Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/refinetreee.cpp b/website/archive/binaries/mac/src/muscle/refinetreee.cpp
deleted file mode 100644 (file)
index 6d8afc6..0000000
--- a/website/archive/binaries/mac/src/muscle/refinetreee.cpp
+++ /dev/null
@@ -1,51 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "profile.h"\r
-#include <stdio.h>\r
-\r
-#define TRACE  0\r
-\r
-void RefineTreeE(MSA &msa, const SeqVect &v, Tree &tree, ProgNode *ProgNodes)\r
-       {\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       if (tree.GetLeafCount() != uSeqCount)\r
-               Quit("Refine tree, tree has different number of nodes");\r
-\r
-       if (uSeqCount < 3)\r
-               return;\r
-\r
-#if    DEBUG\r
-       ValidateMuscleIds(msa);\r
-       ValidateMuscleIds(tree);\r
-#endif\r
-\r
-       const unsigned uNodeCount = tree.GetNodeCount();\r
-       unsigned *uNewNodeIndexToOldNodeIndex= new unsigned[uNodeCount];\r
-\r
-       Tree Tree2;\r
-       TreeFromMSA(msa, Tree2, g_Cluster2, g_Distance2, g_Root2, g_pstrDistMxFileName2);\r
-\r
-#if    DEBUG\r
-       ValidateMuscleIds(Tree2);\r
-#endif\r
-\r
-       DiffTreesE(Tree2, tree, uNewNodeIndexToOldNodeIndex);\r
-\r
-       unsigned uRoot = Tree2.GetRootNodeIndex();\r
-       if (NODE_CHANGED == uNewNodeIndexToOldNodeIndex[uRoot])\r
-               {\r
-               MSA msa2;\r
-               RealignDiffsE(msa, v, Tree2, tree, uNewNodeIndexToOldNodeIndex, msa2, ProgNodes);\r
-               tree.Copy(Tree2);\r
-               msa.Copy(msa2);\r
-#if    DEBUG\r
-               ValidateMuscleIds(msa2);\r
-#endif\r
-               }\r
-\r
-       delete[] uNewNodeIndexToOldNodeIndex;\r
-\r
-       SetCurrentAlignment(msa);\r
-       ProgressStepsDone();\r
-       }\r