Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / fasta2.cpp

diff --git a/website/archive/binaries/mac/src/muscle/fasta2.cpp b/website/archive/binaries/mac/src/muscle/fasta2.cpp
deleted file mode 100644 (file)
index 98b0fa3..0000000
--- a/website/archive/binaries/mac/src/muscle/fasta2.cpp
+++ /dev/null
@@ -1,114 +0,0 @@
-#include "muscle.h"\r
-#include <stdio.h>\r
-#include <errno.h>\r
-\r
-//const int BUFFER_BYTES = 16*1024;\r
-const int BUFFER_BYTES = 128;\r
-const int CR = '\r';\r
-const int NL = '\n';\r
-\r
-#define ADD(c)                                                                                                                 \\r
-               {                                                                                                                               \\r
-               if (Pos >= BufferLength)                                                                                \\r
-                       {                                                                                                                       \\r
-                       const int NewBufferLength = BufferLength + BUFFER_BYTES;        \\r
-                       char *NewBuffer = new char[NewBufferLength];                            \\r
-                       memcpy(NewBuffer, Buffer, BufferLength);                                        \\r
-                       delete[] Buffer;                                                                                        \\r
-                       Buffer = NewBuffer;                                                                                     \\r
-                       BufferLength = NewBufferLength;                                                         \\r
-                       }                                                                                                                       \\r
-               Buffer[Pos++] = c;                                                                                              \\r
-               }\r
-\r
-// Get next sequence from file.\r
-char *GetFastaSeq(FILE *f, unsigned *ptrSeqLength, char **ptrLabel, bool DeleteGaps)\r
-       {\r
-       unsigned BufferLength = 0;\r
-       unsigned Pos = 0;\r
-       char *Buffer = 0;\r
-\r
-       int c = fgetc(f);\r
-       if (EOF == c)\r
-               return 0;\r
-       if ('>' != c)\r
-               Quit("Invalid file format, expected '>' to start FASTA label");\r
-\r
-       for (;;)\r
-               {\r
-               int c = fgetc(f);\r
-               if (EOF == c)\r
-                       Quit("End-of-file or input error in FASTA label");\r
-\r
-       // NL or CR terminates label\r
-               if (NL == c || CR == c)\r
-                       break;\r
-\r
-       // All other characters added to label\r
-               ADD(c)\r
-               }\r
-\r
-// Nul-terminate label\r
-       ADD(0)\r
-       *ptrLabel = Buffer;\r
-\r
-       BufferLength = 0;\r
-       Pos = 0;\r
-       Buffer = 0;\r
-       int PreviousChar = NL;\r
-       for (;;)\r
-               {\r
-               int c = fgetc(f);\r
-               if (EOF == c)\r
-                       {\r
-                       if (feof(f))\r
-                               break;\r
-                       else if (ferror(f))\r
-                               Quit("Error reading FASTA file, ferror=TRUE feof=FALSE errno=%d %s",\r
-                                 errno, strerror(errno));\r
-                       else\r
-                               Quit("Error reading FASTA file, fgetc=EOF feof=FALSE ferror=FALSE errno=%d %s",\r
-                                 errno, strerror(errno));\r
-                       }\r
-\r
-               if ('>' == c)\r
-                       {\r
-                       if (NL == PreviousChar || CR == PreviousChar)\r
-                               {\r
-                               ungetc(c, f);\r
-                               break;\r
-                               }\r
-                       else\r
-                               Quit("Unexpected '>' in FASTA sequence data");\r
-                       }\r
-               else if (isspace(c))\r
-                       ;\r
-               else if (IsGapChar(c))\r
-                       {\r
-                       if (!DeleteGaps)\r
-                               ADD(c)\r
-                       }\r
-               else if (isalpha(c))\r
-                       {\r
-                       c = toupper(c);\r
-                       ADD(c)\r
-                       }\r
-               else if (isprint(c))\r
-                       {\r
-                       Warning("Invalid character '%c' in FASTA sequence data, ignored", c);\r
-                       continue;\r
-                       }\r
-               else\r
-                       {\r
-                       Warning("Invalid byte hex %02x in FASTA sequence data, ignored", (unsigned char) c);\r
-                       continue;\r
-                       }\r
-               PreviousChar = c;\r
-               }\r
-\r
-       if (0 == Pos)\r
-               return GetFastaSeq(f, ptrSeqLength, ptrLabel, DeleteGaps);\r
-\r
-       *ptrSeqLength = Pos;\r
-       return Buffer;\r
-       }\r