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#include "multaln.h"
#define TRACE 0
#define VALIDATE 0
static bool g_bStable = true;
static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
{
short *esA;
short *esB;
PathToEstrings(Path, &esA, &esB);
const unsigned uSeqLength = s.Length();
const unsigned uEdgeCount = Path.GetEdgeCount();
sOut.Clear();
sOut.SetName(s.GetName());
unsigned uPos = 0;
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &Edge = Path.GetEdge(uEdgeIndex);
char cType = Edge.cType;
if (bRight)
{
if (cType == 'I')
cType = 'D';
else if (cType == 'D')
cType = 'I';
}
switch (cType)
{
case 'M':
sOut.AppendChar(s[uPos++]);
break;
case 'D':
sOut.AppendChar('-');
break;
case 'I':
sOut.AppendChar(s[uPos++]);
break;
default:
Quit("PathSeq, invalid edge type %c", cType);
}
}
}
#if VALIDATE
static void MakeRootSeq(const Seq &s, const Tree &GuideTree, unsigned uLeafNodeIndex,
const ProgNode Nodes[], Seq &sRoot)
{
sRoot.Copy(s);
unsigned uNodeIndex = uLeafNodeIndex;
for (;;)
{
unsigned uParent = GuideTree.GetParent(uNodeIndex);
if (NULL_NEIGHBOR == uParent)
break;
bool bRight = (GuideTree.GetLeft(uParent) == uNodeIndex);
uNodeIndex = uParent;
const PWPath &Path = Nodes[uNodeIndex].m_Path;
Seq sTmp;
PathSeq(sRoot, Path, bRight, sTmp);
sRoot.Copy(sTmp);
}
}
#endif // VALIDATE
static short *MakeRootSeqE(const Seq &s, const Tree &GuideTree, unsigned uLeafNodeIndex,
const ProgNode Nodes[], Seq &sRoot, short *Estring1, short *Estring2)
{
short *EstringCurr = Estring1;
short *EstringNext = Estring2;
const unsigned uSeqLength = s.Length();
EstringCurr[0] = uSeqLength;
EstringCurr[1] = 0;
unsigned uNodeIndex = uLeafNodeIndex;
for (;;)
{
unsigned uParent = GuideTree.GetParent(uNodeIndex);
if (NULL_NEIGHBOR == uParent)
break;
bool bRight = (GuideTree.GetLeft(uParent) == uNodeIndex);
uNodeIndex = uParent;
const PWPath &Path = Nodes[uNodeIndex].m_Path;
const short *EstringNode = bRight ?
Nodes[uNodeIndex].m_EstringL : Nodes[uNodeIndex].m_EstringR;
MulEstrings(EstringCurr, EstringNode, EstringNext);
#if TRACE
Log("\n");
Log("Curr=");
LogEstring(EstringCurr);
Log("\n");
Log("Node=");
LogEstring(EstringNode);
Log("\n");
Log("Prod=");
LogEstring(EstringNext);
Log("\n");
#endif
short *EstringTmp = EstringNext;
EstringNext = EstringCurr;
EstringCurr = EstringTmp;
}
EstringOp(EstringCurr, s, sRoot);
#if TRACE
Log("Root estring=");
LogEstring(EstringCurr);
Log("\n");
Log("Root seq=");
sRoot.LogMe();
#endif
return EstringCurr;
}
static unsigned GetFirstNodeIndex(const Tree &tree)
{
if (g_bStable)
return 0;
return tree.FirstDepthFirstNode();
}
static unsigned GetNextNodeIndex(const Tree &tree, unsigned uPrevNodeIndex)
{
if (g_bStable)
{
const unsigned uNodeCount = tree.GetNodeCount();
unsigned uNodeIndex = uPrevNodeIndex;
for (;;)
{
++uNodeIndex;
if (uNodeIndex >= uNodeCount)
return NULL_NEIGHBOR;
if (tree.IsLeaf(uNodeIndex))
return uNodeIndex;
}
}
unsigned uNodeIndex = uPrevNodeIndex;
for (;;)
{
uNodeIndex = tree.NextDepthFirstNode(uNodeIndex);
if (NULL_NEIGHBOR == uNodeIndex || tree.IsLeaf(uNodeIndex))
return uNodeIndex;
}
}
void MakeRootMSA(const SeqVect &v, const Tree &GuideTree, ProgNode Nodes[],
MSA &Aln)
{
assert(v.GetSeqCount() > 1);
#if TRACE
Log("MakeRootMSA Tree=");
GuideTree.LogMe();
#endif
const unsigned uSeqCount = v.GetSeqCount();
unsigned uColCount = uInsane;
unsigned uSeqIndex = 0;
const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
const unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
const PWPath &RootPath = Nodes[uRootNodeIndex].m_Path;
const unsigned uRootColCount = RootPath.GetEdgeCount();
const unsigned uEstringSize = uRootColCount + 1;
short *Estring1 = new short[uEstringSize];
short *Estring2 = new short[uEstringSize];
unsigned uTreeNodeIndex = GetFirstNodeIndex(GuideTree);
do
{
unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);
const Seq &s = *(v[uId]);
Seq sRootE;
short *es = MakeRootSeqE(s, GuideTree, uTreeNodeIndex, Nodes, sRootE,
Estring1, Estring2);
Nodes[uTreeNodeIndex].m_EstringL = EstringNewCopy(es);
#if VALIDATE
Seq sRoot;
MakeRootSeq(s, GuideTree, uTreeNodeIndex, Nodes, sRoot);
if (!sRoot.Eq(sRootE))
{
Log("sRoot=");
sRoot.LogMe();
Log("sRootE=");
sRootE.LogMe();
Quit("Root seqs differ");
}
#endif
#if TRACE
Log("MakeRootSeq=\n");
sRoot.LogMe();
#endif
if (uInsane == uColCount)
{
uColCount = sRootE.Length();
Aln.SetSize(uSeqCount, uColCount);
}
else
{
assert(uColCount == sRootE.Length());
}
Aln.SetSeqName(uSeqIndex, s.GetName());
Aln.SetSeqId(uSeqIndex, uId);
for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
Aln.SetChar(uSeqIndex, uColIndex, sRootE[uColIndex]);
++uSeqIndex;
uTreeNodeIndex = GetNextNodeIndex(GuideTree, uTreeNodeIndex);
}
while (NULL_NEIGHBOR != uTreeNodeIndex);
delete[] Estring1;
delete[] Estring2;
assert(uSeqIndex == uSeqCount);
}
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