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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/tree.h"
#include "libMUSCLE/profile.h"
#include <stdio.h>
namespace muscle {
#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.get(), g_Distance2.get(), g_Root2.get(), g_pstrDistMxFileName2.get());
#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();
}
}
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