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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/tree.h"
#include "libMUSCLE/clust.h"
#include "libMUSCLE/clustsetmsa.h"
#include "libMUSCLE/distcalc.h"
namespace muscle {
static void SaveMSADist(const MSA &msa, MSADist &d, const char *FileName)
{
FILE *f = fopen(FileName, "w");
if (f == 0)
Quit("Cannot create %s", FileName);
unsigned n = msa.GetSeqCount();
for (unsigned i = 0; i < n; ++i)
{
fprintf(f, "%10.10s ", msa.GetSeqName(i));
for (unsigned j = 0; j < n; ++j)
fprintf(f, " %9g", d.ComputeDist(msa, i, j));
fprintf(f, "\n");
}
fclose(f);
}
static void TreeFromMSA_NJ(const MSA &msa, Tree &tree, CLUSTER Cluster,
DISTANCE Distance, const char *SaveFileName)
{
MSADist MD(Distance);
ClustSetMSA Set(msa, MD);
if (SaveFileName != 0)
SaveMSADist(msa, MD, SaveFileName);
Clust C;
C.Create(Set, Cluster);
tree.FromClust(C);
}
static void SaveDC(const DistCalcMSA &DC, const char *FileName)
{
FILE *f = fopen(FileName, "w");
if (f == 0)
Quit("Cannot create %s", FileName);
unsigned n = DC.GetCount();
fprintf(f, "%u\n", n);
float *Dist = new float[n];
for (unsigned i = 0; i < n; ++i)
{
fprintf(f, "%10.10s ", DC.GetName(i));
DC.CalcDistRange(i, Dist);
for (unsigned j = 0; j < i; ++j)
fprintf(f, " %9g", Dist[j]);
fprintf(f, "\n");
}
fclose(f);
}
static void TreeFromMSA_UPGMA(const MSA &msa, Tree &tree, CLUSTER Cluster,
DISTANCE Distance, const char *SaveFileName)
{
LINKAGE Linkage = LINKAGE_Undefined;
switch (Cluster)
{
case CLUSTER_UPGMA:
Linkage = LINKAGE_Avg;
break;
case CLUSTER_UPGMAMin:
Linkage = LINKAGE_Min;
break;
case CLUSTER_UPGMAMax:
Linkage = LINKAGE_Max;
break;
case CLUSTER_UPGMB:
Linkage = LINKAGE_Biased;
break;
default:
Quit("TreeFromMSA_UPGMA, CLUSTER_%u not supported", Cluster);
}
DistCalcMSA DC;
DC.Init(msa, Distance);
if (SaveFileName != 0)
SaveDC(DC, SaveFileName);
UPGMA2(DC, tree, Linkage);
}
void TreeFromMSA(const MSA &msa, Tree &tree, CLUSTER Cluster,
DISTANCE Distance, ROOT Root, const char *SaveFileName)
{
if (CLUSTER_NeighborJoining == Cluster)
TreeFromMSA_NJ(msa, tree, Cluster, Distance, SaveFileName);
else
TreeFromMSA_UPGMA(msa, tree, Cluster, Distance, SaveFileName);
FixRoot(tree, Root);
}
}
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