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#include "pilercr.h"
#include "multaln.h"
void MultipleAlign(SeqVect &Seqs, MSA &Aln)
{
assert(Seqs.GetSeqCount() > 0);
if ((int) Seqs.GetSeqCount() > g_MaxMSASeqs)
Quit("Array length %u, max is %d", Seqs.GetSeqCount(), g_MaxMSASeqs);
if (Seqs.GetSeqCount() == 1)
{
Seq &s = Seqs.GetSeq(0);
s.SetId(0);
Aln.FromSeq(s);
return;
}
unsigned uSeqCount = Seqs.GetSeqCount();
MSA::SetIdCount(g_MaxMSASeqs);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
Seqs.SetSeqId(uSeqIndex, uSeqIndex);
Tree GuideTree;
GetGuideTree(Seqs, GuideTree);
ProgressiveAlign(Seqs, GuideTree, Aln);
}
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