[Seqan-dev] scoring schemes

[Samuel Flores <samuelfloresc@gmail.com>]

Guys,

I can't seem to get globalAlignment to use any scoring scheme otehr than seqan::Simple:

            TAlign align;
            seqan::resize(rows(align), 2);
            assignSource(row(align,0),seqA);
            assignSource(row(align,1),seqB);
            int score = globalAlignment(align, seqan::Score<int,seqan::Simple>(0,-1,-1,gapOpenPenalty));

I tried changing the last line to just:

            int score = globalAlignment(align, seqan::Score<int,Pam>(0,-1,-1,gapOpenPenalty));

and every conceivable variant thereof.  None seem to be recognized, e.g.:


/Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: error: use of undeclared identifier 'Pam'


Can someone tell me how to switch to Blossum, PAM, or some other?

Thanks

Sam