소개

BioJava will run on any computer with a Java virtual machine complying to the Java 2 Standard Edition (J2SE) 1.4 (or later) specifications. Java implementations for Linux, Windows, and Solaris are available to download from Sun’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 BioJava 1.6 (requires Java 1.5+) from the download area .

You can get the legacy version of BioJava 1.5 (requires Java 1.4+) ; or

You can get the legacy release version of BioJava 1.4 here;

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

설치

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:

유닉스 본 쉘 (대부분의 리눅스 배포본이나 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:.

In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. We are working on resolving this.

유닉스 C 쉘 (예: Mac OS X pre-10.3 버전)

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:.

In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. We are working on resolving this.

윈도우즈 명령어

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;.

In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. We are working on resolving this.

윈도우즈 autoexec.bat 파일

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. We are working on resolving this.

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, API documentation and the BioJava in anger section . Finally, you can learn a lot about BioJava by trying the demo programs included in the source distribution (see below).