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‎CHANGELOG.md‎

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BioJava 5.0.0
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=============
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unreleased
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- For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included
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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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### New Features
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BioJava 4.2.0 offers many new features, as well several bug-fixes.
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General
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- Requires Java 7
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- Better logging with SLF4J
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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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AND
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- correct some of the tree evaluator statistics.
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‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java‎

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/**
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* In case if {@link #getID() } in not unique keeps the alternative id, eg. NCBI GI number.
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*
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* This may null.
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*
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* @return
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*/

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java‎

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logger.info("accession id: {}", seq.getAccession().getID());
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Assert.assertNotNull(seq.getAccession().getID());
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// test GID number
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Assert.assertEquals(gi, seq.getAccession().getIdentifier());
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logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
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if( seq.getAccession().getIdentifier() != null) { // GI: in header now optional. See #596
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Assert.assertEquals(gi, seq.getAccession().getIdentifier());
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logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
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}
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// test taxonomy id
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logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
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Assert.assertNotNull(seq.getTaxonomy().getID());

‎biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java‎

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import java.util.List;
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/**
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* A class that take care of the painful mapping
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* A class that can map chromosomal positions to mRNA (coding sequence) positions.
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*
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* @author Andreas Prlic
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*/
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public class ChromosomeMappingTools {
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private static final Logger logger = LoggerFactory.getLogger(ChromosomeMappingTools.class);
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* I have a genomic coordinate, where is it in the Gene?
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* I have a genomic coordinate, where is it on the mRNA
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*
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/**
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* Get the chromosome position mapped onto the mrna CDS transcript position (needs to be divided by 3 to get protein coordinate)
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* Get the chromosome position mapped onto the mRNA CDS transcript position (needs to be divided by 3 to get protein coordinate)
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java‎

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package org.biojava.nbio.structure.test;
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.geometry.SuperPositions;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.PDBFileParser;
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import org.biojava.nbio.structure.io.SSBondImpl;
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import org.biojava.nbio.structure.jama.Matrix;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.List;
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import java.util.Set;
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import javax.vecmath.Matrix4d;
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import org.junit.Test;
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* @author Andreas Prlic
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* @since 1.5
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*/
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public class StructureTest {
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atoms2[1] = g2.getAtom("CA");
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Matrix4d transform = SuperPositions.superpose(
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Calc.atomsToPoints(atoms1), Calc.atomsToPoints(atoms2));
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SVDSuperimposer svds = new SVDSuperimposer(atoms1,atoms2);
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Matrix rotMatrix = svds.getRotation();
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Atom tran = svds.getTranslation();
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Group newGroup = (Group)g2.clone();
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Group newGroup = (Group) g2.clone();
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