[Seqan-dev] local alignment with blosum scoring matrix

[Young-ik Yang <maemukki@yahoo.com>]

Would you let me know which local alignment algorithm support scoring matrix 
such as blosum62?
If any, can you show me a function call or an example?

I am using seqan 1.3.
I am attaching error messages from local alignment call at the end of the 
message.

Thanks,
Youngik.


/home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h: In 
function 'typename seqan::Value<TRight, 0>::Type 
seqan::_alignSmithWaterman(TTrace&, const TStringSet&, const TScore&, typename 
seqan::Value<THolder, 0>::Type&, TIndexPair&, TForbidden&) [with TTrace = 
seqan::String<unsigned char, seqan::Alloc<void> >, TStringSet = 
seqan::Align<seqan::String<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Alloc<void> >, seqan::ArrayGaps>, TScore = seqan::Score<int, 
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Blosum62_> >, TIndexPair = size_t [2], TForbidden = seqan::Nothing]':
/home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h:381:   
instantiated from 'typename seqan::Value<TLeft, 0>::Type 
seqan::_localAlignment(const TStringSet&, const TScore&, seqan::SmithWaterman) 
[with TStringSet = seqan::Align<seqan::String<seqan::SimpleType<unsigned char, 
seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::ArrayGaps>, TScore = 
seqan::Score<int, seqan::ScoreMatrix<seqan::SimpleType<unsigned char, 
seqan::AminoAcid_>, seqan::Blosum62_> >]'
/home/yyang/bin/seqan/seqan/graph_align/graph_align_interface.h:378:   
instantiated from 'TScoreValue seqan::localAlignment(const TStringSet&, const 
seqan::Score<TScoreValue, TScoreSpec>&, TTag) [with TStringSet = 
seqan::Align<seqan::String<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Alloc<void> >, seqan::ArrayGaps>, TScoreValue = int, TSpec = 
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Blosum62_>, TTag = seqan::Tag<seqan::SmithWaterman_>]'
alignment_local.cpp:65:   instantiated from here
/home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h:233: error: 
no match for 'operator[]' in 'str[0]'
/home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h:234: error: 
no match for 'operator[]' in 'str[1]'
/home/yyang/bin/seqan/seqan/score/score_base.h: In function 'TValue 
seqan::score(const seqan::Score<TValue, TSpec>&, TPos1, TPos2, const TSeq1&, 
const TSeq2&) [with TValue = int, TSpec = 
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Blosum62_>, TPos1 = long unsigned int, TPos2 = long unsigned int, TSeq1 = 
seqan::SimpleType<unsigned char, seqan::AminoAcid_>, TSeq2 = 
seqan::SimpleType<unsigned char, seqan::AminoAcid_>]':
/home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h:291:   
instantiated from 'typename seqan::Value<TRight, 0>::Type 
seqan::_alignSmithWaterman(TTrace&, const TStringSet&, const TScore&, typename 
seqan::Value<THolder, 0>::Type&, TIndexPair&, TForbidden&) [with TTrace = 
seqan::String<unsigned char, seqan::Alloc<void> >, TStringSet = 
seqan::Align<seqan::String<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Alloc<void> >, seqan::ArrayGaps>, TScore = seqan::Score<int, 
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Blosum62_> >, TIndexPair = size_t [2], TForbidden = seqan::Nothing]'
/home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h:381:   
instantiated from 'typename seqan::Value<TLeft, 0>::Type 
seqan::_localAlignment(const TStringSet&, const TScore&, seqan::SmithWaterman) 
[with TStringSet = seqan::Align<seqan::String<seqan::SimpleType<unsigned char, 
seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::ArrayGaps>, TScore = 
seqan::Score<int, seqan::ScoreMatrix<seqan::SimpleType<unsigned char, 
seqan::AminoAcid_>, seqan::Blosum62_> >]'
/home/yyang/bin/seqan/seqan/graph_align/graph_align_interface.h:378:   
instantiated from 'TScoreValue seqan::localAlignment(const TStringSet&, const 
seqan::Score<TScoreValue, TScoreSpec>&, TTag) [with TStringSet = 
seqan::Align<seqan::String<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Alloc<void> >, seqan::ArrayGaps>, TScoreValue = int, TSpec = 
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>, 
seqan::Blosum62_>, TTag = seqan::Tag<seqan::SmithWaterman_>]'
alignment_local.cpp:65:   instantiated from here
/home/yyang/bin/seqan/seqan/score/score_base.h:206: error: no match for 
'operator[]' in 'seq1[pos1]'
/home/yyang/bin/seqan/seqan/score/score_base.h:206: error: no match for 
'operator[]' in 'seq2[pos2]'