--- /dev/null
+#include "mltaln.h"
+#include "mtxutl.h"
+
+#define DEBUG 0
+#define TEST 0
+
+#define END_OF_VEC -1
+
+static int maxl;
+static int tsize;
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = NULL;
+ disopt = 0;
+ scoremtx = 1;
+ nblosum = 62;
+ dorp = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'I':
+ disopt = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: -i\n" );
+ exit( 1 );
+ }
+}
+
+void seq_grp_nuc( int *grp, char *seq )
+{
+ int tmp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 4 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\n", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+}
+
+void seq_grp( int *grp, char *seq )
+{
+ int tmp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 6 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\n", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+}
+
+void makecompositiontable_p( short *table, int *pointt )
+{
+ int point;
+
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ table[point]++;
+}
+
+int commonsextet_p( short *table, int *pointt )
+{
+ int value = 0;
+ short tmp;
+ int point;
+ static short *memo = NULL;
+ static int *ct = NULL;
+ static int *cp;
+
+ if( !memo )
+ {
+ memo = (short *)calloc( tsize, sizeof( short ) );
+ if( !memo ) ErrorExit( "Cannot allocate memo\n" );
+ ct = (int *)calloc( MIN( maxl, tsize)+1, sizeof( int ) );
+ if( !ct ) ErrorExit( "Cannot allocate memo\n" );
+ }
+
+ cp = ct;
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ {
+ tmp = memo[point]++;
+ if( tmp < table[point] )
+ value++;
+ if( tmp == 0 ) *cp++ = point;
+// fprintf( stderr, "cp - ct = %d (tsize = %d)\n", cp - ct, tsize );
+ }
+ *cp = END_OF_VEC;
+
+ cp = ct;
+ while( *cp != END_OF_VEC )
+ memo[*cp++] = 0;
+
+ return( value );
+}
+
+void makepointtable_nuc( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ p = n;
+ point = *n++ * 1024;
+ point += *n++ * 256;
+ point += *n++ * 64;
+ point += *n++ * 16;
+ point += *n++ * 4;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 1024;
+ point *= 4;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+void makepointtable( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ p = n;
+ point = *n++ * 7776;
+ point += *n++ * 1296;
+ point += *n++ * 216;
+ point += *n++ * 36;
+ point += *n++ * 6;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 7776;
+ point *= 6;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+int main( int argc, char **argv )
+{
+ int i, j;
+ FILE *fp, *infp;
+ char **seq;
+ int *grpseq;
+ char *tmpseq;
+ int **pointt;
+ static char name[M][B];
+ static int nlen[M];
+ double **mtx;
+ double **mtx2;
+ double score, score0;
+ static short *table1;
+ char b[B];
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ getnumlen( infp );
+#endif
+ rewind( infp );
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ tmpseq = AllocateCharVec( nlenmax+1 );
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ grpseq = AllocateIntVec( nlenmax+1 );
+ pointt = AllocateIntMtx( njob, nlenmax+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ mtx2 = AllocateDoubleMtx( njob, njob );
+ pamN = NOTSPECIFIED;
+
+#if 0
+ FRead( infp, name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+
+ fclose( infp );
+
+ constants( njob, seq );
+
+ if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
+ else tsize = (int)pow( 6, 6 );
+
+ maxl = 0;
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( tmpseq, seq[i] );
+ nlen[i] = strlen( tmpseq );
+ if( nlen[i] < 6 )
+ {
+ fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
+ exit( 1 );
+ }
+ if( nlen[i] > maxl ) maxl = nlen[i];
+ if( dorp == 'd' ) /* nuc */
+ {
+ seq_grp_nuc( grpseq, tmpseq );
+ makepointtable_nuc( pointt[i], grpseq );
+ }
+ else /* amino */
+ {
+ seq_grp( grpseq, tmpseq );
+ makepointtable( pointt[i], grpseq );
+ }
+ }
+ for( i=0; i<njob; i++ )
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "%4d / %4d\r", i+1, njob );
+ }
+ makecompositiontable_p( table1, pointt[i] );
+
+ for( j=i; j<njob; j++ )
+ {
+ score = (double)commonsextet_p( table1, pointt[j] );
+ mtx[i][j] = score;
+ }
+ free( table1 );
+ }
+ for( i=0; i<njob; i++ )
+ {
+ score0 = mtx[i][i];
+ for( j=0; j<njob; j++ )
+ mtx2[i][j] = ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3.0;
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+#if TEST
+ double jscore;
+ jscore = mtx[i][j] / ( MIN( strlen( seq[i] ), strlen( seq[j] ) ) - 2 );
+ fprintf( stdout, "jscore = %f\n", jscore );
+
+ fprintf( stdout, "mtx2[%d][%d] = %f, mtx2[%d][%d] = %f\n", i, j, mtx2[i][j], j, i, mtx2[j][i] );
+#endif
+ mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
+#if TEST
+ fprintf( stdout, "sonokekka mtx2[%d][%d] %f\n", i, j, mtx2[i][j] );
+#endif
+ }
+
+ if( disopt )
+ {
+ for( i=0; i<njob; i++ )
+ {
+ sprintf( b, "=lgth = %04d", nlen[i] );
+ strins( b, name[i] );
+ }
+ }
+
+ fp = fopen( "hat2", "w" );
+ if( !fp ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( fp, njob, name, mtx2 );
+ fclose( fp );
+
+ fprintf( stderr, "\n" );
+ SHOWVERSION;
+ exit( 0 );
+}
git://source.jalview.org / jabaws.git / blobdiff