[Biojava-dev] gaps and basis symbols

[mark.schreiber at novartis.com]

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