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/* About */ Initial changelog
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‎_wikis/BioJava:Download_4.2.0.md

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This release contains over
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[<https://github.com/biojava/biojava/compare/6f8d796fee92edbbcd001c33cdae4f15c5480741>...biojava-4.2.0
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750] commits from 10 contributors.
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750] commits from 16 contributors.
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### New Features
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BioJava 4.2.0 offers a few new features, as well several bug-fixes.
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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 using DSSP
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- Multiple Structure Alignments
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- New MultipleStructureAlignment datastructure supporting flexible
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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,
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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
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(Myers-Turnbull, 2014)
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- Replaced internal graph datastructures with Jgraph
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- Unified StructureIdentifier framework (... complete ....)
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- Improved chemical component framework, now by default providing full
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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
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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
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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
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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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View the <BioJava:Modules> page for a list of current modules.
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‎_wikis/BioJava:Download_4.2.0.mediawiki

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== About ==
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''BioJava'' 4.2.0 has been released and is available using Maven from Maven Central as well as manual download (see below).
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This release contains over [https://github.com/biojava/biojava/compare/6f8d796fee92edbbcd001c33cdae4f15c5480741...biojava-4.2.0 750] commits from 10 contributors.
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This release contains over [https://github.com/biojava/biojava/compare/6f8d796fee92edbbcd001c33cdae4f15c5480741...biojava-4.2.0 750] commits from 16 contributors.
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===New Features===
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BioJava 4.2.0 offers a few new features, as well several bug-fixes.
13-
14-
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
17+
18+
;Biojava-Core
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* New SearchIO framework including blast xml parser
20+
21+
;Biojava-structure
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* Secondary structure assignment using DSSP
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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.
28+
* More complete mmCIF and cif parsing
29+
** Parse bonds, sites, charges
30+
** Better support for non-deposited pdb and mmcif files
31+
* Include CE-Symm algorithm for finding internal symmetry (Myers-Turnbull, 2014)
32+
* Replaced internal graph datastructures with Jgraph
33+
* Unified StructureIdentifier framework (... complete ....)
34+
* Improved chemical component framework, now by default providing full chemical description by using DownloadChemCompProvider
35+
* Optimised memory usage of Residue/Atoms
36+
37+
;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),
45+
* use Sequence and Compound classes from the alignment module
46+
* provide some Wrapper methods to communicate with forester,
47+
* decouple distance matrix calculation from tree constructor,
48+
* provide methods for common distance matrix calculations and framework for user-defined distances,
49+
* update the forester version to have the correct NJ tree constructor AND
50+
* correct some of the tree evaluator statistics.
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