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#include "pilercr.h"
#include "sw.h"
static double CmpSeqsFwd(const Seq &s1, const Seq &s2)
{
unsigned Start1;
unsigned Start2;
std::string Path;
score_t Score = SW(s1, s2, &Start1, &Start2, Path);
if (Score <= 0)
return 0;
return GetFractId(s1, s1, Start1, Start2, Path);
}
static double CmpSeqsBwd(const Seq &s1, const Seq &s2)
{
unsigned Start1;
unsigned Start2;
std::string Path;
Seq s1rev;
s1rev.Copy(s1);
s1rev.RevComp();
score_t Score = SW(s1rev, s2, &Start1, &Start2, Path);
if (Score <= 0)
return 0;
return GetFractId(s1rev, s1, Start1, Start2, Path);
}
static double CmpSeqs(const Seq &s1, const Seq &s2)
{
double IdFwd = CmpSeqsFwd(s1, s2);
if (IdFwd > 0.899)
return IdFwd;
return CmpSeqsBwd(s1, s2);
}
void SaveSeqs(FILE *f, const std::vector<ArrayAln *> AAVec)
{
bool TrimSeqs = FlagOpt("trimseqs");
const size_t ArrayCount = AAVec.size();
for (size_t ArrayIndex = 0; ArrayIndex < ArrayCount; ++ArrayIndex)
{
const ArrayAln &AA = *(AAVec[ArrayIndex]);
const Seq &s = AA.ConsSeq;
if (TrimSeqs)
{
bool Discard = false;
for (size_t ArrayIndex2 = 0; ArrayIndex2 < ArrayIndex; ++ArrayIndex2)
{
const ArrayAln &AA2 = *(AAVec[ArrayIndex2]);
const Seq &s2 = AA2.ConsSeq;
if (CmpSeqs(s, s2) > 0.899)
{
Discard = true;
break;
}
}
if (Discard)
continue;
}
int ArrayLength = GetArrayLength(AA);
char *Label;
int LocalPos = GlobalToLocal(AA.Pos, &Label);
fprintf(f, ">%s[Array%d;Pos=%d]", Label, AA.Id, LocalPos + 1);
unsigned L = s.Length();
for (unsigned i = 0; i < L; ++i)
{
if (i%60 == 0)
fprintf(f, "\n");
fprintf(f, "%c", s[i]);
}
fprintf(f, "\n");
}
}
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