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#include "libMUSCLE/muscle.h"
#include <stdio.h>
#include <errno.h>
namespace muscle {
//const int BUFFER_BYTES = 16*1024;
const int BUFFER_BYTES = 128;
const int CR = '\r';
const int NL = '\n';
#define ADD(c) \
{ \
if (Pos >= BufferLength) \
{ \
const int NewBufferLength = BufferLength + BUFFER_BYTES; \
char *NewBuffer = new char[NewBufferLength]; \
memcpy(NewBuffer, Buffer, BufferLength); \
delete[] Buffer; \
Buffer = NewBuffer; \
BufferLength = NewBufferLength; \
} \
Buffer[Pos++] = c; \
}
// Get next sequence from file.
char *GetFastaSeq(FILE *f, unsigned *ptrSeqLength, char **ptrLabel, bool DeleteGaps)
{
unsigned BufferLength = 0;
unsigned Pos = 0;
char *Buffer = 0;
int c = fgetc(f);
if (EOF == c)
return 0;
// = on a line by itself indicates the end of a Multi-FastA entry in an eXtended Multi-FastA file
if ('=' == c)
{
int c = fgetc(f);
if (NL == c)
return 0;
if (CR == c)
{
c = fgetc(f);
if (NL == c)
return 0;
}
Quit("Invalid file format, '=' may only be used on a line by itself to indicate the end of a MFA entry in an XMFA");
}
if ('>' != c)
Quit("Invalid file format, expected '>' to start FASTA label");
for (;;)
{
int c = fgetc(f);
if (EOF == c)
Quit("End-of-file or input error in FASTA label");
// NL or CR terminates label
if (NL == c || CR == c)
break;
// All other characters added to label
ADD(c)
}
// Nul-terminate label
ADD(0)
*ptrLabel = Buffer;
BufferLength = 0;
Pos = 0;
Buffer = 0;
int PreviousChar = NL;
for (;;)
{
int c = fgetc(f);
if( '=' == c && NL == PreviousChar )
{
ungetc(c, f);
break; // use = on a line by itself to signify the end of a multi-fasta entry
}
if (EOF == c)
{
if (feof(f))
break;
else if (ferror(f))
Quit("Error reading FASTA file, ferror=TRUE feof=FALSE errno=%d %s",
errno, strerror(errno));
else
Quit("Error reading FASTA file, fgetc=EOF feof=FALSE ferror=FALSE errno=%d %s",
errno, strerror(errno));
}
if ('>' == c)
{
if (NL == PreviousChar || CR == PreviousChar)
{
ungetc(c, f);
break;
}
else
Quit("Unexpected '>' in FASTA sequence data");
}
else if (isspace(c))
;
else if (IsGapChar(c))
{
if (!DeleteGaps)
ADD(c)
}
else if (isalpha(c))
{
c = toupper(c);
ADD(c)
}
else if (isprint(c))
{
Warning("Invalid character '%c' in FASTA sequence data, ignored", c);
continue;
}
else
{
Warning("Invalid byte hex %02x in FASTA sequence data, ignored", (unsigned char) c);
continue;
}
PreviousChar = c;
}
if (0 == Pos)
return GetFastaSeq(f, ptrSeqLength, ptrLabel, DeleteGaps);
*ptrSeqLength = Pos;
return Buffer;
}
}
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