[Biococoa-dev] mass calculator bug

[Alexander Griekspoor]

> I need some help from you DNA dudes here.
>
> Looking at the methods, they are all very similar, until the lines:
>
>         if ( [selfSymbol isRepresentedByBase: entrySymbol]  || 
> [entrySymbol isRepresentedByBase: selfSymbol] ) {
>
> or variants thereof.  After that I really don't follow the flow of the 
> code, too many counters and symbols ;-)
>
> Here's my question:  isRepresentedByBase a specific test that is only 
> needed for bases, or should amino acids be tested the same way using a 
> similar method?
Yes, it is because of the whole ambiguity problem of DNA,  for example, 
if you have the sequence ATWG then TWG is a subsequence, but so is TAG 
and TTG.

> What I am trying to get at is to see if it is possible to have a 
> separate method to test the entrySymbol and selfSymbol that goes in 
> BCNucleotideDNA and BCAminoAcid  (or BCSequenceDNA and 
> BCSequenceProtein). Then we can keep all the rangeOfSubsequence in 
> BCSequence.
Perhaps it's indeed a good plan to let BCSymbol have the 
isRepresentedBySymbol method that BCNucleotideDNA overrides to check 
for ambiguous bases as well, that way BCSequence could have the general 
methods.

Furthermore, I as wondering if it's nice to have two complemented 
methods here:
- isRepresentedBySymbol   A isRepresentedBySymbol W but not vice versa
- representsSymbol 		    W representsSymbol A but not vice versa
It's also nice to add this particular example to the headerdoc.

the line would then become:
         if ( [selfSymbol isRepresentedBySymbol: entrySymbol]  || 
[selfSymbol representsSymbol: entrySymbol] ) {

But John knows more on this, so perhaps it's already there.

> BTW, just saw that there is also a method subSequenceInRange which 
> doesn't do all the checking - I guess I wrote that one ;D
Well, if the modus is 'strict' and want to check if a a sequence is 
exactly the same symbolwise (ATWG == ATWG but not ATAG), you don't need 
the checking, so it's nice to have anyway!

Alex

*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

                             iRNAi, do you?
              http://www.mekentosj.com/irnai

*********************************************************