Re: [Seqan-dev] scoring schemes

From: Rahn, René <rene.maerker@fu-berlin.de>
To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
Date: Mon, 17 Feb 2014 10:48:50 +0100
Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
Subject: Re: [Seqan-dev] scoring schemes

Hey Sam,

if you want to use scoring matrices you need to use a different specialization of our Score class. To use scoring schemes like the Pam or Blosum matrices you need to use the following code:

Score<int, ScoreMatrix<AminoAcid, Pam120_> > scorePam120(gap, gapOpen);

You can also use our shortcuts to make the code look nicer. You can find a list of all available shortcuts here: http://docs.seqan.de/seqan/1.4.1/SPEC_Score+_Matrix.html.

For the example above this would look like:

Pam120 scorePam120(gap, gapOpen);

I hope that will solve your problem!

Kind regards,

René Rahn

On Feb 17, 2014, at 12:32 AM, Samuel Flores <samuelfloresc@gmail.com> wrote:

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
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