Welcome to BioJava.
BioJava is an open-source initiative with the aim of providing the
biological community with objects for representing and manipulating
biological information. We hope that it becomes the one-stop solution for
every-day biological programming.
This distribution contains the BioJava classes and resources, along with
scripts for building the .class files and the documentation tree. The CVS
directories are arranged as follows:
biojava-live
|
|- apps : Java source files for user applications
|
|- demos : a selection of demo programs
|
|- demos-obsolete : demo programs for deperecated API
|
|- docs : documentation
|
|- dtd : dtd's relevant to Blast parsing
|
|- manifest : manifest file for building jars
|
|- reports : reports (currently test logs, this is not included in the
| distirubtion but is autogenerated when you run JUnit)
|
|- resources : resource files - images, xml documents
|
|- src : Java source files and package documentation
|
|- selfSignedCertificate : key required for self-signing of biojava.jar
|
|- taglets : Custom javadoc taglets for biojava
|
|- tests : Java unit test source files
|
BioJava requires Java >= 1.5 to build.
BioJava uses the CLI component of the Jakarta Commons project for its
user application components. We currently include CLI 1.0 in the
source tree. For more information, see:
http://jakarta.apache.org/
BioJava uses the DBCP, Pool & Collections components of the Jakarta Commons project for its
database connection pooling components. The current versions included in the CVS are DBCP 1.1
, Pool 1.1 and Collections 2.1. For more information, see:
http://jakarta.apache.org/
BioJava now uses the Java based build tool Ant, supplied by the Apache
Jakarta Project (see http://ant.apache.org/). To build the project,
change to biojava-live and type:
ant clean;
ant ;
ant javadocs-biojava;
If you have Ant >= 1.3 and the Java based unit testing tool JUnit (see
http://www.junit.org) you can run the supplied tests. To build and run
the tests, change directory to biojava-live and type:
ant runtests
To check for edits type:
> cvs update
and then for each directory under src with at least one modified file, build
the package.
To use biojava, put biojava.jar, bytecode.jar, jgrapht-jdk1.5.jar and commons-cli.jar into your
classpath.
To sign biojava.jar using a self signed certificate do:
ant sign
to verify that a biojava.jar has a valid signature do:
jarsigner -verify biojava.jar
BioJava uses Ant to build the demos. To build the demos, change
directory to biojava-live and type:
ant compile-demos
To run the demos change directory to demos. Most have either a comment
explaining their purpose, or will print out a usage message when run
without arguments.
Mail the BioJava mailing list (biojava-l@biojava.org) for more details.
For more techical discussion use biojava-dev@biojava.org
This product includes software developed by the
Apache Software Foundation (http://www.apache.org/).