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#include "pilercr.h"
static void OutputDetailHeader(const ArrayAln &AA)
{
unsigned RepeatColCount = (unsigned) AA.Repeats[0].size();
char *Label;
GlobalToLocal(AA.Pos, &Label);
Out("\n\n");
Out("Array %d\n", AA.Id);
Out(">%s\n", Label);
Out("\n");
Out(" Pos Repeat %%id Spacer Left flank Repeat");
int Blanks = (int) RepeatColCount - 6;
for (int i = 0; i < Blanks; ++i)
Out(" ");
Out(" Spacer\n");
Out("========== ====== ====== ====== ========== ");
// 1234567890 123456 123456 123456 1234567890
for (unsigned i = 0; i < RepeatColCount; ++i)
Out("=");
Out(" ======\n");
}
int GetAvgSpacerLength(const ArrayAln &AA)
{
size_t RepeatCount = AA.Repeats.size();
size_t Sum = 0;
for (size_t RepeatIndex = 0; RepeatIndex < RepeatCount - 1; ++RepeatIndex)
Sum += AA.Spacers[RepeatIndex].size();
return (int) (Sum / (RepeatCount - 1));
}
int GetAvgRepeatLength(const ArrayAln &AA)
{
size_t RepeatCount = AA.Repeats.size();
size_t Sum = 0;
for (size_t RepeatIndex = 0; RepeatIndex < RepeatCount; ++RepeatIndex)
Sum += AA.Repeats[RepeatIndex].size();
return (int) (Sum / RepeatCount);
}
static void OutputDetailFooter(const ArrayAln &AA)
{
unsigned RepeatColCount = (unsigned) AA.Repeats[0].size();
Out("========== ====== ====== ====== ========== ");
for (unsigned i = 0; i < RepeatColCount; ++i)
Out("=");
Out("\n");
int RepeatCount = (int) AA.Repeats.size();
int RepeatLength = (int) AA.Repeats[0].size();
int SpacerLength = GetAvgSpacerLength(AA);
Out("%10d %6d %6d ",
RepeatCount, RepeatLength, SpacerLength);
assert(AA.AlignedConsSeq.size() == RepeatColCount);
for (unsigned i = 0; i < RepeatColCount; ++i)
Out("%c", AA.AlignedConsSeq[i]);
Out("\n");
}
static double GetRepeatPctId(const ArrayAln &AA, size_t RepeatIndex)
{
assert(RepeatIndex < AA.Repeats.size());
const std::string &Repeat = AA.Repeats[RepeatIndex];
const Seq &ConsSeq = AA.AlignedConsSeq;
size_t RepeatLength = Repeat.size();
assert(ConsSeq.size() == RepeatLength);
int Same = 0;
for (size_t i = 0; i < RepeatLength; ++i)
{
if (toupper(ConsSeq[i]) == toupper(Repeat[i]))
++Same;
}
return 100.0 * (double) Same / (double) RepeatLength;
}
static void OutDetailRepeat(const ArrayAln &AA, size_t RepeatIndex, int &Pos)
{
const std::string &LeftFlank = AA.LeftFlanks[RepeatIndex];
const std::string &Repeat = AA.Repeats[RepeatIndex];
const std::string &Spacer = AA.Spacers[RepeatIndex];
const Seq &ConsSeq = AA.AlignedConsSeq;
size_t LeftFlankLength = LeftFlank.size();
size_t RepeatLength = Repeat.size();
size_t SpacerLength = Spacer.size();
assert(LeftFlankLength == g_FlankSize);
double PctId = GetRepeatPctId(AA, RepeatIndex);
const ContigData &Contig = GlobalPosToContig(Pos);
const char *Label = Contig.Label;
char *TmpLabel;
int LocalLo = GlobalToLocal(Pos, &TmpLabel);
// Pos Repeat %id Spacer Left flank Repeat
// ========== ====== ====== ====== ========== ======
// 1234567890 123456 123456 123456 1234567890
Out("%10d %6d %6.1f ",
LocalLo + 1, // 1-based for user's benefit
RepeatLength,
PctId);
const size_t RepeatCount = AA.Repeats.size();
if (RepeatIndex == RepeatCount - 1)
Out(" ");
else
Out("%6d ", SpacerLength);
for (size_t i = 0; i < LeftFlankLength; ++i)
Out("%c", LeftFlank[i]);
Out(" ");
for (size_t i = 0; i < RepeatLength; ++i)
{
if (Repeat[i] == ConsSeq[i])
{
if (Repeat[i] == '-')
Out("-");
else
Out(".");
}
else
Out("%c", Repeat[i]);
}
Out(" ");
for (size_t i = 0; i < SpacerLength; ++i)
Out("%c", Spacer[i]);
Out("\n");
Pos += (int) (RepeatLength + SpacerLength);
}
void OutDetailAA(const ArrayAln &AA)
{
OutputDetailHeader(AA);
int Pos = AA.Pos;
size_t RepeatCount = AA.Repeats.size();
for (size_t RepeatIndex = 0; RepeatIndex < RepeatCount; ++RepeatIndex)
OutDetailRepeat(AA, RepeatIndex, Pos);
OutputDetailFooter(AA);
}
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