IAligner * CAlignTest::NewAligner( EAlignmentAlgo algo, int xdropoff ) const
{
// if( xdropoff == 0 ) return new CAligner_HSP();
switch( algo ) {
case eAlignment_fast: return new CAligner_fast();
case eAlignment_HSP: return new CAligner_HSP();
case eAlignment_SW:
do {
auto_ptr<CAligner_SW> swalign( new CAligner_SW() );
swalign->SetMatrix().resize( 2*xdropoff + 1 );
return swalign.release();
} while(0); break;
default: THROW( logic_error, "Bad value for m_algo" );
}
}
int main (int argc, char *argv[]) {
char seq1[ MAXSEQ ]; // input seq1
char seq2[ MAXSEQ ]; // input seq2
char bts1[ MAXSEQ ]; // back trace seq1
char bts2[ MAXSEQ ]; // back trace seq2
char aln[ MAXSEQ ]; // the one line alignment string
int swas; // smith-waterman alginment score
int c; // options
char infile1[ MAXFNL ]; // input file1
char infile2[ MAXFNL ]; // input file2
int simple; // output controls
// options
while ( ( c = getopt( argc, argv, "ha:b:i:j:s" ) ) != EOF )
switch (c) {
case 'h':
usage();
break;
case 'a':
strcpy(seq1, optarg);
break;
case 'b':
strcpy(seq2, optarg);
break;
case 'i':
strcpy(infile1, optarg);
break;
case 'j':
strcpy(infile2, optarg);
break;
case 's':
simple = 1;
break;
}
if ( argc == 1 ) {
usage();
}
// check if sequences were passed by file
if ( ( infile1[0] != '\0' ) && ( infile2[0] != '\0' ) ) {
readseq( infile1, seq1 );
readseq( infile2, seq2 );
}
// check if sequences are ready
if ( ( seq1[0] == '\0' ) || ( seq2[0] == '\0' ) ) {
printf("Error: insufficent input sequences found!\n");
usage();
}
// covert sequences to UPPER case
upper( seq1 );
upper( seq2 );
// do smith-waterman alignment
swas = swalign( seq1, seq2, bts1, bts2, aln );
// output alignment
if ( simple == 1 ) {
printf("%d\n", swas);
puts(bts1);
puts(aln);
puts(bts2);
} else {
printf("Smith-Waterman Alignment:\n\n");
printf("Score:\t%d\n\n", swas);
print_align( bts1, bts2, aln );
}
}
