source: branches/nameserver/GDE/MUSCLE/src/refinetree.cpp

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

void RefineTree(MSA &msa, Tree &tree)
        {
        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

        unsigned *IdToDiffsLeafNodeIndex = new unsigned[uSeqCount];
        unsigned uDiffsCount = uSeqCount;
        Tree Tree2;
        for (unsigned uIter = 0; uIter < g_uMaxTreeRefineIters; ++uIter)
                {
                TreeFromMSA(msa, Tree2, g_Cluster2, g_Distance2, g_Root2, g_pstrDistMxFileName2);

#if     DEBUG
                ValidateMuscleIds(Tree2);
#endif

                Tree Diffs;
                DiffTrees(Tree2, tree, Diffs, IdToDiffsLeafNodeIndex);

                tree.Copy(Tree2);

                const unsigned uNewDiffsNodeCount = Diffs.GetNodeCount();
                const unsigned uNewDiffsCount = (uNewDiffsNodeCount - 1)/2;

                if (0 == uNewDiffsCount || uNewDiffsCount >= uDiffsCount)
                        {
                        ProgressStepsDone();
                        break;
                        }
                uDiffsCount = uNewDiffsCount;

                MSA msa2;
                RealignDiffs(msa, Diffs, IdToDiffsLeafNodeIndex, msa2);

#if     DEBUG
                ValidateMuscleIds(msa2);
#endif

                msa.Copy(msa2);
                SetCurrentAlignment(msa);
                }

        delete[] IdToDiffsLeafNodeIndex;
        }