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#include "pilercr.h"
#define TRACE 0
// Best entry is one with largest number
// of distances smaller than the threshold
static int FindBest(const std::vector<ArrayData *> &ADVec,
const DistFunc &DF, BoolVec &Done, IntVec &Cluster)
{
Cluster.clear();
const int Count = DF.GetCount();
IntVec NrUnderThresh;
for (int i = 0; i < Count; ++i)
NrUnderThresh.push_back(0);
for (int i = 0; i < Count; ++i)
{
if (Done[i])
continue;
for (int j = 0; j < Count; ++j)
{
if (i == j || Done[j])
continue;
#if TRACE
Log("Dist(");
ADVec[i]->ConsSeq.LogMeSeqOnly();
Log(",");
ADVec[j]->ConsSeq.LogMeSeqOnly();
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])
continue;
if (DF.GetDist(Best, i) <= g_ClusterMaxDist)
{
Done[i] = true;
Cluster.push_back(i);
}
}
}
return Best;
}
void ClusterCons(const std::vector<ArrayData *> &ADVec, IntVecVec &Clusters)
{
SeqVect Seqs;
const size_t ArrayCount = ADVec.size();
for (size_t i = 0; i < ArrayCount; ++i)
{
const ArrayData &AD = *(ADVec[i]);
Seq *s = new Seq;
s->Copy(AD.ConsSeq);
Seqs.push_back(s);
}
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(ADVec, DF, Done, Cluster);
if (Best == -1)
break;
Clusters.push_back(Cluster);
}
for (size_t i = 0; i < ArrayCount; ++i)
{
if (!Done[i])
{
IntVec Cluster;
Cluster.push_back(i);
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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