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<h2>TODO list for The BioCocoa Project</h2>
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<p>General:</p>
<ul>
<li>Look for more places to use NSData in more places to replace the symbolArray</li>
<li>Implementation of a mutable sequence class</li>
<li>Update the documentation and headerdoc entries to reflect the new BCSequence/NSData structure</li>
<li>Update the test code to reflect the new BCSequence/NSData structure</li>
</ul>
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<p>Koen's list:</p>
<ul>
<li>help with BCFeature and BCAnnotation classes</li>
<li>Work more on BCSequenceReader and BCSequenceWriter classes</li>
<li>Start working on BCScanner and BCDigest class</li>
<li>Add more headerdoc entries</li>
<li>Add specialized views (low priority)</li>
<li>Set up the initial wiki page</li>
</ul>
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<p>Charles' agenda = what I want to do in order of priority:</p>
<ul>
<li>add dev-doc to explain BCSequence et al. design</li>
<li>implement tests for symbol sets --> idea: systematically use the whole alphabet - BTW, need X for proteins??</li>
<li>implement tests for translation</li>
<li>get the sequence IO to a point equivalent to the current BioCocoa release (well, first, understand how it works!)</li>
<li>have a look at the BCAppKit and BCSequenceView, see if I can do something (at least write a couple of emails...)</li>
<li>help to get a more complete demo app with all of that</li>
<li>make BCSymbol more consistent (specifically have a 'symbolForChar:' method for all classes instead of current methods)</li>
<li>see if I can help to improve BCSequenceCodon</li>
</ul>
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<p>Scott's list:</p>
<ul>
<li>Need symbol types that allow for soft and hard masking (BCSymbolSet)</li>
<li>Init with NSData verifies symbol set (BCSequence)</li>
<li>Memory efficient reading of sequences to handle whole genomes (BCSequenceReader)</li>
<li>Add protein sequence support in suffix array (BCSuffixArray)</li>
<li>Break up suffix array too large for memory into smaller ones on disk, then merge</li>
<li>Add test cases for BCSuffixArray</li>
<li>Add dev doc for BCSuffixArray</li>
<li>Finish maximum common prefix class (BCMCP)</li>
<li>Add test cases for BCMCP</li>
<li>Add dev doc for BCMCP</li>
<li>Multi-core thread support</li>
</ul>
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