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#include "muscle.h"
#include "msa.h"
#include "tree.h"
#include "profile.h"
#include "pwpath.h"
#define TRACE 0
// Progressive alignment according to a diffs tree.
static void MakeNode(const MSA &msaIn, const Tree &Diffs, unsigned uDiffsNodeIndex,
const unsigned IdToDiffsTreeNodeIndex[], ProgNode &Node)
{
const unsigned uSeqCount = msaIn.GetSeqCount();
unsigned *Ids = new unsigned[uSeqCount];
unsigned uSeqsInDiffCount = 0;
for (unsigned uId = 0; uId < uSeqCount; ++uId)
{
if (IdToDiffsTreeNodeIndex[uId] == uDiffsNodeIndex)
{
Ids[uSeqsInDiffCount] = uId;
++uSeqsInDiffCount;
}
}
if (0 == uSeqsInDiffCount)
Quit("MakeNode: no seqs in diff");
MSASubsetByIds(msaIn, Ids, uSeqsInDiffCount, Node.m_MSA);
#if DEBUG
ValidateMuscleIds(Node.m_MSA);
#endif
DeleteGappedCols(Node.m_MSA);
delete[] Ids;
}
void RealignDiffs(const MSA &msaIn, const Tree &Diffs,
const unsigned IdToDiffsTreeNodeIndex[], MSA &msaOut)
{
assert(Diffs.IsRooted());
#if TRACE
Log("RealignDiffs\n");
Log("Diff tree:\n");
Diffs.LogMe();
#endif
const unsigned uNodeCount = Diffs.GetNodeCount();
if (uNodeCount%2 == 0)
Quit("RealignDiffs: Expected odd number of nodes");
const unsigned uMergeCount = (uNodeCount - 1)/2;
ProgNode *ProgNodes = new ProgNode[uNodeCount];
unsigned uJoin = 0;
SetProgressDesc("Refine tree");
for (unsigned uDiffsNodeIndex = Diffs.FirstDepthFirstNode();
NULL_NEIGHBOR != uDiffsNodeIndex;
uDiffsNodeIndex = Diffs.NextDepthFirstNode(uDiffsNodeIndex))
{
if (Diffs.IsLeaf(uDiffsNodeIndex))
{
assert(uDiffsNodeIndex < uNodeCount);
if (uDiffsNodeIndex >= uNodeCount)
Quit("TreeNodeIndex=%u NodeCount=%u\n", uDiffsNodeIndex, uNodeCount);
ProgNode &Node = ProgNodes[uDiffsNodeIndex];
MakeNode(msaIn, Diffs, uDiffsNodeIndex, IdToDiffsTreeNodeIndex, Node);
Node.m_uLength = Node.m_MSA.GetColCount();
}
else
{
Progress(uJoin, uMergeCount);
++uJoin;
const unsigned uMergeNodeIndex = uDiffsNodeIndex;
ProgNode &Parent = ProgNodes[uMergeNodeIndex];
const unsigned uLeft = Diffs.GetLeft(uDiffsNodeIndex);
const unsigned uRight = Diffs.GetRight(uDiffsNodeIndex);
ProgNode &Node1 = ProgNodes[uLeft];
ProgNode &Node2 = ProgNodes[uRight];
PWPath Path;
AlignTwoMSAs(Node1.m_MSA, Node2.m_MSA, Parent.m_MSA, Path);
#if TRACE
{
Log("Combined:\n");
Parent.m_MSA.LogMe();
}
#endif
Node1.m_MSA.Clear();
Node2.m_MSA.Clear();
}
}
ProgressStepsDone();
unsigned uRootNodeIndex = Diffs.GetRootNodeIndex();
const ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];
msaOut.Copy(RootProgNode.m_MSA);
#if DEBUG
AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);
#endif
delete[] ProgNodes;
ProgNodes = 0;
}
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