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BioJava is an open-source project dedicated to providing a Java framework for processing biological data.

Improve error messages in AlignmentGui

Show an error if the selected output directory is unwritable.
Use message dialogs for errors rather than stdout.
latest commit ea33b1240b
Spencer Bliven sbliven authored April 17, 2014
Octocat-spinner-32 biojava3-aa-prop [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-alignment [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-core [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-genome [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-modfinder more removal of excessive StructureException #54 April 02, 2014
Octocat-spinner-32 biojava3-ontology [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-phylo [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-protein-disorder [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-sequencing [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-structure-gui Improve error messages in AlignmentGui April 17, 2014
Octocat-spinner-32 biojava3-structure Removing more deprecated methods April 04, 2014
Octocat-spinner-32 biojava3-survival [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 biojava3-ws [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 development Also don't add 'final' everywhere. I think that's probably a little o… August 09, 2013
Octocat-spinner-32 integrationtest Making test throw exception if PDB_DIR not set April 03, 2014
Octocat-spinner-32 protein-comparison-tool [maven-release-plugin] prepare for next development iteration March 25, 2014
Octocat-spinner-32 .gitignore Ignoring some more temp files May 08, 2013
Octocat-spinner-32 .travis.yml Create .travis.yml April 27, 2013
Octocat-spinner-32 LICENSE moving the last ant based trunk to a branch September 15, 2009
Octocat-spinner-32 ignore.txt moving the last ant based trunk to a branch September 15, 2009
Octocat-spinner-32 pom.xml Added long pdb-vs-mmcif-parsing test and fixed small issues in parsing March 27, 2014
Octocat-spinner-32 readme.md updating version nr. March 25, 2014
readme.md

Welcome to BioJava v.3

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

BioJava is licensed under LGPL 2.1.

Please visit our homepage.

Documentation

The BioJava Cookbook is a collection of simple examples that teach the basics for how to work with BioJava. We are also working on a tutorial for biojava (currently only for protein structure modules).

Maven Repository

The Maven Repository contains the jars of all releases, as well as SNAPSHOT builds of the latest code base.

Quick Installation

If you are using Maven you can add the BioJava repository by adding the following XML to your project pom.xml file:

    <repositories>
      <repository>
        <id>biojava-maven-repo</id>
        <name>BioJava repository</name>
        <url>http://www.biojava.org/download/maven/</url>           
      </repository>
    </repositories>

    <dependencies>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava3-core</artifactId>
        <version>3.0.8</version>
      </dependency>
      <!-- other biojava jars as needed -->
    </dependencies>

Build Status

Build Status

Mailing Lists

BioJava has two main mailing lists. In order to avoid SPAM both lists only accept postings from list members. Anybody can become a list member, so please subscribe before you post. If you send without being subscribed your mail might get stuck in the moderation loop, which can cause several weeks of delay (no fun to read through all that spam).

biojava-l general discussion list

This list is intended for general discussion, advice, questions, offers of help, announcements, expressions of appreciation, bugs found in release code and requests for features.

biojava-dev developers list

This list is intended for more technical discussions about API design, bugs in git development code, performance issues and things that might not be of interest to the more casual user.

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