source: branches/lib/GDE/MUSCLE/src/refinetreee.cpp

#include "muscle.h"
#include "msa.h"
#include "tree.h"
#include "profile.h"
#include <stdio.h>

#define TRACE   0

void RefineTreeE(MSA &msa, const SeqVect &v, Tree &tree, ProgNode *ProgNodes)
        {
        const unsigned uSeqCount = msa.GetSeqCount();
        if (tree.GetLeafCount() != uSeqCount)
                Quit("Refine tree, tree has different number of nodes");

        if (uSeqCount < 3)
                return;

#if     DEBUG
        ValidateMuscleIds(msa);
        ValidateMuscleIds(tree);
#endif

        const unsigned uNodeCount = tree.GetNodeCount();
        unsigned *uNewNodeIndexToOldNodeIndex= new unsigned[uNodeCount];

        Tree Tree2;
        TreeFromMSA(msa, Tree2, g_Cluster2, g_Distance2, g_Root2, g_pstrDistMxFileName2);

#if     DEBUG
        ValidateMuscleIds(Tree2);
#endif

        DiffTreesE(Tree2, tree, uNewNodeIndexToOldNodeIndex);

        unsigned uRoot = Tree2.GetRootNodeIndex();
        if (NODE_CHANGED == uNewNodeIndexToOldNodeIndex[uRoot])
                {
                MSA msa2;
                RealignDiffsE(msa, v, Tree2, tree, uNewNodeIndexToOldNodeIndex, msa2, ProgNodes);
                tree.Copy(Tree2);
                msa.Copy(msa2);
#if     DEBUG
                ValidateMuscleIds(msa2);
#endif
                }

        delete[] uNewNodeIndexToOldNodeIndex;

        SetCurrentAlignment(msa);
        ProgressStepsDone();
        }