binaries/src/muscle/fasta2.cpp

   1 #include "muscle.h"\r
   2 #include <stdio.h>\r
   3 #include <errno.h>\r
   4 \r
   5 //const int BUFFER_BYTES = 16*1024;\r
   6 const int BUFFER_BYTES = 128;\r
   7 const int CR = '\r';\r
   8 const int NL = '\n';\r
   9 \r
  10 #define ADD(c)                                                                                                                  \\r
  11                 {                                                                                                                               \\r
  12                 if (Pos >= BufferLength)                                                                                \\r
  13                         {                                                                                                                       \\r
  14                         const int NewBufferLength = BufferLength + BUFFER_BYTES;        \\r
  15                         char *NewBuffer = new char[NewBufferLength];                            \\r
  16                         memcpy(NewBuffer, Buffer, BufferLength);                                        \\r
  17                         delete[] Buffer;                                                                                        \\r
  18                         Buffer = NewBuffer;                                                                                     \\r
  19                         BufferLength = NewBufferLength;                                                         \\r
  20                         }                                                                                                                       \\r
  21                 Buffer[Pos++] = c;                                                                                              \\r
  22                 }\r
  23 \r
  24 // Get next sequence from file.\r
  25 char *GetFastaSeq(FILE *f, unsigned *ptrSeqLength, char **ptrLabel, bool DeleteGaps)\r
  26         {\r
  27         unsigned BufferLength = 0;\r
  28         unsigned Pos = 0;\r
  29         char *Buffer = 0;\r
  30 \r
  31         int c = fgetc(f);\r
  32         if (EOF == c)\r
  33                 return 0;\r
  34         if ('>' != c)\r
  35                 Quit("Invalid file format, expected '>' to start FASTA label");\r
  36 \r
  37         for (;;)\r
  38                 {\r
  39                 int c = fgetc(f);\r
  40                 if (EOF == c)\r
  41                         Quit("End-of-file or input error in FASTA label");\r
  42 \r
  43         // NL or CR terminates label\r
  44                 if (NL == c || CR == c)\r
  45                         break;\r
  46 \r
  47         // All other characters added to label\r
  48                 ADD(c)\r
  49                 }\r
  50 \r
  51 // Nul-terminate label\r
  52         ADD(0)\r
  53         *ptrLabel = Buffer;\r
  54 \r
  55         BufferLength = 0;\r
  56         Pos = 0;\r
  57         Buffer = 0;\r
  58         int PreviousChar = NL;\r
  59         for (;;)\r
  60                 {\r
  61                 int c = fgetc(f);\r
  62                 if (EOF == c)\r
  63                         {\r
  64                         if (feof(f))\r
  65                                 break;\r
  66                         else if (ferror(f))\r
  67                                 Quit("Error reading FASTA file, ferror=TRUE feof=FALSE errno=%d %s",\r
  68                                   errno, strerror(errno));\r
  69                         else\r
  70                                 Quit("Error reading FASTA file, fgetc=EOF feof=FALSE ferror=FALSE errno=%d %s",\r
  71                                   errno, strerror(errno));\r
  72                         }\r
  73 \r
  74                 if ('>' == c)\r
  75                         {\r
  76                         if (NL == PreviousChar || CR == PreviousChar)\r
  77                                 {\r
  78                                 ungetc(c, f);\r
  79                                 break;\r
  80                                 }\r
  81                         else\r
  82                                 Quit("Unexpected '>' in FASTA sequence data");\r
  83                         }\r
  84                 else if (isspace(c))\r
  85                         ;\r
  86                 else if (IsGapChar(c))\r
  87                         {\r
  88                         if (!DeleteGaps)\r
  89                                 ADD(c)\r
  90                         }\r
  91                 else if (isalpha(c))\r
  92                         {\r
  93                         c = toupper(c);\r
  94                         ADD(c)\r
  95                         }\r
  96                 else if (isprint(c))\r
  97                         {\r
  98                         Warning("Invalid character '%c' in FASTA sequence data, ignored", c);\r
  99                         continue;\r
 100                         }\r
 101                 else\r
 102                         {\r
 103                         Warning("Invalid byte hex %02x in FASTA sequence data, ignored", (unsigned char) c);\r
 104                         continue;\r
 105                         }\r
 106                 PreviousChar = c;\r
 107                 }\r
 108 \r
 109         if (0 == Pos)\r
 110                 return GetFastaSeq(f, ptrSeqLength, ptrLabel, DeleteGaps);\r
 111 \r
 112         *ptrSeqLength = Pos;\r
 113         return Buffer;\r
 114         }\r