Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/refinetree.cpp b/website/archive/binaries/mac/src/muscle/refinetree.cpp
deleted file mode 100644 (file)
index 313bbed..0000000
--- a/website/archive/binaries/mac/src/muscle/refinetree.cpp
+++ /dev/null
@@ -1,59 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "profile.h"\r
-#include <stdio.h>\r
-\r
-void RefineTree(MSA &msa, Tree &tree)\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
-       unsigned *IdToDiffsLeafNodeIndex = new unsigned[uSeqCount];\r
-       unsigned uDiffsCount = uSeqCount;\r
-       Tree Tree2;\r
-       for (unsigned uIter = 0; uIter < g_uMaxTreeRefineIters; ++uIter)\r
-               {\r
-               TreeFromMSA(msa, Tree2, g_Cluster2, g_Distance2, g_Root2, g_pstrDistMxFileName2);\r
-\r
-#if    DEBUG\r
-               ValidateMuscleIds(Tree2);\r
-#endif\r
-\r
-               Tree Diffs;\r
-               DiffTrees(Tree2, tree, Diffs, IdToDiffsLeafNodeIndex);\r
-\r
-               tree.Copy(Tree2);\r
-\r
-               const unsigned uNewDiffsNodeCount = Diffs.GetNodeCount();\r
-               const unsigned uNewDiffsCount = (uNewDiffsNodeCount - 1)/2;\r
-\r
-               if (0 == uNewDiffsCount || uNewDiffsCount >= uDiffsCount)\r
-                       {\r
-                       ProgressStepsDone();\r
-                       break;\r
-                       }\r
-               uDiffsCount = uNewDiffsCount;\r
-\r
-               MSA msa2;\r
-               RealignDiffs(msa, Diffs, IdToDiffsLeafNodeIndex, msa2);\r
-\r
-#if    DEBUG\r
-               ValidateMuscleIds(msa2);\r
-#endif\r
-\r
-               msa.Copy(msa2);\r
-               SetCurrentAlignment(msa);\r
-               }\r
-\r
-       delete[] IdToDiffsLeafNodeIndex;\r
-       }\r