BioJava is composed of several submodules, one per broad bioinformatics topic. biojava-core contains general core methods that are shared across different modules.

• Fork the repo
• On your fork branch off master (Ignore all other branches)
• Submit pull request from your branch to the biojava/biojava master branch
• If you are submitting a fix related to an existing issue be sure to include '#' in the commit message to make processing your pull request easier.

• Please use the provided formatting xml file in /development/eclipse (intellij users can import the formatter file)
• Please add javadocs following standard java conventions. Javadocs are a must for public facing API methods.
• Add @author tags to class javadocs.
• Be sure to add @since tags whenever adding a new public-facing API method/field/class.
• Removed unused imports and variables or any other obvious compiler warning.
• Please handle exceptions carefully. Follow the "Throw early, catch late" philosophy, see #111.
• Add tutorial docs to the biojava-tutorial repository

• We use junit 4 for testing. Some older tests are in junit 3, but all new ones should be 4.
• Unit tests should cover reasonably the code. The tests should go into the src/test/main/ directory of the corresponding biojava module.
• We store heavier and longer running tests into the biojava-integrationtest module
• Try minimising use of external resources in tests. We haven't been very good at that in the past.