[Seqan-dev] Scoring mit Blosum62

[Hannes Hauswedell <hauswedell@mi.fu-berlin.de>]

Hallo wieder!

bez. der lokal/semi-global-Frage warte ich auf Antwort von David.

Ich bin gerade an dem BLASTX-Modus meiner Bachelor-Arbeit. Dabei komme 
ich nicht weiter. Ich möchte einfach mit einer Blosum62 ein Alignment 
scoren, dazu benutze ich als Aufruf (jenach Option wird hier das 
Nucleotide oder das Protein-Scoring verwendet):


int score = globalAlignment(align,
                            (options.blastMode == 1)
                              ? options.blastNScoring
                              : options.blastPScoring,
                            Gotoh());

Vorher habe ich das nur mit blastNScoring gemacht, problemlos. 
BlastNScoring ist vom Typ Score<int>, BlastPScoring ist vom Typ 
Blosum62. 

Der Compiler spuckt dabei als Fehler aus:

/usr/include/c++/4.2/bits/stl_algobase.h:283: error: cannot convert 
'seqan::Score<int, seqan::Simple>' to 'char' in assignment

Die etwas längeren Vorlauf habe ich angehangen.

Danke für Tipps!

Gruß,
Hannes

/usr/include/c++/4.2/bits/stl_algobase.h: In static member function 'static _OI std::__copy<_BoolType, std::random_access_iterator_tag>::copy(_II, _II, _OI) [with _II = seqan::Score<int, seqan::Simple>*, _OI = char*, bool _BoolType = false]':                                                                                           
/usr/include/c++/4.2/bits/stl_algobase.h:315:   instantiated from '_OI std::__copy_aux(_II, _II, _OI) [with _II = seqan::Score<int, seqan::Simple>*, _OI = char*]'                                                                                                                                                                           
/usr/include/c++/4.2/bits/stl_algobase.h:340:   instantiated from 'static _OI std::__copy_normal<<anonymous>, <anonymous> >::__copy_n(_II, _II, _OI) [with _II = seqan::Score<int, seqan::Simple>*, _OI = char*, bool <anonymous> = false, bool <anonymous> = false]'                                                                        
/usr/include/c++/4.2/bits/stl_algobase.h:401:   instantiated from '_OutputIterator std::copy(_InputIterator, _InputIterator, _OutputIterator) [with _InputIterator = seqan::Score<int, seqan::Simple>*, _OutputIterator = char*]'                                                                                                            
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/basic/basic_alphabet_interface.h:509:   instantiated from 'void seqan::_arrayCopyForward_Default(TSource1, TSource2, TTarget) [with TTarget = char*, TSource1 = seqan::Score<int, seqan::Simple>*, TSource2 = seqan::Score<int, seqan::Simple>*]'                                                                                                                                                                                                                                                                                                                                
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/basic/basic_alphabet_interface.h:518:   instantiated from 'void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = char*, TSource1 = seqan::Score<int, seqan::Simple>*, TSource2 = seqan::Score<int, seqan::Simple>*]'                                                                                                                                                                                                                                                                                                                                         
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/basic/basic_alphabet_trait_basic.h:102:   instantiated from 'void seqan::_arrayConstructCopy_Pointer(TValueSource*, TValueSource*, TValueTarget*, seqan::True) [with TValueSource = seqan::Score<int, seqan::Simple>, TValueTarget = char]'                                                                                                                                                                                                                                                                                                                                      
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/basic/basic_alphabet_trait_basic.h:132:   instantiated from 'void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = seqan::Score<int, seqan::Simple>, TValueTarget = char]'               
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/sequence/string_base.h:764:   instantiated from 'static void seqan::_Assign_String<TExpand>::assign_(TTarget&, TSource&) [with TTarget = seqan::String<char, seqan::Alloc<void> >, TSource = const seqan::String<seqan::Score<int, seqan::Simple>, seqan::Alloc<void> >, TExpand = const seqan::Tag<seqan::TagGenerous_>]'                                                                                                                                                                                                                                                       
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/sequence/string_base.h:812:   instantiated from 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>) [with TTargetValue = char, TTargetSpec = seqan::Alloc<void>, TSource = seqan::String<seqan::Score<int, seqan::Simple>, seqan::Alloc<void> >, TExpand = seqan::TagGenerous_]'                                                                                                                                                                                                                                                              
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/sequence/string_base.h:772:   instantiated from 'static void seqan::_Assign_String<TExpand>::assign_(TTarget&, TSource&) [with TTarget = seqan::String<char, seqan::Alloc<void> >, TSource = const seqan::Score<int, seqan::Simple>, TExpand = const seqan::Tag<seqan::TagGenerous_>]'                                                                                                                                                                                                                                                                                           
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/sequence/string_base.h:812:   instantiated from 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>) [with TTargetValue = char, TTargetSpec = seqan::Alloc<void>, TSource = seqan::Score<int, seqan::Simple>, TExpand = seqan::TagGenerous_]'                                                                                                                                                                                                                                                                                                  
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/sequence/string_base.h:746:   instantiated from 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&) [with TTargetValue = char, TTargetSpec = seqan::Alloc<void>, TSource = seqan::Score<int, seqan::Simple>]'        
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/sequence/string_alloc.h:79:   instantiated from 'seqan::String<TValue, seqan::Alloc<void> >::String(const TSource&) [with TSource = seqan::Score<int, seqan::Simple>, TValue = char]'                                               
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/score/score_matrix.h:312:   instantiated from 'void seqan::loadScoreMatrix(seqan::Score<TValue, seqan::ScoreMatrix<TSequenceValue, TSpec> >&, TString&) [with TValue = int, TSequenceValue = seqan::SimpleType<unsigned char, seqan::_AminoAcid>, TSpec = seqan::_Blosum62, TString = const seqan::Score<int, seqan::Simple>]'                                                                                                                                                                                                                                                   
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/../../../../seqan/projects/library/seqan/score/score_matrix.h:92:   instantiated from 'seqan::Score<TValue, seqan::ScoreMatrix<TSequenceValue, TSpec> >::Score(const TString&, TValue) [with TString = seqan::Score<int, seqan::Simple>, TValue = int, TSequenceValue = seqan::SimpleType<unsigned char, seqan::_AminoAcid>, TSpec = seqan::_Blosum62]'                                                                                                                                                                                                                                                                   
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/outputFormat_withBlast.h:1132:   instantiated from 'void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<const seqan::Tag<seqan::Default_> > >&, std::map<unsigned int, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int>, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int> > > >&, const TReads&, TCounts&, const TReadNames&, std::string, std::string, seqan::RazerSOptions<TSpec>&) [with TMatches = seqan::String<seqan::ReadMatch<int>, seqan::Alloc<void> >, TGenomeNames = seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<const seqan::Tag<seqan::Default_> > >, TReads = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5Q>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, TReadNames = seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<const seqan::Tag<seqan::Default_> > >, TCounts = seqan::String<seqan::String<short unsigned int, seqan::Alloc<void> >, seqan::Alloc<void> >, TSpec = seqan::RazerBlastSSpec<false, false>]'
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/razer_blast_s.cpp:191:   instantiated from 'int mapReads(const char*, const char**, const char*, seqan::RazerSOptions<TSpec>&) [with TSpec = seqan::RazerBlastSSpec<false, false>]'
/home/hannes/devel/seqan/teaching/master/hauswedell/razerblasts/razer_blast_s.cpp:1636:   instantiated from here
/usr/include/c++/4.2/bits/stl_algobase.h:283: error: cannot convert 'seqan::Score<int, seqan::Simple>' to 'char' in assignment
gmake[2]: *** [CMakeFiles/razerblasts.dir/razer_blast_s.cpp.o] Fehler 1
gmake[1]: *** [CMakeFiles/razerblasts.dir/all] Fehler 2
gmake: *** [all] Fehler 2