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 <[email protected]> Reply-To: biojava/biojava <[email protected]> To: biojava/biojava <[email protected]> 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 — You are receiving this because you are subscribed to this thread. View it on GitHub <https://github.com/biojava/biojava/releases/tag/biojava-4.2.0> _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
