[biojava/biojava] BioJava 4.2.0

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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