source: trunk/GDE/MUSCLE/src/fastdist.cpp

#include "muscle.h"
#include "distfunc.h"
#include "seqvect.h"

void DistPWScoreDist(const SeqVect &v, DistFunc &DF);

void DistUnaligned(const SeqVect &v, DISTANCE DistMethod, DistFunc &DF)
        {
        const unsigned uSeqCount = v.Length();

        switch (DistMethod)
                {
        case DISTANCE_Kmer6_6:
                DistKmer6_6(v, DF);
                break;

        case DISTANCE_Kmer20_3:
                DistKmer20_3(v, DF);
                break;

        case DISTANCE_Kmer20_4:
                FastDistKmer(v, DF);
                break;

        case DISTANCE_Kbit20_3:
                DistKbit20_3(v, DF);
                break;

        case DISTANCE_Kmer4_6:
                DistKmer4_6(v, DF);
                break;

        case DISTANCE_PWKimura:
                DistPWKimura(v, DF);
                break;

        case DISTANCE_PWScoreDist:
                DistPWScoreDist(v, DF);
                break;

        default:
                Quit("DistUnaligned, unsupported distance method %d", DistMethod);
                }

//      const char **SeqNames = (const char **) malloc(uSeqCount*sizeof(char *));
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                {
                const Seq &s = *(v[uSeqIndex]);

                const char *ptrName = s.GetName();
                unsigned uId = s.GetId();

                DF.SetName(uSeqIndex, ptrName);
                DF.SetId(uSeqIndex, uId);
                }
        }