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#include "pilercr.h"
#include "sw.h"
static void AllocAA(ArrayAln &AA, int RepeatCount)
{
for (int i = 0; i < RepeatCount; ++i)
{
AA.LeftFlanks.push_back(*new std::string);
AA.Repeats.push_back(*new std::string);
AA.Spacers.push_back(*new std::string);
}
}
static ArrayAln *CopyAA(const ArrayAln &AA)
{
ArrayAln *NewAA = new ArrayAln;
*NewAA = AA;
return NewAA;
}
static bool EqAA(const ArrayAln &AA1, const ArrayAln &AA2)
{
if (AA1.Id != AA2.Id)
return false;
if (AA1.Pos != AA2.Pos)
return false;
const size_t RepeatCount = AA1.Repeats.size();
if (RepeatCount != AA2.Repeats.size())
return false;
for (unsigned RepeatIndex = 0; RepeatIndex < RepeatCount; ++RepeatIndex)
{
if (AA1.Repeats != AA2.Repeats)
return false;
if (AA1.LeftFlanks != AA2.LeftFlanks)
return false;
if (AA1.Spacers != AA2.Spacers)
return false;
}
return true;
}
static size_t UngappedLength(const std::string &s)
{
size_t Length = 0;
for (size_t i = 0; i < s.size(); ++i)
if (s[i] != '-')
++Length;
return Length;
}
int GetArrayLength(const ArrayAln &AA)
{
size_t Length = 0;
const size_t RepeatCount = AA.Repeats.size();
for (size_t RepeatIndex = 0; RepeatIndex < RepeatCount; ++RepeatIndex)
{
size_t RepeatLength = UngappedLength(AA.Repeats[RepeatIndex]);
Length += RepeatLength;
if (RepeatIndex != RepeatCount - 1)
{
size_t SpacerLength = AA.Spacers[RepeatIndex].size();
Length += SpacerLength;
}
}
return (int) Length;
}
void AlignArray(const ArrayData &AD, ArrayAln &AA)
{
const IntVec &PileIndexes = AD.PileIndexes;
std::vector<RowData> Rows;
size_t RowCount = PileIndexes.size();
Rows.resize(RowCount);
AllocAA(AA, (int) RowCount);
AA.Id = AD.Id;
const unsigned ConsSeqLen = AD.ConsSeq.Length();
char *ConsSeqStr = all(char, ConsSeqLen+1);
AD.ConsSeq.ToString(ConsSeqStr, ConsSeqLen+1);
SeqVect HitSeqs;
int RowIndex = 0;
for_CIntVec(PileIndexes, p)
{
RowData &Row = Rows[RowIndex++];
int PileIndex = *p;
assert(PileIndex >= 0 && PileIndex < g_PileCount);
Seq *PileSeq = new Seq;
int Lo;
int Hi;
PileToSeq(g_Piles, PileIndex, *PileSeq, &Lo, &Hi);
unsigned PileSeqLen = PileSeq->Length();
char *PileSeqStr = all(char, PileSeqLen+1);
PileSeq->ToString(PileSeqStr, PileSeqLen+1);
std::string Path;
unsigned PileOffset;
unsigned ConsOffset;
SWSimple(PileSeqStr, PileSeqLen, ConsSeqStr, ConsSeqLen, &PileOffset,
&ConsOffset, Path);
Row.PctId = GetPctId(PileSeqStr+PileOffset, ConsSeqStr+ConsOffset, Path.c_str());
const PileData &Pile = g_Piles[PileIndex];
Row.RepeatLo = Lo + PileOffset;
int RepeatLength = PathALength(Path.c_str());
Row.RepeatLength = RepeatLength;
Seq *HitSeq = new Seq;
const int ToPos = PileOffset + RepeatLength - 1;
for (int Pos = PileOffset; Pos <= ToPos; ++Pos)
HitSeq->push_back(PileSeqStr[Pos]);
HitSeq->SetName("hit");
HitSeq->SetId(0);
HitSeqs.push_back(HitSeq);
}
freemem(ConsSeqStr);
ConsSeqStr = 0;
Seq *ConsSeq = new Seq;
ConsSeq->Copy(AD.ConsSeq);
HitSeqs.push_back(ConsSeq);
MSA Aln;
MultipleAlign(HitSeqs, Aln);
if (g_LogAlns)
{
Out("Refined alignment array %d:\n", AD.Id);
Aln.LogMe();
Out("\n");
}
const unsigned ColCount = Aln.GetColCount();
int SumSpacerLengths = 0;
for (size_t RowIndex = 0; RowIndex < RowCount; ++RowIndex)
{
const RowData &Row = Rows[RowIndex];
char *Label;
int LocalRepeatLo = GlobalToLocal(Row.RepeatLo, &Label);
int NextLo = -1;
int Hi = -1;
int SpacerLength = -1;
if (RowIndex + 1 != RowCount)
{
NextLo = Rows[RowIndex+1].RepeatLo;
Hi = Row.RepeatLo + Row.RepeatLength - 1;
SpacerLength = NextLo - Hi;
if (SpacerLength < 4)
{
AA.Repeats.clear();
AA.Spacers.clear();
AA.LeftFlanks.clear();
return;
}
}
// Left flank
const ContigData &Contig = GlobalPosToContig(Row.RepeatLo);
int ContigFrom = Contig.From;
int ContigTo = ContigFrom + Contig.Length - 1;
int LeftFlankStartPos = Row.RepeatLo - g_FlankSize;
int LeftFlankBlanks = 0;
if (LeftFlankStartPos < ContigFrom)
{
LeftFlankStartPos = ContigFrom;
LeftFlankBlanks = g_FlankSize - (Row.RepeatLo - ContigFrom);
}
std::string &LeftFlank = AA.LeftFlanks[RowIndex];
for (int i = 0; i < LeftFlankBlanks; ++i)
LeftFlank += ' ';
for (int Pos = LeftFlankStartPos; Pos < Row.RepeatLo; ++Pos)
LeftFlank += g_SeqQ[Pos];
// Repeat
std::string &Repeat = AA.Repeats[RowIndex];
for (unsigned Col = 0; Col < ColCount; ++Col)
Repeat += Aln.GetChar((unsigned) RowIndex, Col);
// Spacer
std::string &Spacer = AA.Spacers[RowIndex];
if (RowIndex + 1 == RowCount)
{
int RightFlankPos = Row.RepeatLo + Row.RepeatLength;
int ToPos = RightFlankPos + 9;
if (ToPos >= ContigTo)
ToPos = ContigTo;
for (int Pos = RightFlankPos; Pos <= ToPos; ++Pos)
Spacer += g_SeqQ[Pos];
}
else
{
for (int Pos = Hi + 1; Pos < NextLo; ++Pos)
Spacer += g_SeqQ[Pos];
}
}
AA.Pos = Rows[0].RepeatLo;
FixBounds(AA);
GetConsSeqAA(AA, AA.AlignedConsSeq);
AA.ConsSeq.Copy(AA.AlignedConsSeq);
StripBlanksAndGaps(AA.ConsSeq);
}
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