binaries/src/muscle/refine.cpp

   1 #include "muscle.h"\r
   2 #include "textfile.h"\r
   3 #include "seqvect.h"\r
   4 #include "distfunc.h"\r
   5 #include "msa.h"\r
   6 #include "tree.h"\r
   7 #include "clust.h"\r
   8 #include "profile.h"\r
   9 #include "clustsetmsa.h"\r
  10 \r
  11 void Refine()\r
  12         {\r
  13         SetOutputFileName(g_pstrOutFileName);\r
  14         SetInputFileName(g_pstrInFileName);\r
  15         SetStartTime();\r
  16 \r
  17         SetMaxIters(g_uMaxIters);\r
  18         SetSeqWeightMethod(g_SeqWeight1);\r
  19 \r
  20         TextFile fileIn(g_pstrInFileName);\r
  21         MSA msa;\r
  22         msa.FromFile(fileIn);\r
  23 \r
  24         const unsigned uSeqCount = msa.GetSeqCount();\r
  25         if (0 == uSeqCount)\r
  26                 Quit("No sequences in input file");\r
  27 \r
  28         ALPHA Alpha = ALPHA_Undefined;\r
  29         switch (g_SeqType)\r
  30                 {\r
  31         case SEQTYPE_Auto:\r
  32                 Alpha = msa.GuessAlpha();\r
  33                 break;\r
  34 \r
  35         case SEQTYPE_Protein:\r
  36                 Alpha = ALPHA_Amino;\r
  37                 break;\r
  38 \r
  39         case SEQTYPE_DNA:\r
  40                 Alpha = ALPHA_DNA;\r
  41                 break;\r
  42 \r
  43         case SEQTYPE_RNA:\r
  44                 Alpha = ALPHA_RNA;\r
  45                 break;\r
  46 \r
  47         default:\r
  48                 Quit("Invalid SeqType");\r
  49                 }\r
  50         SetAlpha(Alpha);\r
  51         msa.FixAlpha();\r
  52 \r
  53         SetPPScore();\r
  54         if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)\r
  55                 SetPPScore(PPSCORE_SPN);\r
  56 \r
  57         MSA::SetIdCount(uSeqCount);\r
  58 \r
  59 // Initialize sequence ids.\r
  60 // From this point on, ids must somehow propogate from here.\r
  61         for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
  62                 msa.SetSeqId(uSeqIndex, uSeqIndex);\r
  63         SetMuscleInputMSA(msa);\r
  64 \r
  65         Tree GuideTree;\r
  66         TreeFromMSA(msa, GuideTree, g_Cluster2, g_Distance2, g_Root2);\r
  67         SetMuscleTree(GuideTree);\r
  68 \r
  69         if (g_bAnchors)\r
  70                 RefineVert(msa, GuideTree, g_uMaxIters);\r
  71         else\r
  72                 RefineHoriz(msa, GuideTree, g_uMaxIters, false, false);\r
  73 \r
  74         ValidateMuscleIds(msa);\r
  75         ValidateMuscleIds(GuideTree);\r
  76 \r
  77 //      TextFile fileOut(g_pstrOutFileName, true);\r
  78 //      msa.ToFile(fileOut);\r
  79         MuscleOutput(msa);\r
  80         }\r