Mac binaries

[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
new file mode 100644 (file)
index 0000000..6d8afc6
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/refinetreee.cpp
@@ -0,0 +1,51 @@
+#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