1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
#include "pilercr.h"
#define TRACE 0
void AlignCluster(std::vector<ArrayAln *> &AAVec, const IntVec &Cluster,
Seq &ConsSymbols)
{
#if TRACE
Log("AlignCluster:\n");
#endif
SeqVect Seqs;
const size_t ClusterSize = Cluster.size();
for (size_t i = 0; i < ClusterSize ; ++i)
{
size_t ArrayIndex = Cluster[i];
Seq *s = new Seq;
#if TRACE
ADVec[ArrayIndex]->ConsSeq.LogMe();
Log("\n");
#endif
const ArrayAln &AA = *(AAVec[ArrayIndex]);
s->Copy(AA.ConsSeq);
if (AA.ClusterRevComp && ClusterSize > 1)
s->RevComp();
Seqs.push_back(s);
}
MSA Aln;
MultipleAlign(Seqs, Aln);
#if TRACE
Aln.LogMe();
#endif
GetConsSymbols(Aln, ConsSymbols);
for (size_t i = 0; i < ClusterSize ; ++i)
{
size_t ArrayIndex = Cluster[i];
Aln.GetSeq((unsigned) i, AAVec[ArrayIndex]->AlignedConsSeq);
#if TRACE
Log("Aligned=");
AAVec[i]->AlignedConsSeq.LogMe();
#endif
}
}
|
