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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