/* read a fasta file and pass the sequence to an array */
void readseq (char filename[], char seq[]) {
FILE *file; // hold fasta file
int i; // index for seq[]
char line[ MAXCOL ]; // store each line
int j; // index for line[]
file = fopen( filename, "r" );
if ( file == NULL ) {
printf("Error: file %s does not exist!\n", filename);
exit(1);
}
i = 0;
while ( fgets( line, sizeof line, file ) ) {
/* if a fasta header line was found */
if ( line[0] == '>' ) continue;
/* now try to parse the fasta body */
for ( j = 0; j < strlen(line); j++ ) {
if ( isnuc( line[j] ) ) seq[i++] = line[j];
}
} // end of while
seq[i] = '\0';
fclose( file );
} // end readseq
//// read and filter a line of input sequence from the file stream
void Gene::readline( char linebuff[], int const chars )
{
// use temporary filter container to avoid constly multiple redimensioning
std::vector< char > clean( chars );
int nclean(0);
// filter as rapidly as possible
for ( int i(0); i < chars; ++i ) {
char const thischar = linebuff[i];
if ( isnuc(thischar) ) clean[nclean++] = thischar;
}
sequence_.insert( sequence_.end(), clean.begin(), clean.begin() + nclean );
}
