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#include "muscle.h"
#include "tree.h"
#include "seqvect.h"
#include "profile.h"
#include "msa.h"
#include "pwpath.h"
#include "distfunc.h"
#include "textfile.h"
#include "estring.h"
#define TRACE 0
#define VALIDATE 0
#define TRACE_LENGTH_DELTA 0
ProgNode *ProgressiveAlignE(const SeqVect &v, const Tree &GuideTree, MSA &a)
{
assert(GuideTree.IsRooted());
#if TRACE
Log("GuideTree:\n");
GuideTree.LogMe();
#endif
const unsigned uSeqCount = v.Length();
const unsigned uNodeCount = 2*uSeqCount - 1;
const unsigned uIterCount = uSeqCount - 1;
WEIGHT *Weights = new WEIGHT[uSeqCount];
CalcClustalWWeights(GuideTree, Weights);
ProgNode *ProgNodes = new ProgNode[uNodeCount];
unsigned uJoin = 0;
unsigned uTreeNodeIndex = GuideTree.FirstDepthFirstNode();
SetProgressDesc("Align node");
do
{
if (GuideTree.IsLeaf(uTreeNodeIndex))
{
if (uTreeNodeIndex >= uNodeCount)
Quit("TreeNodeIndex=%u NodeCount=%u\n", uTreeNodeIndex, uNodeCount);
ProgNode &Node = ProgNodes[uTreeNodeIndex];
unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);
if (uId >= uSeqCount)
Quit("Seq index out of range");
const Seq &s = *(v[uId]);
Node.m_MSA.FromSeq(s);
Node.m_MSA.SetSeqId(0, uId);
Node.m_uLength = Node.m_MSA.GetColCount();
Node.m_Weight = Weights[uId];
// TODO: Term gaps settable
Node.m_Prof = ProfileFromMSA(Node.m_MSA, g_scoreGapOpen, true);
Node.m_EstringL = 0;
Node.m_EstringR = 0;
#if TRACE
Log("Leaf id=%u\n", uId);
Log("MSA=\n");
Node.m_MSA.LogMe();
Log("Profile (from MSA)=\n");
ListProfile(Node.m_Prof, Node.m_uLength, &Node.m_MSA);
#endif
}
else
{
Progress(uJoin, uSeqCount - 1);
++uJoin;
const unsigned uMergeNodeIndex = uTreeNodeIndex;
ProgNode &Parent = ProgNodes[uMergeNodeIndex];
const unsigned uLeft = GuideTree.GetLeft(uTreeNodeIndex);
const unsigned uRight = GuideTree.GetRight(uTreeNodeIndex);
ProgNode &Node1 = ProgNodes[uLeft];
ProgNode &Node2 = ProgNodes[uRight];
#if TRACE
Log("AlignTwoMSAs:\n");
#endif
AlignTwoProfs(
Node1.m_Prof, Node1.m_uLength, Node1.m_Weight,
Node2.m_Prof, Node2.m_uLength, Node2.m_Weight,
Parent.m_Path,
&Parent.m_Prof, &Parent.m_uLength);
#if TRACE_LENGTH_DELTA
{
unsigned L = Node1.m_uLength;
unsigned R = Node2.m_uLength;
unsigned P = Parent.m_Path.GetEdgeCount();
unsigned Max = L > R ? L : R;
unsigned d = P - Max;
Log("LD%u;%u;%u;%u\n", L, R, P, d);
}
#endif
PathToEstrings(Parent.m_Path, &Parent.m_EstringL, &Parent.m_EstringR);
Parent.m_Weight = Node1.m_Weight + Node2.m_Weight;
#if VALIDATE
{
#if TRACE
Log("AlignTwoMSAs:\n");
#endif
PWPath TmpPath;
AlignTwoMSAs(Node1.m_MSA, Node2.m_MSA, Parent.m_MSA, TmpPath);
ProfPos *P1 = ProfileFromMSA(Node1.m_MSA, g_scoreGapOpen, true);
ProfPos *P2 = ProfileFromMSA(Node2.m_MSA, g_scoreGapOpen, true);
unsigned uLength = Parent.m_MSA.GetColCount();
ProfPos *TmpProf = ProfileFromMSA(Parent.m_MSA, g_scoreGapOpen, true);
#if TRACE
Log("Node1 MSA=\n");
Node1.m_MSA.LogMe();
Log("Node1 prof=\n");
ListProfile(Node1.m_Prof, Node1.m_MSA.GetColCount(), &Node1.m_MSA);
Log("Node1 prof (from MSA)=\n");
ListProfile(P1, Node1.m_MSA.GetColCount(), &Node1.m_MSA);
AssertProfsEq(Node1.m_Prof, Node1.m_uLength, P1, Node1.m_MSA.GetColCount());
Log("Node2 prof=\n");
ListProfile(Node2.m_Prof, Node2.m_MSA.GetColCount(), &Node2.m_MSA);
Log("Node2 MSA=\n");
Node2.m_MSA.LogMe();
Log("Node2 prof (from MSA)=\n");
ListProfile(P2, Node2.m_MSA.GetColCount(), &Node2.m_MSA);
AssertProfsEq(Node2.m_Prof, Node2.m_uLength, P2, Node2.m_MSA.GetColCount());
TmpPath.AssertEqual(Parent.m_Path);
Log("Parent MSA=\n");
Parent.m_MSA.LogMe();
Log("Parent prof=\n");
ListProfile(Parent.m_Prof, Parent.m_uLength, &Parent.m_MSA);
Log("Parent prof (from MSA)=\n");
ListProfile(TmpProf, Parent.m_MSA.GetColCount(), &Parent.m_MSA);
#endif // TRACE
AssertProfsEq(Parent.m_Prof, Parent.m_uLength,
TmpProf, Parent.m_MSA.GetColCount());
delete[] P1;
delete[] P2;
delete[] TmpProf;
}
#endif // VALIDATE
Node1.m_MSA.Clear();
Node2.m_MSA.Clear();
// Don't delete profiles, may need them for tree refinement.
//delete[] Node1.m_Prof;
//delete[] Node2.m_Prof;
//Node1.m_Prof = 0;
//Node2.m_Prof = 0;
}
uTreeNodeIndex = GuideTree.NextDepthFirstNode(uTreeNodeIndex);
}
while (NULL_NEIGHBOR != uTreeNodeIndex);
ProgressStepsDone();
if (g_bBrenner)
MakeRootMSABrenner((SeqVect &) v, GuideTree, ProgNodes, a);
else
MakeRootMSA(v, GuideTree, ProgNodes, a);
#if VALIDATE
{
unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
const ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];
AssertMSAEq(a, RootProgNode.m_MSA);
}
#endif
return ProgNodes;
}
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