website/archive/binaries/mac/src/muscle/refinetree.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 void RefineTree(MSA &msa, Tree &tree)\r
   8         {\r
   9         const unsigned uSeqCount = msa.GetSeqCount();\r
  10         if (tree.GetLeafCount() != uSeqCount)\r
  11                 Quit("Refine tree, tree has different number of nodes");\r
  12 \r
  13         if (uSeqCount < 3)\r
  14                 return;\r
  15 \r
  16 #if     DEBUG\r
  17         ValidateMuscleIds(msa);\r
  18         ValidateMuscleIds(tree);\r
  19 #endif\r
  20 \r
  21         unsigned *IdToDiffsLeafNodeIndex = new unsigned[uSeqCount];\r
  22         unsigned uDiffsCount = uSeqCount;\r
  23         Tree Tree2;\r
  24         for (unsigned uIter = 0; uIter < g_uMaxTreeRefineIters; ++uIter)\r
  25                 {\r
  26                 TreeFromMSA(msa, Tree2, g_Cluster2, g_Distance2, g_Root2, g_pstrDistMxFileName2);\r
  27 \r
  28 #if     DEBUG\r
  29                 ValidateMuscleIds(Tree2);\r
  30 #endif\r
  31 \r
  32                 Tree Diffs;\r
  33                 DiffTrees(Tree2, tree, Diffs, IdToDiffsLeafNodeIndex);\r
  34 \r
  35                 tree.Copy(Tree2);\r
  36 \r
  37                 const unsigned uNewDiffsNodeCount = Diffs.GetNodeCount();\r
  38                 const unsigned uNewDiffsCount = (uNewDiffsNodeCount - 1)/2;\r
  39 \r
  40                 if (0 == uNewDiffsCount || uNewDiffsCount >= uDiffsCount)\r
  41                         {\r
  42                         ProgressStepsDone();\r
  43                         break;\r
  44                         }\r
  45                 uDiffsCount = uNewDiffsCount;\r
  46 \r
  47                 MSA msa2;\r
  48                 RealignDiffs(msa, Diffs, IdToDiffsLeafNodeIndex, msa2);\r
  49 \r
  50 #if     DEBUG\r
  51                 ValidateMuscleIds(msa2);\r
  52 #endif\r
  53 \r
  54                 msa.Copy(msa2);\r
  55                 SetCurrentAlignment(msa);\r
  56                 }\r
  57 \r
  58         delete[] IdToDiffsLeafNodeIndex;\r
  59         }\r