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#include "pilercr.h"
#include "multaln.h"
#define TRACE 0
void PileToSeq(const std::vector<PileData> &Piles, int PileIndex, Seq &s,
int *ptrPosLo, int *ptrPosHi)
{
const int PileCount = (int) Piles.size();
assert(PileIndex >= 0 && PileIndex < PileCount);
const PileData &Pile = Piles[PileIndex];
const ContigData &Contig = GlobalPosToContig(Pile.Lo);
int Lo = Pile.Lo - g_HitPadding;
int Hi = Pile.Hi + g_HitPadding;
if (Lo < Contig.From)
Lo = Contig.From;
int ContigTo = Contig.From + Contig.Length - 1;
if (Hi >= ContigTo)
Hi = ContigTo;
int Length = Hi - Lo + 1;
assert(Length > 0);
int n = (int) strlen(Contig.Label) + 64;
char *Name = all(char, n);
sprintf(Name, "%s:%d-%d", Contig.Label, Lo, Hi);
s.SetName(Name);
freemem(Name);
s.reserve(Length);
for (int Pos = Lo; Pos <= Hi; ++Pos)
s.push_back(g_SeqQ[Pos]);
*ptrPosLo = Lo;
*ptrPosHi = Hi;
}
static void OutputArrayHeaderSim()
{
Out("\n\n");
Out("Array Sequence Position Length # Copies Repeat Spacer + Consensus\n");
Out("===== ================ ========== ========== ======== ====== ====== = =========\n");
}
static void OutputArrayHeaderPos()
{
Out("\n");
Out("Array Sequence Position Length # Copies Repeat Spacer Distance Consensus\n");
Out("===== ================ ========== ========== ======== ====== ====== ========== =========\n");
}
static void OutputArraySummaryLineSim(const ArrayAln &AA)
{
const ContigData &Contig = GlobalPosToContig(AA.Pos);
const char *Label = Contig.Label;
int ArrayLength = GetArrayLength(AA);
int RepeatCount = (int) AA.Repeats.size();
int AvgRepeatLength = GetAvgRepeatLength(AA);
int AvgSpacerLength = GetAvgSpacerLength(AA);
char Strand = (AA.ClusterRevComp ? '-' : '+');
char *TmpLabel;
int LocalLo = GlobalToLocal(AA.Pos, &TmpLabel);
Out("%5d %16.16s %10d %10d %8d %6d %6d %c ",
AA.Id, Label, LocalLo + 1, ArrayLength, RepeatCount, AvgRepeatLength,
AvgSpacerLength, Strand);
const Seq &s = AA.AlignedConsSeq;
int Len = s.Length();
for (int i = 0; i < Len; ++i)
Out("%c", s.GetChar(i));
Out("\n");
}
static void OutputArraySummaryLinePos(const ArrayAln &AA, int Distance)
{
const ContigData &Contig = GlobalPosToContig(AA.Pos);
const char *Label = Contig.Label;
int ArrayLength = GetArrayLength(AA);
int RepeatCount = (int) AA.Repeats.size();
int AvgRepeatLength = GetAvgRepeatLength(AA);
int AvgSpacerLength = GetAvgSpacerLength(AA);
char *TmpLabel;
int LocalLo = GlobalToLocal(AA.Pos, &TmpLabel);
Out("%5d %16.16s %10d %10d %8d %6d %6d ",
AA.Id, Label, LocalLo + 1, ArrayLength, RepeatCount, AvgRepeatLength, AvgSpacerLength);
if (Distance == -1)
Out(" ");
else
Out("%10d ", Distance);
const Seq &s = AA.ConsSeq;
int Len = s.Length();
for (int i = 0; i < Len; ++i)
Out("%c", s.GetChar(i));
Out("\n");
}
static void OutputArrayFooter(const Seq &ConsSymbols)
{
for (int i = 0; i < (5+2+16+2+10+2+10+8+2+6+2+6+2+2+3); i++)
Out(" ");
int Len = ConsSymbols.Length();
for (int i = 0; i < Len; ++i)
Out("%c", ConsSymbols.GetChar(i));
Out("\n");
}
static bool ByPos(const ArrayAln *A1, const ArrayAln *A2)
{
return A1->Pos < A2->Pos;
}
void OutArrays(std::vector<ArrayAln *> &AAVec)
{
IntVecVec Clusters;
ClusterConsRC(AAVec, Clusters);
const size_t ClusterCount = Clusters.size();
Progress("Creating report");
// Detail report
Out("\n");
Out("\n");
Out("DETAIL REPORT\n");
Out("\n");
const size_t ArrayCount = AAVec.size();
for (size_t ArrayIndex = 0; ArrayIndex < ArrayCount; ++ArrayIndex)
{
const ArrayAln &AA = *(AAVec[ArrayIndex]);
OutDetailAA(AA);
}
// Summary reports
Out("\n");
Out("\n");
Out("SUMMARY BY SIMILARITY\n");
Out("\n");
OutputArrayHeaderSim();
for (size_t ClusterIndex = 0; ClusterIndex < ClusterCount; ++ClusterIndex)
{
const IntVec &Cluster = Clusters[ClusterIndex];
Seq ConsSymbols;
AlignCluster(AAVec, Cluster, ConsSymbols);
const size_t ArrayCount = Cluster.size();
for (size_t i = 0; i < ArrayCount; ++i)
{
unsigned ArrayIndex = Cluster[i];
ArrayAln &AA = *(AAVec[ArrayIndex]);
if (ArrayCount == 1)
AA.ClusterRevComp = false;
OutputArraySummaryLineSim(AA);
}
if (ArrayCount > 1)
OutputArrayFooter(ConsSymbols);
Out("\n");
}
Out("\n");
Out("\n");
Out("SUMMARY BY POSITION\n");
Out("\n");
std::sort(AAVec.begin(), AAVec.end(), ByPos);
int LastContigIndex = -1;
int LastPos = -1;
for (size_t ArrayIndex = 0; ArrayIndex < ArrayCount; ++ArrayIndex)
{
const ArrayAln &AA = *(AAVec[ArrayIndex]);
int Pos = AA.Pos;
int ContigIndex = GlobalPosToContigIndex(Pos);
if (ContigIndex != LastContigIndex)
{
LastPos = -1;
const ContigData &Contig = GlobalPosToContig(Pos);
Out("\n");
Out("\n");
Out(">");
Out(Contig.Label);
Out("\n");
OutputArrayHeaderPos();
LastContigIndex = Contig.Index;
}
int Distance = -1;
if (ArrayIndex > 0)
Distance = DistanceAA(*(AAVec[ArrayIndex-1]), AA);
OutputArraySummaryLinePos(AA, Distance);
}
}
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