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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
|
#include "libMUSCLE/muscle.h"
#include "libMUSCLE/seqvect.h"
#include "libMUSCLE/distfunc.h"
#include "libMUSCLE/clust.h"
#include "libMUSCLE/clustsetdf.h"
#include "libMUSCLE/tree.h"
#include "libMUSCLE/clust.h"
#include "libMUSCLE/distcalc.h"
#include <math.h>
namespace muscle {
static void TreeFromSeqVect_NJ(const DistFunc &DF, CLUSTER Cluster, Tree &tree)
{
ClustSetDF CSD(DF);
Clust C;
C.Create(CSD, Cluster);
tree.FromClust(C);
}
static void TreeFromSeqVect_UPGMA(const DistFunc &DF, CLUSTER Cluster, Tree &tree)
{
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("TreeFromSeqVect_UPGMA, CLUSTER_%u not supported", Cluster);
}
DistCalcDF DC;
DC.Init(DF);
UPGMA2(DC, tree, Linkage);
}
static void SaveDF(const SeqVect &v, DistFunc &d, const char *FileName)
{
FILE *f = fopen(FileName, "w");
if (f == 0)
Quit("Cannot create %s", FileName);
unsigned n = v.GetSeqCount();
fprintf(f, "%u\n", n);
for (unsigned i = 0; i < n; ++i)
{
fprintf(f, "%10.10s ", v.GetSeqName(i));
for (unsigned j = 0; j < i; ++j)
fprintf(f, " %9g", d.GetDist(i, j));
fprintf(f, "\n");
}
fclose(f);
}
void TreeFromSeqVect(const SeqVect &v, Tree &tree, CLUSTER Cluster,
DISTANCE Distance, ROOT Root, const char *SaveFileName)
{
DistFunc DF;
DistUnaligned(v, Distance, DF);
if (SaveFileName != 0)
SaveDF(v, DF, SaveFileName);
if (CLUSTER_NeighborJoining == Cluster)
TreeFromSeqVect_NJ(DF, Cluster, tree);
else
TreeFromSeqVect_UPGMA(DF, Cluster, tree);
FixRoot(tree, Root);
}
}
|
