5 void arguments( int argc, char *argv[] )
9 ppenalty = NOTSPECIFIED;
10 ppenalty_ex = NOTSPECIFIED;
11 poffset = NOTSPECIFIED;
12 kimuraR = NOTSPECIFIED;
14 scoremtx = NOTSPECIFIED;
16 while( --argc > 0 && (*++argv)[0] == '-' )
18 while ( ( c = *++argv[0] ) )
23 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
24 fprintf( stderr, "ppenalty = %d\n", ppenalty );
28 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
29 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
33 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
34 fprintf( stderr, "poffset = %d\n", poffset );
38 kimuraR = atoi( *++argv );
39 fprintf( stderr, "kimuraR = %d\n", kimuraR );
49 fprintf( stderr, "illegal option %c\n", c );
59 cut = atof( (*argv) );
65 int main( int ac, char **av )
68 static char name[M][B], **seq;
70 extern double score_calc_for_score( int, char ** );
77 seq = AllocateCharMtx( njob, nlenmax );
79 readData( stdin, name, nlen, seq );
81 if( !isaligned( njob, seq ) ) ErrorExit( "Not aligned." );
83 constants( njob, seq );
85 score = score_calc_for_score( njob, seq );
86 if( scoremtx == 0 ) score += offset;
88 fprintf( stdout, "score = %f\n", score );
89 if ( scoremtx == 0 ) fprintf( stdout, "JTT %dPAM\n", pamN );
90 else if( scoremtx == 1 ) fprintf( stdout, "Dayhoff( machigai ga aru )\n" );
91 else if( scoremtx == 2 ) fprintf( stdout, "M-Y\n" );
92 else if( scoremtx == -1 ) fprintf( stdout, "DNA 1:%d\n", kimuraR );
94 fprintf( stdout, "gap penalty = %+6.2f, %+6.2f, %+6.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );