binaries/src/muscle/savebest.cpp

   1 #include "muscle.h"\r
   2 #include "msa.h"\r
   3 #include "textfile.h"\r
   4 #include <time.h>\r
   5 \r
   6 MSA *ptrBestMSA;\r
   7 static const char *pstrOutputFileName;\r
   8 \r
   9 void SetOutputFileName(const char *out)\r
  10         {\r
  11         pstrOutputFileName = out;\r
  12         }\r
  13 \r
  14 void SetCurrentAlignment(MSA &msa)\r
  15         {\r
  16         ptrBestMSA = &msa;\r
  17         }\r
  18 \r
  19 void SaveCurrentAlignment()\r
  20         {\r
  21         static bool bCalled = false;\r
  22         if (bCalled)\r
  23                 {\r
  24                 fprintf(stderr,\r
  25                   "\nRecursive call to SaveCurrentAlignment, giving up attempt to save.\n");\r
  26                 exit(EXIT_FatalError);\r
  27                 }\r
  28 \r
  29         if (0 == ptrBestMSA)\r
  30                 {\r
  31                 fprintf(stderr, "\nAlignment not completed, cannot save.\n");\r
  32                 Log("Alignment not completed, cannot save.\n");\r
  33                 exit(EXIT_FatalError);\r
  34                 }\r
  35 \r
  36         if (0 == pstrOutputFileName)\r
  37                 {\r
  38                 fprintf(stderr, "\nOutput file name not specified, cannot save.\n");\r
  39                 exit(EXIT_FatalError);\r
  40                 }\r
  41 \r
  42         fprintf(stderr, "\nSaving current alignment ...\n");\r
  43 \r
  44         TextFile fileOut(pstrOutputFileName, true);\r
  45         ptrBestMSA->ToFASTAFile(fileOut);\r
  46 \r
  47         fprintf(stderr, "Current alignment saved to \"%s\".\n", pstrOutputFileName);\r
  48         Log("Current alignment saved to \"%s\".\n", pstrOutputFileName);\r
  49         }\r
  50 \r
  51 void CheckMaxTime()\r
  52         {\r
  53         if (0 == g_ulMaxSecs)\r
  54                 return;\r
  55 \r
  56         time_t Now = time(0);\r
  57         time_t ElapsedSecs = Now - GetStartTime();\r
  58         if (ElapsedSecs <= (time_t) g_ulMaxSecs)\r
  59                 return;\r
  60 \r
  61         Log("Max time %s exceeded, elapsed seconds = %ul\n",\r
  62           MaxSecsToStr(), ElapsedSecs);\r
  63 \r
  64         SaveCurrentAlignment();\r
  65         exit(EXIT_Success);\r
  66         }\r