source: branches/stable/GDE/MUSCLE/src/dosp.cpp

#include "muscle.h"
#include "textfile.h"
#include "msa.h"
#include "objscore.h"
#include "tree.h"
#include "profile.h"

void DoSP()
        {
        TextFile f(g_pstrSPFileName);

        MSA a;
        a.FromFile(f);

        ALPHA Alpha = ALPHA_Undefined;
        switch (g_SeqType)
                {
        case SEQTYPE_Auto:
                Alpha = a.GuessAlpha();
                break;

        case SEQTYPE_Protein:
                Alpha = ALPHA_Amino;
                break;

        case SEQTYPE_DNA:
                Alpha = ALPHA_DNA;
                break;

        case SEQTYPE_RNA:
                Alpha = ALPHA_RNA;
                break;

        default:
                Quit("Invalid SeqType");
                }
        SetAlpha(Alpha);
        a.FixAlpha();

        SetPPScore();

        const unsigned uSeqCount = a.GetSeqCount();
        if (0 == uSeqCount)
                Quit("No sequences in input file %s", g_pstrSPFileName);

        MSA::SetIdCount(uSeqCount);
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                a.SetSeqId(uSeqIndex, uSeqIndex);

        SetSeqWeightMethod(g_SeqWeight1);
        Tree tree;
        TreeFromMSA(a, tree, g_Cluster2, g_Distance2, g_Root2);
        SetMuscleTree(tree);
        SetMSAWeightsMuscle((MSA &) a);

        SCORE SP = ObjScoreSP(a);

        Log("File=%s;SP=%.4g\n", g_pstrSPFileName, SP);
        fprintf(stderr, "File=%s;SP=%.4g\n", g_pstrSPFileName, SP);
        }