source: branches/profile/GDE/MUSCLE/src/profile.cpp

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

bool TreeNeededForWeighting(SEQWEIGHT s)
        {
        switch (s)
                {
        case SEQWEIGHT_ClustalW:
        case SEQWEIGHT_ThreeWay:
                return true;
        default:
                return false;
                }
        }

static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree)
        {
        const unsigned uSeqCount = msa.GetSeqCount();
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                msa.SetSeqId(uSeqIndex, uSeqIndex);

        if (TreeNeededForWeighting(g_SeqWeight2))
                {
                TreeFromMSA(msa, tree, g_Cluster2, g_Distance2, g_Root1);
                SetMuscleTree(tree);
                }
        return ProfileFromMSA(msa);
        }

void ProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut)
        {
        //ALPHA Alpha = ALPHA_Undefined;
        //switch (g_SeqType)
        //      {
        //case SEQTYPE_Auto:
        //      Alpha = msa1.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);

        //msa1.FixAlpha();
        //msa2.FixAlpha();

        unsigned uLength1;
        unsigned uLength2;

        uLength1 = msa1.GetColCount();
        uLength2 = msa2.GetColCount();

        Tree tree1;
        Tree tree2;
        ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);
        ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);

        PWPath Path;
        ProfPos *ProfOut;
        unsigned uLengthOut;
        Progress("Aligning profiles");
        AlignTwoProfs(Prof1, uLength1, 1.0, Prof2, uLength2, 1.0, Path, &ProfOut, &uLengthOut);

        Progress("Building output");
        AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);
        }

// Do profile-profile alignment
void Profile()
        {
        if (0 == g_pstrFileName1 || 0 == g_pstrFileName2)
                Quit("-profile needs -in1 and -in2");

        SetSeqWeightMethod(g_SeqWeight1);

        TextFile file1(g_pstrFileName1);
        TextFile file2(g_pstrFileName2);

        MSA msa1;
        MSA msa2;
        MSA msaOut;

        Progress("Reading %s", g_pstrFileName1);
        msa1.FromFile(file1);
        Progress("%u seqs %u cols", msa1.GetSeqCount(), msa1.GetColCount());

        Progress("Reading %s", g_pstrFileName2);
        msa2.FromFile(file2);
        Progress("%u seqs %u cols", msa2.GetSeqCount(), msa2.GetColCount());

        ALPHA Alpha = ALPHA_Undefined;
        switch (g_SeqType)
                {
        case SEQTYPE_Auto:
                Alpha = msa1.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 seq type");
                }
        SetAlpha(Alpha);

        msa1.FixAlpha();
        msa2.FixAlpha();

        SetPPScore();
        if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
                SetPPScore(PPSCORE_SPN);

        const unsigned uSeqCount1 = msa1.GetSeqCount();
        const unsigned uSeqCount2 = msa2.GetSeqCount();
        const unsigned uSumSeqCount = uSeqCount1 + uSeqCount2;
        MSA::SetIdCount(uSumSeqCount);

        ProfileProfile(msa1, msa2, msaOut);

        Progress("Writing output");
        MuscleOutput(msaOut);
        }