Re: [Seqan-dev] multiLocalAlignment function

[andres.burgos@irisa.fr]

Hi Tobias, thanks for your reply, I'll take a closer look at the code so
maybe I'll figure it out, but the example will still be helpful.

Danke schoen!
Andres

> Hello Andres,
>
> The multi-local alignment algorithm we have implemented is the one from
> Waterman and Eggert.
> It returns possibly overlapping local alignments, so it is not a repeated
> match finder.
>
> It is implemented in
> ./seqan/graph_align/graph_align_smith_waterman_clump.h and
> as you can see at the bottom of the file it repeatedly calls the standard
> smith-waterman
> alignment algorithm. Each found local alignment is then forbidden in the
> next run.
>
> I send you an example on how to use it on Monday.
>
> Best regards,
> Tobias
>
>
> ________________________________________
> From: seqan-dev-bounces@lists.fu-berlin.de
> [seqan-dev-bounces@lists.fu-berlin.de] On Behalf Of andres.burgos@irisa.fr
> [andres.burgos@irisa.fr]
> Sent: Friday, August 21, 2009 6:01 PM
> To: seqan-dev@lists.fu-berlin.de
> Subject: [Seqan-dev] multiLocalAlignment function
>
> Hi!
>
> I'm currently trying to make work the function
>
> multiLocalAlignment(graph, edgeMap, score, numAlign, tag)
>
> but I can't success, so I was hoping to get some help, since it's not
> documented on the web site. I was also wondering weather this function
> would return overlapping or non-overlapping alignments.
>
> Ok, so here is the code I'm working on:
>
>     typedef seqan::String<seqan::AminoAcid> TString;
>     typedef seqan::StringSet<TString, seqan::Dependent<> > TStringSet;
>     typedef seqan::Graph<seqan::Alignment<TStringSet, seqan::AminoAcid> >
> TGraph;
>
>     TStringSet str;
>     TString s1 ("some string");
>     TString s2 ("some other string");
>
>     seqan::appendValue(str, s1);
>     seqan::appendValue(str, s2);
>
>     seqan::Score<int, seqan::Pam<> > pam (250, -1, 0);
>     TGraph g(str);
>
>     seqan::String<seqan::IntervalTreeNode<seqan::IntervalAndCargo<int,
> int> > > propMap;
>     seqan::resizeEdgeMap(g, propMap);
>
>     seqan::multiLocalAlignment(g, propMap, pam, 10,
> seqan::SmithWaterman());
>
> This won't compile, throwing this error:
>
> ../seqan-1.1/seqan/graph_align/graph_align_interface.h: In function ?void
> seqan::multiLocalAlignment(seqan::Graph<seqan::Alignment<TStringSet,
> TCargo, TSpec> >&, TPropertyMap&, const seqan::Score<TScoreValue,
> TSpec2>&, TSize, TTag) [with TStringSet =
> seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
> seqan::_AminoAcid>, seqan::Alloc<void> >, seqan::Dependent<const
> seqan::Tag<seqan::TagGenerous_> > >, TCargo = seqan::SimpleType<unsigned
> char, seqan::_AminoAcid>, TSpec = const seqan::Tag<seqan::Default_>,
> TPropertyMap =
> seqan::String<seqan::IntervalTreeNode<seqan::IntervalAndCargo<int, char>,
> seqan::StorePointsOnly>, seqan::Alloc<void> >, TScoreValue = int, TSpec2 =
> seqan::Pam<seqan::SimpleType<unsigned char, seqan::_AminoAcid>,
> seqan::Pam_Data_Dayhoff_MDM78>, TSize = int, TTag =
> seqan::Tag<seqan::SmithWaterman_>]?:
> readers/SWReader.cc:26:   instantiated from here
> ../seqan-1.1/seqan/graph_align/graph_align_interface.h:234: error: no
> matching function for call to
> ?_localAlignment(seqan::String<seqan::Fragment<unsigned int,
> seqan::ExactFragment<const seqan::Tag<seqan::Default_> > >,
> seqan::Alloc<void> >&,
> seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
> seqan::_AminoAcid>, seqan::Alloc<void> >, seqan::Dependent<const
> seqan::Tag<seqan::TagGenerous_> > >&,
> seqan::String<seqan::IntervalTreeNode<seqan::IntervalAndCargo<int, char>,
> seqan::StorePointsOnly>, seqan::Alloc<void> >&, const seqan::Score<int,
> seqan::Pam<seqan::SimpleType<unsigned char, seqan::_AminoAcid>,
> seqan::Pam_Data_Dayhoff_MDM78> >&, int&,
> seqan::Tag<seqan::SmithWaterman_>)?
> make: *** [readers/SWReader.o] Error 1
>
> So, maybe an example would make things clearer...
>
> Thanks in advance,
> Andres
>
>
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