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<TITLE>Nomenclature</TITLE>
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<BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
Could we agree on the following names? If anyone prefers another one, let it know, but it would be nice if we can decide what to take (saves a lot of typing ;-) <BR>
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BCSymbol (instead of BCSequenceUnit) <BR>
| <BR>
| <BR>
------------ BCNucleotide (instead of BCBase) <BR>
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------------ BCAminoAcid <BR>
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------------ etc (think BCSaccharide and alikes) <BR>
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I think BCFunctionalGroup should be a feature (like phosphates) and not a symbol, but perhaps I am wrong here. <BR>
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For sequences I would propose to take the names Koen already mentioned: <BR>
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BCSequence <BR>
| <BR>
| <BR>
----------------BCSequenceDNA <BR>
| <BR>
| <BR>
----------------BCSequenceProtein <BR>
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</SPAN></FONT></BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Okay, the BCSequenceDNA was just a first stab at thinking of the methods we’d want. Once I filled them in, I’d think about which ones would work generally across all sequences, and move them to the superclass, which I haven’t defined yet. What you saw was the twistings of my mind in action ;)<BR>
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That said, mentally I was reserving BCSequence as the wrapper for a type of sequence and all the additions – features, format conversion, etc. I was thinking more along the lines of:<BR>
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BCSequenceGeneric<BR>
| <BR>
BCSequence | <BR>
Contains an |<BR>
Instance of -> ----------------BCSequenceDNA <BR>
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| <BR>
----------------BCSequenceProtein <BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>That said, it would violate the naming conventions I’d argued for, so I hereby reject my own thinking. Given that, what do we call the wrapper object on the left then?<BR>
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I think this all makes life a bit simpler to implement John. I like the addition of the proposed equality testing methods you mention: <BR>
- (BOOL) complementsNucleotide: (BCNucleotide *)entry; (would be BCNucleotide specific) <BR>
- (BOOL) representsSymbol: (BCSymbol *) entry; (do you mean here to test whether this base belongs to an ambiguous group?) <BR>
And would like to add: <BR>
- (BOOL) isEqualToSymbol: (BCSymbol *) entry; <BR>
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</SPAN></FONT></BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Wouldn’t NSObject’s “isEqual” method work just as well here?<BR>
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And the second method (which I wrote this morning) looks like:<BR>
</SPAN></FONT><FONT SIZE="2"><FONT FACE="Monaco, Courier New"><SPAN STYLE='font-size:10.0px'>- (<FONT COLOR="#760F50">BOOL</FONT>) representsBase: (BCSequenceDNABase *) entry {<BR>
<FONT COLOR="#760F50">if</FONT> ( [[<FONT COLOR="#760F50">self</FONT> matches] containsObject: entry] )<BR>
<FONT COLOR="#760F50">return</FONT> <FONT COLOR="#760F50">YES</FONT>;<BR>
<FONT COLOR="#760F50">return</FONT> <FONT COLOR="#760F50">NO</FONT>; <BR>
}<BR>
</SPAN></FONT></FONT><BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>It works if you have an ambiguous base as self, and get handed another base.<BR>
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JT<BR>
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