BioJava:GetStartedLegacy

Introduction

Welcome to BioJava 1 or BioJava Legacy. BioJava Legacy is the continuation of the old BioJava core while a new code base, BioJava 3, is currently being developed. As of the concurrent release of BioJava and BioJava , many functionalities are still not available in BioJava 3 and differences between their respective sequence models may make BioJava 1 a valid option for your project.

To find out more about BioJava 1, check any of the following entry points:

Tutorial to learn about symbols, sequence, and events.
Cook Book, also famously known as BioJava in Anger, to find out many code snippets.
BioJavax Extension which provides sophisticated event-based methods to read, write, and manipulate sequence files.

Installation

BioJava 1 will run on any computer with a Java virtual machine complying to the Java 2 Standard Edition (J2SE) 1.5 (or later) specifications. Java implementations for Linux, Windows, and Solaris are available to download from Oracle’s java website. Recent versions of MacOS X include a suitable Java implementation as standard. Java is also available on many other platforms: if in doubt, contact your vendor. BioJava binaries are distributed in .jar (Java ARchive) format.

You can get the latest version from the download page BioJava (requires Java 1.5+).

You can also integrate BioJava with NetBeans IDE. To find out how follow this link.

None of these .jar files need to be unpacked for normal use – simply place them in a convenient directory. To use BioJava, add the required JAR files to your CLASSPATH environment variable. The exact syntax varies between platforms. The text is wrapped due to limited space. The actual commands should be on a single line:

UNIX Bourne-type shells (the default with most Linux distributions and MacOS 10.3)

export CLASSPATH=/home/thomas/biojava-live.jar:/home/thomas/bytecode.jar:
                        /home/thomas/commons-cli.jar:
                        /home/thomas/commons-collections-2.1.jar:
                        /home/thomas/commons-dbcp-1.1.jar:
                        /home/thomas/commons-pool-1.1.jar:.

UNIX C-type shell (for example: versions of Mac OS X pre-10.3)

setenv CLASSPATH /home/thomas/biojava-live.jar:/home/thomas/bytecode.jar:
                        /home/thomas/commons-cli.jar:
                        /home/thomas/commons-collections-2.1.jar:
                        /home/thomas/commons-dbcp-1.1.jar:
                        /home/thomas/commons-pool-1.1.jar:.

Windows from command line

set CLASSPATH C:\biojava-live.jar;C:\bytecode.jar;C:\commons-cli.jar;
C:\commons-collections-2.1.jar;C:\commons-dbcp-1.1.jar;
C:\commons-dbcp-1.1.jar;.

Windows autoexec.bat files

set CLASSPATH=C:\biojava-live.jar;C:\bytecode.jar;C:\commons-cli.jar;
C:\commons-collections-2.1.jar;C:\commons-dbcp-1.1.jar;
C:\commons-pool-1.1.jar;.

In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. Note: Since version 1.8, BioJava is modular and the scripts need to be adjusted to incorporate submodules.

It is also possible to “install” JAR files onto your system by copying them into your Java installation’s extensions directory. On most Unix systems, this is named ${JAVA_HOME}/jre/lib/ext. On Mac OS X there is a per-user extensions directory called ~/Library/Java/Extensions (you may have to create this directory yourself). For other platforms, consult your Java vendor.

You can now compile and run BioJava programs using the javac and java commands. You might like to look at the tutorial, [http://www.biojava.org/docs/api API documentation] and the Legacy Cookbook section. Finally, you can learn a lot about BioJava by trying the demo programs included in the source distribution (see below).

Building your own

If you want to modify BioJava, you can obtain a copy of the source code from the Maven repository of the download area. Source releases are distributed in .tar.gz format. You can also obtain up-to-the-minute source code.

Since version 1.8, BioJava Legacy 1.8 requires Maven for the build process. We are also providing a BioJava specific Maven repository at http://biojava.org/download/maven/ .

Building the demo programs

The source distribution contains a number of small demo programs. Once you have a working biojava.jar on your classpath, these can be compiled directly using javac from the demos directory.

(unix)
cd demos
javac seq/TestEmbl.java
java seq.TestEmbl seq/AL121903.embl

(windows)
cd demos
javac seq\TestEmbl.java
java seq.TestEmbl seq\AL121903.embl