TODO

## TODO list for The BioCocoa Project

General:

- Look for more places to use NSData in more places to replace the symbolArray
- Implementation of a mutable sequence class
- Update the documentation and headerdoc entries to reflect the new BCSequence/NSData structure
- Update the test code to reflect the new BCSequence/NSData structure

Koen's list:

- help with BCFeature and BCAnnotation classes
- Work more on BCSequenceReader and BCSequenceWriter classes
- Start working on BCScanner and BCDigest class
- Add more headerdoc entries
- Add specialized views (low priority)
- Set up the initial wiki page

Charles' agenda = what I want to do in order of priority:

- add dev-doc to explain BCSequence et al. design
- implement tests for symbol sets --> idea: systematically use the whole alphabet - BTW, need X for proteins??
- implement tests for translation
- get the sequence IO to a point equivalent to the current BioCocoa release (well, first, understand how it works!)
- have a look at the BCAppKit and BCSequenceView, see if I can do something (at least write a couple of emails...)
- help to get a more complete demo app with all of that
- make BCSymbol more consistent (specifically have a 'symbolForChar:' method for all classes instead of current methods)
- see if I can help to improve BCSequenceCodon

Scott's list:

- Need symbol types that allow for soft and hard masking (BCSymbolSet)
- Init with NSData verifies symbol set (BCSequence)
- Memory efficient reading of sequences to handle whole genomes (BCSequenceReader)
- Add protein sequence support in suffix array (BCSuffixArray)
- Break up suffix array too large for memory into smaller ones on disk, then merge
- Add test cases for BCSuffixArray
- Add dev doc for BCSuffixArray
- Finish maximum common prefix class (BCMCP)
- Add test cases for BCMCP
- Add dev doc for BCMCP
- Multi-core thread support

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