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#include "pilercr.h"
#define TRACE 0
// ClusterConsRC:
// Cluster consensus sequences considering the sequence
// or its reverse complement, but not both.
// Best entry is one with largest number
// of distances smaller than the threshold
// Indexes into DistFunc are 2i for i'th array,
// 2i+2 for reverse complement of i'th array.
static int FindBest(std::vector<ArrayAln *> &AAVec, const DistFunc &DF,
BoolVec &Done, IntVec &Cluster)
{
Cluster.clear();
const int ArrayCount = (int) AAVec.size();
const int Count = DF.GetCount();
assert(Count == 2*ArrayCount);
IntVec NrUnderThresh;
for (int i = 0; i < Count; ++i)
NrUnderThresh.push_back(0);
for (int i = 0; i < Count; ++i)
{
if (Done[i/2])
continue;
for (int j = 0; j < Count; ++j)
{
if (i == j || Done[j/2])
continue;
#if TRACE
Log("Dist(");
AAVec[i/2]->ConsSeq.LogMeSeqOnly();
if (i%2 == 1)
Log("-");
else
Log("+");
Log(",");
AAVec[j/2]->ConsSeq.LogMeSeqOnly();
if (j%2 == 1)
Log("-");
else
Log("+");
Log(") = %.1f", DF.GetDist(i, j));
#endif
if (DF.GetDist(i, j) <= g_ClusterMaxDist)
{
#if TRACE
Log(" Under\n");
#endif
++(NrUnderThresh[i]);
}
else
{
#if TRACE
Log(" Over\n");
#endif
;
}
}
}
#if TRACE
{
Log("FindBest:\n");
for (int i = 0; i < Count; ++i)
Log(" i=%d Done=%c NrUnder=%d\n", i, Done[i] ? 'T' : 'F', NrUnderThresh[i]);
}
#endif
int Best = -1;
unsigned BestCount = 0;
for (int i = 0; i < Count; ++i)
{
if (NrUnderThresh[i] > BestCount)
{
Best = i;
BestCount = NrUnderThresh[i];
}
}
if (Best >= 0)
{
for (int i = 0; i < Count; ++i)
{
if (Done[i/2])
continue;
if (DF.GetDist(Best, i) <= g_ClusterMaxDist)
{
ArrayAln &AA = *(AAVec[i/2]);
AA.ClusterRevComp = (i%2 == 1);
Done[i/2] = true;
Cluster.push_back(i/2);
}
}
}
if (Cluster.size() == 0)
return -1;
return Best;
}
// Enforce convention that first array is + strand.
static void FixStrand(std::vector<ArrayAln *> &AAVec, IntVec &Cluster)
{
int First = Cluster.front();
const ArrayAln &FirstAA = *(AAVec[First]);
if (!FirstAA.ClusterRevComp)
return;
const size_t N = Cluster.size();
for (size_t i = 0; i < N; ++i)
{
int ArrayIndex = Cluster[i];
assert(ArrayIndex < (int) AAVec.size());
ArrayAln &AA = *(AAVec[ArrayIndex]);
AA.ClusterRevComp = !AA.ClusterRevComp;
}
}
void ClusterConsRC(std::vector<ArrayAln *> &AAVec, IntVecVec &Clusters)
{
SeqVect Seqs;
const size_t ArrayCount = AAVec.size();
for (size_t i = 0; i < ArrayCount; ++i)
{
const ArrayAln &AA = *(AAVec[i]);
Seqs.push_back((Seq *) &AA.ConsSeq);
Seq *r = new Seq;
r->Copy(AA.ConsSeq);
r->RevComp();
Seqs.push_back(r);
}
DistFunc DF;
KmerDist(Seqs, DF);
#if TRACE
DF.LogMe();
#endif
BoolVec Done;
for (size_t i = 0; i < ArrayCount; ++i)
Done.push_back(false);
for (;;)
{
IntVec Cluster;
int Best = FindBest(AAVec, DF, Done, Cluster);
if (Best == -1)
break;
FixStrand(AAVec, Cluster);
Clusters.push_back(Cluster);
}
for (size_t i = 0; i < ArrayCount; ++i)
{
if (!Done[i])
{
IntVec Cluster;
Cluster.push_back(i);
FixStrand(AAVec, Cluster);
Clusters.push_back(Cluster);
}
}
#if TRACE
{
Log("%d clusters\n", (int) Clusters.size());
for (size_t i = 0; i < (int) Clusters.size(); ++i)
{
const IntVec &Cluster = Clusters[i];
Log(" ");
size_t N = Cluster.size();
for (size_t j = 0; j < N; ++j)
Log(" %d", Cluster[j]);
Log("\n");
}
}
#endif
}
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