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#include "mltaln.h"
#define DEBUG 0
void arguments( int argc, char *argv[] )
{
int c;
ppenalty = NOTSPECIFIED;
ppenalty_ex = NOTSPECIFIED;
poffset = NOTSPECIFIED;
kimuraR = NOTSPECIFIED;
pamN = NOTSPECIFIED;
scoremtx = NOTSPECIFIED;
while( --argc > 0 && (*++argv)[0] == '-' )
{
while ( ( c = *++argv[0] ) )
{
switch( c )
{
case 'f':
ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
fprintf( stderr, "ppenalty = %d\n", ppenalty );
--argc;
goto nextoption;
case 'g':
ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
--argc;
goto nextoption;
case 'h':
poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
fprintf( stderr, "poffset = %d\n", poffset );
--argc;
goto nextoption;
case 'k':
kimuraR = atoi( *++argv );
fprintf( stderr, "kimuraR = %d\n", kimuraR );
--argc;
goto nextoption;
case 'D':
scoremtx = -1;
break;
case 'P':
scoremtx = 0;
break;
default:
fprintf( stderr, "illegal option %c\n", c );
argc = 0;
break;
}
}
nextoption:
;
}
if( argc == 1 )
{
cut = atof( (*argv) );
argc--;
}
}
int main( int ac, char **av )
{
int nlen[M];
static char name[M][B], **seq;
double score;
extern double score_calc_for_score( int, char ** );
arguments( ac, av );
getnumlen( stdin );
rewind( stdin );
seq = AllocateCharMtx( njob, nlenmax );
readData( stdin, name, nlen, seq );
if( !isaligned( njob, seq ) ) ErrorExit( "Not aligned." );
constants( njob, seq );
score = score_calc_for_score( njob, seq );
if( scoremtx == 0 ) score += offset;
fprintf( stdout, "score = %f\n", score );
if ( scoremtx == 0 ) fprintf( stdout, "JTT %dPAM\n", pamN );
else if( scoremtx == 1 ) fprintf( stdout, "Dayhoff( machigai ga aru )\n" );
else if( scoremtx == 2 ) fprintf( stdout, "M-Y\n" );
else if( scoremtx == -1 ) fprintf( stdout, "DNA 1:%d\n", kimuraR );
fprintf( stdout, "gap penalty = %+6.2f, %+6.2f, %+6.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
exit( 0 );
}
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