binaries/src/muscle/muscleout.cpp

   1 #include "muscle.h"\r
   2 #include "msa.h"\r
   3 #include "params.h"\r
   4 #include "textfile.h"\r
   5 \r
   6 static void DoOutput(MSA &msa)\r
   7         {\r
   8         bool AnyOutput = false;\r
   9 \r
  10 // Value options\r
  11         if (g_pstrFASTAOutFileName)\r
  12                 {\r
  13                 TextFile File(g_pstrFASTAOutFileName, true);\r
  14                 msa.ToFASTAFile(File);\r
  15                 AnyOutput = true;\r
  16                 }\r
  17 \r
  18         if (g_pstrMSFOutFileName)\r
  19                 {\r
  20                 TextFile File(g_pstrMSFOutFileName, true);\r
  21                 msa.ToMSFFile(File);\r
  22                 AnyOutput = true;\r
  23                 }\r
  24 \r
  25         if (g_pstrClwOutFileName)\r
  26                 {\r
  27                 TextFile File(g_pstrClwOutFileName, true);\r
  28                 msa.ToAlnFile(File);\r
  29                 AnyOutput = true;\r
  30                 }\r
  31 \r
  32         if (g_pstrClwStrictOutFileName)\r
  33                 {\r
  34                 g_bClwStrict = true;\r
  35                 TextFile File(g_pstrClwStrictOutFileName, true);\r
  36                 msa.ToAlnFile(File);\r
  37                 AnyOutput = true;\r
  38                 }\r
  39 \r
  40         if (g_pstrHTMLOutFileName)\r
  41                 {\r
  42                 TextFile File(g_pstrHTMLOutFileName, true);\r
  43                 msa.ToHTMLFile(File);\r
  44                 AnyOutput = true;\r
  45                 }\r
  46 \r
  47         if (g_pstrPHYIOutFileName)\r
  48                 {\r
  49                 TextFile File(g_pstrPHYIOutFileName, true);\r
  50                 msa.ToPhyInterleavedFile(File);\r
  51                 AnyOutput = true;\r
  52                 }\r
  53 \r
  54         if (g_pstrPHYSOutFileName)\r
  55                 {\r
  56                 TextFile File(g_pstrPHYSOutFileName, true);\r
  57                 msa.ToPhySequentialFile(File);\r
  58                 AnyOutput = true;\r
  59                 }\r
  60 \r
  61 // Flag options, at most one used (because only one -out filename)\r
  62         TextFile fileOut(g_pstrOutFileName, true);\r
  63         if (g_bFASTA)\r
  64                 {\r
  65                 msa.ToFASTAFile(fileOut);\r
  66                 AnyOutput = true;\r
  67                 }\r
  68         else if (g_bMSF)\r
  69                 {\r
  70                 msa.ToMSFFile(fileOut);\r
  71                 AnyOutput = true;\r
  72                 }\r
  73         else if (g_bAln)\r
  74                 {\r
  75                 msa.ToAlnFile(fileOut);\r
  76                 AnyOutput = true;\r
  77                 }\r
  78         else if (g_bHTML)\r
  79                 {\r
  80                 msa.ToHTMLFile(fileOut);\r
  81                 AnyOutput = true;\r
  82                 }\r
  83         else if (g_bPHYI)\r
  84                 {\r
  85                 msa.ToPhyInterleavedFile(fileOut);\r
  86                 AnyOutput = true;\r
  87                 }\r
  88         else if (g_bPHYS)\r
  89                 {\r
  90                 msa.ToPhySequentialFile(fileOut);\r
  91                 AnyOutput = true;\r
  92                 }\r
  93 \r
  94 // If -out option was given but no flags, output as FASTA\r
  95         if (!AnyOutput)\r
  96                 msa.ToFASTAFile(fileOut);\r
  97         \r
  98         fileOut.Close();\r
  99 \r
 100         if (0 != g_pstrScoreFileName)\r
 101                 WriteScoreFile(msa);\r
 102         }\r
 103 \r
 104 void MuscleOutput(MSA &msa)\r
 105         {\r
 106         MHackEnd(msa);\r
 107         if (g_bStable)\r
 108                 {\r
 109                 MSA msaStable;\r
 110                 Stabilize(msa, msaStable);\r
 111                 msa.Clear();    // save memory\r
 112                 DoOutput(msaStable);\r
 113                 }\r
 114         else\r
 115                 DoOutput(msa);\r
 116         }\r