Hi All!
Just forwarding for interest: the latest Biojava release is looking great!
Jim
···
-------- Forwarded Message --------
Subject: [biojava/biojava] BioJava 4.2.0
Date: Tue, 19 Apr 2016 02:16:45 -0700
From: Spencer Bliven <notifications@github.com>
Reply-To: biojava/biojava <noreply@github.com>
To: biojava/biojava <biojava@noreply.github.com>
BioJava 4.2.0 is compatible with *Java 7 and 8*.
About
/BioJava/ 4.2.0 has been released and is available using Maven from
Maven Central as well as manual download (see below).
This release contains over
750
<https://github.com/biojava/biojava/compare/6f8d796fee92edbbcd001c33cdae4f15c5480741...biojava-4.2.0>
commits from 16 contributors.
New Features
BioJava 4.2.0 offers many new features, as well several bug-fixes.
General
* Requires Java 7
* Better logging with SLF4J
Biojava-Core
* New SearchIO framework including blast xml parser
Biojava-structure
* Secondary structure assignment (DSSP compatible)
* Multiple Structure Alignments
o New MultipleStructureAlignment datastructure supporting flexible
and order-independent alignments
o MultipleMC algorithm
+ Can use any pairwise StructureAlignment implementation
o serialize and parse multiple structure alignments as XML files,
output as Text, FatCat, FASTA, Rotation Matrices, etc.
* More complete mmCIF and cif parsing
o Parse bonds, sites, charges
o Better support for non-deposited pdb and mmcif files
* Include CE-Symm algorithm for finding internal symmetry
(Myers-Turnbull, 2014)
* Replaced internal graph datastructures with Jgraph
* Unified StructureIdentifier framework
* Improved chemical component framework, now by default providing full
chemical description by using DownloadChemCompProvider
* Optimised memory usage of Residue/Atoms
Biojava-structure-gui
* MultipleAlignmentGUI for visualizing Multiple Structure Alignments
with Jmol
* SymmetryDisplay for visualizing internal symmetry
Biojava-Phylo
* Use Forester 1.038
* Significant bug fixes
* use SubstitutionMatrices in the core module (instead of imported
Jalview matrices),
* use Sequence and Compound classes from the alignment module
* provide some Wrapper methods to communicate with forester,
* decouple distance matrix calculation from tree constructor,
* provide methods for common distance matrix calculations and
framework for user-defined distances,
* update the forester version to have the correct NJ tree constructor AND
* correct some of the tree evaluator statistics.
View the BioJava:Modules page for a list of current modules.
Maven Download
BioJava 4.2.0 requires Maven <http://maven.apache.org/> for the build
process. All BioJava jar files are available via Maven Central as of
this release.
You can create a BioJava dependency by adding the following XML to your
project pom.xml file:
<dependencies> <dependency> <groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId> <version>4.2.0</version>
</dependency> <!-- other biojava jars as needed --> </dependencies> |
Manual Download
Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-core/4.2.0/biojava-core-4.2.0.jar>
biojava-core-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-core/4.2.0/biojava-core-4.2.0-sources.jar>
biojava-core-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-core/4.2.0/biojava-core-4.2.0-javadoc.jar>
biojava-alignment biojava-alignment-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-alignment/4.2.0/biojava-alignment-4.2.0.jar>
biojava-alignment-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-alignment/4.2.0/biojava-alignment-4.2.0-sources.jar>
biojava-alignment-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-alignment/4.2.0/biojava-alignment-4.2.0-javadoc.jar>
biojava-genome biojava-genome-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-genome/4.2.0/biojava-genome-4.2.0.jar>
biojava-genome-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-genome/4.2.0/biojava-genome-4.2.0-sources.jar>
biojava-genome-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-genome/4.2.0/biojava-genome-4.2.0-javadoc.jar>
biojava-structure biojava-structure-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-structure/4.2.0/biojava-structure-4.2.0.jar>
biojava-structure-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-structure/4.2.0/biojava-structure-4.2.0-sources.jar>
biojava-structure-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-structure/4.2.0/biojava-structure-4.2.0-javadoc.jar>
biojava-structure-gui biojava-structure-gui-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-structure-gui/4.2.0/biojava-structure-gui-4.2.0.jar>
biojava-structure-gui-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-structure-gui/4.2.0/biojava-structure-gui-4.2.0-sources.jar>
biojava-structure-gui-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-structure-gui/4.2.0/biojava-structure-gui-4.2.0-javadoc.jar>
biojava-phylo biojava-phylo-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-phylo/4.2.0/biojava-phylo-4.2.0.jar>
biojava-phylo-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-phylo/4.2.0/biojava-phylo-4.2.0-sources.jar>
biojava-phylo-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-phylo/4.2.0/biojava-phylo-4.2.0-javadoc.jar>
biojava-modfinder biojava-modfinder-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-modfinder/4.2.0/biojava-modfinder-4.2.0.jar>
biojava-modfinder-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-modfinder/4.2.0/biojava-modfinder-4.2.0-sources.jar>
biojava-modfinder-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-modfinder/4.2.0/biojava-modfinder-4.2.0-javadoc.jar>
biojava-ws biojava-ws-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-ws/4.2.0/biojava-ws-4.2.0.jar>
biojava-ws-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-ws/4.2.0/biojava-ws-4.2.0-sources.jar>
biojava-ws-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-ws/4.2.0/biojava-ws-4.2.0-javadoc.jar>
biojava-aa-prop biojava-aa-prop-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-aa-prop/4.2.0/biojava-aa-prop-4.2.0.jar>
biojava-aa-prop-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-aa-prop/4.2.0/biojava-aa-prop-4.2.0-sources.jar>
biojava-aa-prop-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-aa-prop/4.2.0/biojava-aa-prop-4.2.0-javadoc.jar>
biojava-ontology biojava-ontology-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-ontology/4.2.0/biojava-ontology-4.2.0.jar>
biojava-ontology-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-ontology/4.2.0/biojava-ontology-4.2.0-sources.jar>
biojava-ontology-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-ontology/4.2.0/biojava-ontology-4.2.0-javadoc.jar>
biojava-survival biojava-survival-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-survival/4.2.0/biojava-survival-4.2.0.jar>
biojava-survival-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-survival/4.2.0/biojava-survival-4.2.0-sources.jar>
biojava-survival-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-survival/4.2.0/biojava-survival-4.2.0-javadoc.jar>
biojava-protein-disorder biojava-protein-disorder-4.2.0.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-protein-disorder/4.2.0/biojava-protein-disorder-4.2.0.jar>
biojava-protein-disorder-4.2.0-sources.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-protein-disorder/4.2.0/biojava-protein-disorder-4.2.0-sources.jar>
biojava-protein-disorder-4.2.0-javadoc.jar
<https://repo1.maven.org/maven2/org/biojava/biojava-protein-disorder/4.2.0/biojava-protein-disorder-4.2.0-javadoc.jar>
Browse API docs
You can also browse the documentation at BioJava 4.2.0
api <http://www.biojava.org/docs/api4.2.0/>
Release Date
BioJava 4.2.0 has been released on March 10th, 2015
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