binaries/src/muscle/dosp.cpp

   1 #include "muscle.h"\r
   2 #include "textfile.h"\r
   3 #include "msa.h"\r
   4 #include "objscore.h"\r
   5 #include "tree.h"\r
   6 #include "profile.h"\r
   7 \r
   8 void DoSP()\r
   9         {\r
  10         TextFile f(g_pstrSPFileName);\r
  11 \r
  12         MSA a;\r
  13         a.FromFile(f);\r
  14 \r
  15         ALPHA Alpha = ALPHA_Undefined;\r
  16         switch (g_SeqType)\r
  17                 {\r
  18         case SEQTYPE_Auto:\r
  19                 Alpha = a.GuessAlpha();\r
  20                 break;\r
  21 \r
  22         case SEQTYPE_Protein:\r
  23                 Alpha = ALPHA_Amino;\r
  24                 break;\r
  25 \r
  26         case SEQTYPE_DNA:\r
  27                 Alpha = ALPHA_DNA;\r
  28                 break;\r
  29 \r
  30         case SEQTYPE_RNA:\r
  31                 Alpha = ALPHA_RNA;\r
  32                 break;\r
  33 \r
  34         default:\r
  35                 Quit("Invalid SeqType");\r
  36                 }\r
  37         SetAlpha(Alpha);\r
  38         a.FixAlpha();\r
  39 \r
  40         SetPPScore();\r
  41 \r
  42         const unsigned uSeqCount = a.GetSeqCount();\r
  43         if (0 == uSeqCount)\r
  44                 Quit("No sequences in input file %s", g_pstrSPFileName);\r
  45 \r
  46         MSA::SetIdCount(uSeqCount);\r
  47         for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
  48                 a.SetSeqId(uSeqIndex, uSeqIndex);\r
  49 \r
  50         SetSeqWeightMethod(g_SeqWeight1);\r
  51         Tree tree;\r
  52         TreeFromMSA(a, tree, g_Cluster2, g_Distance2, g_Root2);\r
  53         SetMuscleTree(tree);\r
  54         SetMSAWeightsMuscle((MSA &) a);\r
  55 \r
  56         SCORE SP = ObjScoreSP(a);\r
  57 \r
  58         Log("File=%s;SP=%.4g\n", g_pstrSPFileName, SP);\r
  59         fprintf(stderr, "File=%s;SP=%.4g\n", g_pstrSPFileName, SP);\r
  60         }\r