[Biojava-dev] gaps and basis symbols

[mark.schreiber at novartis.com]

Further to this ...

Investigating a bit further it seems that AlphabetManager.xml denotes an 
<ambiguityMapping> for "-"  ,  "." and " ". It denotes a <gapMapping> for 
"~".

I'm not sure if this is an oversight or if this was intentional. Should 
they not all be <gapMapping>s?? Are not all gaps created equal? If I edit 
this in my copy of AlphabetManager.xml then everything seems to work and 
the JUnit tests still pass. It seems odd though, given that this has not 
been spotted before I am thinking it is intentional.

Should I commit these changes to CVS???

- Mark 





Mark Schreiber/GP/Novartis at PH
Sent by: biojava-dev-bounces at portal.open-bio.org
10/21/2005 03:58 PM

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] gaps and basis symbols


Hello -

There seems to be a slightly strange relationship between gaps and 
AlphabetManager.getGapSymbol(). If I take (for example) the 
SymbolTokenization of DNA and ask it for the Symbol associated with "-" it 

gives me back a BasisSymbol that is composed of a List that contains only 
the GapSymbol from AlphabetManager.

This leads to the slightly weird problem that the Symbol returned != 
AlphabetManager.getGapSymbol() which is what I expected. This also causes 
some curious problems with serialization that may or may not be related. 
Regardless, why does the "-" token not map directly to the GapSymbol in a 
singleton manner rather than mapping to the BasisSymbol composed of a List 

of only the GapSymbol.

Can any biojava mystics illucidate some wisdom on this?

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910
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