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

   1 #include "muscle.h"\r
   2 #include "msa.h"\r
   3 #include "tree.h"\r
   4 #include "profile.h"\r
   5 #include <stdio.h>\r
   6 \r
   7 #define TRACE   0\r
   8 \r
   9 void RefineTreeE(MSA &msa, const SeqVect &v, Tree &tree, ProgNode *ProgNodes)\r
  10         {\r
  11         const unsigned uSeqCount = msa.GetSeqCount();\r
  12         if (tree.GetLeafCount() != uSeqCount)\r
  13                 Quit("Refine tree, tree has different number of nodes");\r
  14 \r
  15         if (uSeqCount < 3)\r
  16                 return;\r
  17 \r
  18 #if     DEBUG\r
  19         ValidateMuscleIds(msa);\r
  20         ValidateMuscleIds(tree);\r
  21 #endif\r
  22 \r
  23         const unsigned uNodeCount = tree.GetNodeCount();\r
  24         unsigned *uNewNodeIndexToOldNodeIndex= new unsigned[uNodeCount];\r
  25 \r
  26         Tree Tree2;\r
  27         TreeFromMSA(msa, Tree2, g_Cluster2, g_Distance2, g_Root2, g_pstrDistMxFileName2);\r
  28 \r
  29 #if     DEBUG\r
  30         ValidateMuscleIds(Tree2);\r
  31 #endif\r
  32 \r
  33         DiffTreesE(Tree2, tree, uNewNodeIndexToOldNodeIndex);\r
  34 \r
  35         unsigned uRoot = Tree2.GetRootNodeIndex();\r
  36         if (NODE_CHANGED == uNewNodeIndexToOldNodeIndex[uRoot])\r
  37                 {\r
  38                 MSA msa2;\r
  39                 RealignDiffsE(msa, v, Tree2, tree, uNewNodeIndexToOldNodeIndex, msa2, ProgNodes);\r
  40                 tree.Copy(Tree2);\r
  41                 msa.Copy(msa2);\r
  42 #if     DEBUG\r
  43                 ValidateMuscleIds(msa2);\r
  44 #endif\r
  45                 }\r
  46 \r
  47         delete[] uNewNodeIndexToOldNodeIndex;\r
  48 \r
  49         SetCurrentAlignment(msa);\r
  50         ProgressStepsDone();\r
  51         }\r