Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / treefrommsa.cpp

diff --git a/website/archive/binaries/mac/src/muscle/treefrommsa.cpp b/website/archive/binaries/mac/src/muscle/treefrommsa.cpp
deleted file mode 100644 (file)
index 36d3166..0000000
--- a/website/archive/binaries/mac/src/muscle/treefrommsa.cpp
+++ /dev/null
@@ -1,97 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "clust.h"\r
-#include "clustsetmsa.h"\r
-#include "distcalc.h"\r
-\r
-static void SaveMSADist(const MSA &msa, MSADist &d, const char *FileName)\r
-       {\r
-       FILE *f = fopen(FileName, "w");\r
-       if (f == 0)\r
-               Quit("Cannot create %s", FileName);\r
-\r
-       unsigned n = msa.GetSeqCount();\r
-       for (unsigned i = 0; i < n; ++i)\r
-               {\r
-               fprintf(f, "%10.10s  ", msa.GetSeqName(i));\r
-               for (unsigned j = 0; j < n; ++j)\r
-                       fprintf(f, "  %9g", d.ComputeDist(msa, i, j));\r
-               fprintf(f, "\n");\r
-               }\r
-       fclose(f);\r
-       }\r
-\r
-static void TreeFromMSA_NJ(const MSA &msa, Tree &tree, CLUSTER Cluster,\r
-  DISTANCE Distance, const char *SaveFileName)\r
-       {\r
-       MSADist MD(Distance);\r
-       ClustSetMSA Set(msa, MD);\r
-\r
-       if (SaveFileName != 0)\r
-               SaveMSADist(msa, MD, SaveFileName);\r
-\r
-       Clust C;\r
-       C.Create(Set, Cluster);\r
-\r
-       tree.FromClust(C);\r
-       }\r
-\r
-static void SaveDC(const DistCalcMSA &DC, const char *FileName)\r
-       {\r
-       FILE *f = fopen(FileName, "w");\r
-       if (f == 0)\r
-               Quit("Cannot create %s", FileName);\r
-\r
-       unsigned n = DC.GetCount();\r
-       fprintf(f, "%u\n", n);\r
-       float *Dist = new float[n];\r
-       for (unsigned i = 0; i < n; ++i)\r
-               {\r
-               fprintf(f, "%10.10s  ", DC.GetName(i));\r
-               DC.CalcDistRange(i, Dist);\r
-               for (unsigned j = 0; j < i; ++j)\r
-                       fprintf(f, "  %9g", Dist[j]);\r
-               fprintf(f, "\n");\r
-               }\r
-       fclose(f);\r
-       }\r
-\r
-static void TreeFromMSA_UPGMA(const MSA &msa, Tree &tree, CLUSTER Cluster,\r
-  DISTANCE Distance, const char *SaveFileName)\r
-       {\r
-       LINKAGE Linkage = LINKAGE_Undefined;\r
-       switch (Cluster)\r
-               {\r
-       case CLUSTER_UPGMA:\r
-               Linkage = LINKAGE_Avg;\r
-               break;\r
-       case CLUSTER_UPGMAMin:\r
-               Linkage = LINKAGE_Min;\r
-               break;\r
-       case CLUSTER_UPGMAMax:\r
-               Linkage = LINKAGE_Max;\r
-               break;\r
-       case CLUSTER_UPGMB:\r
-               Linkage = LINKAGE_Biased;\r
-               break;\r
-       default:\r
-               Quit("TreeFromMSA_UPGMA, CLUSTER_%u not supported", Cluster);\r
-               }\r
-       \r
-       DistCalcMSA DC;\r
-       DC.Init(msa, Distance);\r
-       if (SaveFileName != 0)\r
-               SaveDC(DC, SaveFileName);\r
-       UPGMA2(DC, tree, Linkage);\r
-       }\r
-\r
-void TreeFromMSA(const MSA &msa, Tree &tree, CLUSTER Cluster,\r
-  DISTANCE Distance, ROOT Root, const char *SaveFileName)\r
-       {\r
-       if (CLUSTER_NeighborJoining == Cluster)\r
-               TreeFromMSA_NJ(msa, tree, Cluster, Distance, SaveFileName);\r
-       else\r
-               TreeFromMSA_UPGMA(msa, tree, Cluster, Distance, SaveFileName);\r
-       FixRoot(tree, Root);\r
-       }\r