In Febuary 2007 several current and former BioJava core developers met at the EBI in Cambridge, UK to discuss future directions in BioJava. The following is a summary of what was discussed. –Mark 03:16, 15 March 2007 (EDT)


It was generally felt we should release as soon as possible! Although it is not bug free, completely documented/ tested etc it is probably still better than previous releases. Because we are encouraging people to use 1.5-beta2 instead of 1.4 it is pretty much the official version.

Exception Handling

It was generally felt that where possible exceptions that are unlikely and that would only happen in situations that the developer might expect should be runtime exceptions and not checked exceptions. More generally, problems caused by bad programming should be runtime exceptions. Problems caused by the user doing something odd should be checked exceptions.

An example is the ChangeVetoExceptions which will only occur if the developer has set up change listeners. This has been changed to a runtime (unchecked) exception in BJ1.5-beta2.

Things like IllegalSymbolException are probably errors caused by the user. For example the user provides a Protein fasta file when the program expects DNA. A well constructed program could respond in a better way than just crashing with a stack trace. For example it could prompt for a different file.

Checked exceptions create a development and learning burden and we should reduce them where appropriate.

Suggestions of other exceptions that should be unchecked are welcome. It is simple to convert a checked to unchecked exception it is not possible to go the other way so we should properly discuss each example.

Java 5 (JDK1.5)

It was decided that immediately after the release of BJ1.5 we should adopt and allow language features and API’s from JDK1.5

Bug fixes and regression testing

The bugzilla system is an excellent way for us to track bugs. Where possible we should encourage bug reports to the mailing list to be entered in bugzilla as well to make sure they are not missed.

To make sure bugs do not re-emerge it was suggested that JUnit tests be created for individual bugs. Given that each test is probably very simple it shouldn’t be too much of a burden to create them. Netbeans and Eclipse have very good JUnit wizards to make this even simpler.

I suggest that the tests could reside in a package like org.biojava.regression package. The tests could be named after the bug id, eg –Mark 03:16, 15 March 2007 (EDT)

New Classes and API’s

New classes should be accompanied by complete javadocs of all public and protected methods, including @param, @exception and @return tags. Modern IDEs have good wizards to point out methods that are not properly documented.

I would like to make this automated so that code checked into the repository is rejected or an email is sent out to indicate that docs are not complete. –Mark 03:16, 15 March 2007 (EDT)

New classes should have an accompanying JUnit test that covers all methods. People frequently miss equals(), hashcode(), compare() but these have behaviour contracts that require they are all in logical agreement. Strange and hard to debug behaviour arises if they are not tested properly. The toString() method should also be tested if it has been over-ridden because people start to rely on the value it produces.

Can a check for a JUnit test be automated?? –Mark 03:16, 15 March 2007 (EDT)

Subversion and Maven

There was some discussion about biojava switching to subversion after the 1.5 release and possibly using Maven2 instead of Ant for building.

Does someone want to organize this?? –Mark 03:16, 15 March 2007 (EDT)

Dropping the GUI API

Developments in Java graphics probably make it such that the BioJava GUI API shouldn’t be part of BioJava. There are now several ways to generate graphics depending on what the display is. Eg Swing for GUI, SVG for web, JSF/AJAX for dynamic web etc. There for the GUI package might best be a seperate project.

In addition the GUI model has not been updated to make use of features in RichSequence. If it is not maintained it could be distributed as a seperate JAR that would be an optional download for those who need it.

User Survey

It would be useful to perform a user survey to get an idea of what people want, what they use biojava for etc. Any volunteers to organise this??? –Mark 03:26, 15 March 2007 (EDT)

Code Audit

There are now several tools that check the quality of code, coverage of unit tests, documentation etc. It was felt that it would be useful to perform an ‘audit’ of the code base to get an idea of the quality.

Could people with some experience of these tools make some suggestions? –Mark 03:27, 15 March 2007 (EDT)

BioJava publication

The biojava 1.5 release should be accompanied by a applications note in Bioinformatics or similar. Matthew drew the short straw :) –Mark 03:29, 15 March 2007 (EDT)