[Biojava-dev] Code checkout

[Scooter Willis]

Andy

Yesterday when I was fighting code updates I only pulled the source tree and not the test source(forgot). So all test cases passing was only true for all old test cases. TranslationTest is failing on multiFrameTranslation. This could be a result of all the code changes we made or something you are working on. I didn't try to fix and the test case fails but all others pass.

I also commented out the GCStats test case where not sure if that should be in the genome module or functionality that should be in the core.

Your test case coverage is amazing. When are you going to get around to actually writing code that does something! Kidding of course and you have set the bar very high....

I moved FastaReaderHelper and FastaWriterHelper to the sequence.io package as they were in the sequence package. Not sure if we should adopt the Helper naming convention but I like having a class designed to bring together code abstraction in easy to use working code. The newbie programmer is not going to invest time in figuring out how to read a fasta file with all the flexibility we are providing so typical use cases can be represented in the helper class. It also makes it easier to have modular working examples in one place. The helper classes should all have static methods and very few lines of code per method.

Scooter