website/archive/binaries/mac/src/muscle/treefrommsa.cpp

   1 #include "muscle.h"\r
   2 #include "msa.h"\r
   3 #include "tree.h"\r
   4 #include "clust.h"\r
   5 #include "clustsetmsa.h"\r
   6 #include "distcalc.h"\r
   7 \r
   8 static void SaveMSADist(const MSA &msa, MSADist &d, const char *FileName)\r
   9         {\r
  10         FILE *f = fopen(FileName, "w");\r
  11         if (f == 0)\r
  12                 Quit("Cannot create %s", FileName);\r
  13 \r
  14         unsigned n = msa.GetSeqCount();\r
  15         for (unsigned i = 0; i < n; ++i)\r
  16                 {\r
  17                 fprintf(f, "%10.10s  ", msa.GetSeqName(i));\r
  18                 for (unsigned j = 0; j < n; ++j)\r
  19                         fprintf(f, "  %9g", d.ComputeDist(msa, i, j));\r
  20                 fprintf(f, "\n");\r
  21                 }\r
  22         fclose(f);\r
  23         }\r
  24 \r
  25 static void TreeFromMSA_NJ(const MSA &msa, Tree &tree, CLUSTER Cluster,\r
  26   DISTANCE Distance, const char *SaveFileName)\r
  27         {\r
  28         MSADist MD(Distance);\r
  29         ClustSetMSA Set(msa, MD);\r
  30 \r
  31         if (SaveFileName != 0)\r
  32                 SaveMSADist(msa, MD, SaveFileName);\r
  33 \r
  34         Clust C;\r
  35         C.Create(Set, Cluster);\r
  36 \r
  37         tree.FromClust(C);\r
  38         }\r
  39 \r
  40 static void SaveDC(const DistCalcMSA &DC, const char *FileName)\r
  41         {\r
  42         FILE *f = fopen(FileName, "w");\r
  43         if (f == 0)\r
  44                 Quit("Cannot create %s", FileName);\r
  45 \r
  46         unsigned n = DC.GetCount();\r
  47         fprintf(f, "%u\n", n);\r
  48         float *Dist = new float[n];\r
  49         for (unsigned i = 0; i < n; ++i)\r
  50                 {\r
  51                 fprintf(f, "%10.10s  ", DC.GetName(i));\r
  52                 DC.CalcDistRange(i, Dist);\r
  53                 for (unsigned j = 0; j < i; ++j)\r
  54                         fprintf(f, "  %9g", Dist[j]);\r
  55                 fprintf(f, "\n");\r
  56                 }\r
  57         fclose(f);\r
  58         }\r
  59 \r
  60 static void TreeFromMSA_UPGMA(const MSA &msa, Tree &tree, CLUSTER Cluster,\r
  61   DISTANCE Distance, const char *SaveFileName)\r
  62         {\r
  63         LINKAGE Linkage = LINKAGE_Undefined;\r
  64         switch (Cluster)\r
  65                 {\r
  66         case CLUSTER_UPGMA:\r
  67                 Linkage = LINKAGE_Avg;\r
  68                 break;\r
  69         case CLUSTER_UPGMAMin:\r
  70                 Linkage = LINKAGE_Min;\r
  71                 break;\r
  72         case CLUSTER_UPGMAMax:\r
  73                 Linkage = LINKAGE_Max;\r
  74                 break;\r
  75         case CLUSTER_UPGMB:\r
  76                 Linkage = LINKAGE_Biased;\r
  77                 break;\r
  78         default:\r
  79                 Quit("TreeFromMSA_UPGMA, CLUSTER_%u not supported", Cluster);\r
  80                 }\r
  81         \r
  82         DistCalcMSA DC;\r
  83         DC.Init(msa, Distance);\r
  84         if (SaveFileName != 0)\r
  85                 SaveDC(DC, SaveFileName);\r
  86         UPGMA2(DC, tree, Linkage);\r
  87         }\r
  88 \r
  89 void TreeFromMSA(const MSA &msa, Tree &tree, CLUSTER Cluster,\r
  90   DISTANCE Distance, ROOT Root, const char *SaveFileName)\r
  91         {\r
  92         if (CLUSTER_NeighborJoining == Cluster)\r
  93                 TreeFromMSA_NJ(msa, tree, Cluster, Distance, SaveFileName);\r
  94         else\r
  95                 TreeFromMSA_UPGMA(msa, tree, Cluster, Distance, SaveFileName);\r
  96         FixRoot(tree, Root);\r
  97         }\r