アライメント

gistfile1.cpp

#include <iostream>
#include <string>

#include <seqan/sequence.h>
#include <seqan/align.h>

using namespace seqan;

int main ()
{
    typedef String <char> TSequence;
    typedef Align<TSequence,ArrayGaps> TAlign; 
    typedef Row<TAlign>::Type TRow;
    
    TSequence seq1 = "LVLGEGPHLANGSARGLSQRKRPLEEGNKGHGHSKFRPKKRRKPQGPILP";
    TSequence seq2 = "AVLGEGPHLANGSARGLSCRKRPLEEGNKGHGHSKFRPKKRRKPQGPILP";
    TAlign align;
        
    resize(rows(align), 2);
    assignSource(row(align,0), seq1);
    assignSource(row(align,1), seq2);
    
    ::std::cout << align;
    TRow &row1 = row(align, 0);
    TRow &row2 = row(align, 1);
    
    insertGap(row1, 2);
    insertGap(row2, 5);
    
    ::std::cout << align;
    
    ::std::cout << ::std::endl << "ViewToSource1";
    
    for ( unsigned i = 0; i <length(row1); i++ ) {
        ::std::cout << toSourcePosition(row1, i)<<",";
        ::std::cout << ::std::endl << "ViewToSource2";
        
        for ( unsigned i = 0; i < length(row2); i++){
            ::std::cout << toViewPosition(row2, i);
            ::std::cout << ::std::endl;
            
            return  0;
        }
    }
}

/*

      0     .    :    .    :    .    :    .    :    .    : 
        LVLGEGPHLANGSARGLSQRKRPLEEGNKGHGHSKFRPKKRRKPQGPILP
         ||||||||||||||||| |||||||||||||||||||||||||||||||
        AVLGEGPHLANGSARGLSCRKRPLEEGNKGHGHSKFRPKKRRKPQGPILP


      0     .    :    .    :    .    :    .    :    .    : 
        LV-LGEGPHLANGSARGLSQRKRPLEEGNKGHGHSKFRPKKRRKPQGPIL
         |    ||||||||||||| ||||||||||||||||||||||||||||||
        AVLGE-GPHLANGSARGLSCRKRPLEEGNKGHGHSKFRPKKRRKPQGPIL

     50   
        P
        |
        P



ViewToSource10,
ViewToSource20
*/