i = 0; i < fMsa.getNumberOfSequences(); i++) {
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sb.append(">" + fMsa.getIdentifier(i) + "\n");
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sb.append(fMsa.getSequenceAsString(i) + "\n");
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sb.append(">" + fMsa.getIdentifier(i) + System.lineSeparator());
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sb.append(fMsa.getSequenceAsString(i) + System.lineSeparator());
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}
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String forester = sb.toString();
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‎biojava-core/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-core</artifactId>

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java‎

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private static final String TREMBLID_PATTERN = "[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}";
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public static final Pattern UP_AC_PATTERN = Pattern.compile("(" + SPID_PATTERN + "|" + TREMBLID_PATTERN + ")");
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private static String uniprotbaseURL = "http://www.uniprot.org"; //"http://pir.uniprot.org";
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public static final String DEFAULT_UNIPROT_BASE_URL = "https://www.uniprot.org";
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private static String uniprotbaseURL = DEFAULT_UNIPROT_BASE_URL;
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private static String uniprotDirectoryCache = null;
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private String sequence;
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private CompoundSet<C> compoundSet;

‎biojava-genome/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-genome</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-integrationtest/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-integrationtest</artifactId>
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<packaging>jar</packaging>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>5.1.0-SNAPSHOT</version>
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<version>5.1.1-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java‎

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assertEquals(3, multiModelBioAssemblies.get(0).getPolyChains(0).size() + multiModelBioAssemblies.get(0).getPolyChains(1).size());
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// 3 chains in flattened structure in bioassembly 1
147147
assertEquals(3, flattenedBioAssemblies.get(0).getPolyChains().size());
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// 3 chains divided into 2 models in bioassembly 2
150-
assertEquals(3, multiModelBioAssemblies.get(1).getPolyChains(0).size() + multiModelBioAssemblies.get(0).getPolyChains(1).size());
150+
assertEquals(3, multiModelBioAssemblies.get(1).getPolyChains(0).size() + multiModelBioAssemblies.get(1).getPolyChains(1).size());
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// 3 chains in flattened structure in bioassembly 2
152152
assertEquals(3, flattenedBioAssemblies.get(1).getPolyChains().size());
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155154
// chain ids and names don't contain underscores in multimodel
156155
for (int modelIdx = 0; modelIdx<multiModelBioAssemblies.get(0).nrModels(); modelIdx++) {

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