binaries/src/muscle/fasta.cpp

   1 #include "muscle.h"\r
   2 #include <stdio.h>\r
   3 #include <ctype.h>\r
   4 #include "msa.h"\r
   5 #include "textfile.h"\r
   6 \r
   7 const unsigned FASTA_BLOCK = 60;\r
   8 \r
   9 void MSA::FromFASTAFile(TextFile &File)\r
  10         {\r
  11         Clear();\r
  12 \r
  13         FILE *f = File.GetStdioFile();\r
  14         \r
  15         unsigned uSeqCount = 0;\r
  16         unsigned uColCount = uInsane;\r
  17         for (;;)\r
  18                 {\r
  19                 char *Label;\r
  20                 unsigned uSeqLength;\r
  21                 char *SeqData = GetFastaSeq(f, &uSeqLength, &Label, false);\r
  22                 if (0 == SeqData)\r
  23                         break;\r
  24                 AppendSeq(SeqData, uSeqLength, Label);\r
  25                 }\r
  26         }\r
  27 \r
  28 void MSA::ToFASTAFile(TextFile &File) const\r
  29         {\r
  30         const unsigned uColCount = GetColCount();\r
  31         assert(uColCount > 0);\r
  32         const unsigned uLinesPerSeq = (GetColCount() - 1)/FASTA_BLOCK + 1;\r
  33         const unsigned uSeqCount = GetSeqCount();\r
  34 \r
  35         for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
  36                 {\r
  37                 File.PutString(">");\r
  38                 File.PutString(GetSeqName(uSeqIndex));\r
  39                 File.PutString("\n");\r
  40 \r
  41                 unsigned n = 0;\r
  42                 for (unsigned uLine = 0; uLine < uLinesPerSeq; ++uLine)\r
  43                         {\r
  44                         unsigned uLetters = uColCount - uLine*FASTA_BLOCK;\r
  45                         if (uLetters > FASTA_BLOCK)\r
  46                                 uLetters = FASTA_BLOCK;\r
  47                         for (unsigned i = 0; i < uLetters; ++i)\r
  48                                 {\r
  49                                 char c = GetChar(uSeqIndex, n);\r
  50                                 File.PutChar(c);\r
  51                                 ++n;\r
  52                                 }\r
  53                         File.PutChar('\n');\r
  54                         }\r
  55                 }\r
  56         }\r