--- /dev/null
+#include "mltaln.h"
+#include <sys/types.h>
+#include <unistd.h>
+#define DEBUG 0
+#define TEST 0
+
+
+int howmanyx( char *s )
+{
+ int val = 0;
+ if( scoremtx == -1 )
+ {
+ do
+ {
+ if( !strchr( "atgcuATGCU", *s ) ) val++;
+ } while( *++s );
+ }
+ else
+ {
+ do
+ {
+ if( !strchr( "ARNDCQEGHILKMFPSTWYV", *s ) ) val++;
+ } while( *++s );
+ }
+ return( val );
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = NULL;
+ disopt = 0;
+ divpairscore = 0;
+ swopt = "";
+
+ 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 'I':
+ disopt = 1;
+ break;
+ case 'A':
+ swopt = "-A";
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: -i\n" );
+ exit( 1 );
+ }
+}
+
+int main( int argc, char *argv[] )
+{
+ int ktuple;
+ int i, j;
+ FILE *hat2p;
+ FILE *hat3p;
+ FILE *infp;
+ char **seq = NULL; // by D.Mathog
+ char **seq1;
+ static char name[M][B];
+ static char name1[M][B];
+ static int nlen1[M];
+ double **mtx;
+ double **mtx2;
+ static int nlen[M];
+ char b[B];
+ double max;
+ char com[1000];
+ int opt[M];
+ int res;
+ char *home;
+ char *fastapath;
+ char queryfile[B];
+ char datafile[B];
+ char fastafile[B];
+ char hat2file[B];
+ int pid = (int)getpid();
+ LocalHom **localhomtable, *tmpptr;
+#if 0
+ home = getenv( "HOME" );
+#else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */
+ home = NULL;
+#endif
+ fastapath = getenv( "FASTA_4_MAFFT" );
+ if( !fastapath )
+ fastapath = "fasta34";
+
+#if DEBUG
+ if( home ) fprintf( stderr, "home = %s\n", home );
+#endif
+ if( !home ) home = "";
+ sprintf( queryfile, "%s/tmp/query-%d", home, pid );
+ sprintf( datafile, "%s/tmp/data-%d", home, pid );
+ sprintf( fastafile, "%s/tmp/fasta-%d", home, pid );
+ sprintf( hat2file, "hat2-%d", pid );
+
+
+ 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
+ dorp = NOTSPECIFIED;
+ getnumlen( infp );
+#endif
+
+ if( dorp == 'd' )
+ {
+ scoremtx = -1;
+ pamN = NOTSPECIFIED;
+ }
+ else
+ {
+ nblosum = 62;
+ scoremtx = 1;
+ }
+ constants( njob, seq );
+
+ rewind( infp );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ seq1 = AllocateCharMtx( 2, nlenmax+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ mtx2 = AllocateDoubleMtx( njob, njob );
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ }
+ }
+
+#if 0
+ FRead( infp, name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ if( scoremtx == -1 ) ktuple = 6;
+ else ktuple = 1;
+
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( seq1[0], seq[i] );
+ strcpy( seq[i], seq1[0] );
+ }
+ for( j=0; j<njob; j++ )
+ {
+ sprintf( name1[j], "+==========+%d ", j );
+ nlen1[j] = nlen[j];
+ }
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob, name1, nlen1, seq );
+ fclose( hat2p );
+
+ for( i=0; i<njob; i++ )
+ {
+// fprintf( stderr, "### i = %d\n", i );
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
+ fclose( hat2p );
+
+ seq1[0] = seq[i];
+ nlen1[0] = nlen[i];
+
+ hat2p = fopen( queryfile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open queryfile." );
+ WriteForFasta( hat2p, 1, name1+i, nlen1, seq1 );
+ fclose( hat2p );
+
+
+ if( scoremtx == -1 )
+ sprintf( com, "%s %s -z3 -m10 -n -Q -b%d -E%d -d%d %s %s %d > %s", fastapath, swopt, M, M, M, queryfile, datafile, ktuple, fastafile );
+ else
+ sprintf( com, "%s %s -z3 -m10 -Q -b%d -E%d -d%d %s %s %d > %s", fastapath, swopt, M, M, M, queryfile, datafile, ktuple, fastafile );
+ res = system( com );
+ if( res ) ErrorExit( "error in fasta" );
+
+
+
+ hat2p = fopen( fastafile, "r" );
+ if( hat2p == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ if( scoremtx == -1 )
+ res = ReadFasta34m10_nuc( hat2p, mtx[i], i, name1, localhomtable[i] );
+ else
+ res = ReadFasta34m10( hat2p, mtx[i], i, name1, localhomtable[i] );
+ fclose( hat2p );
+
+ if( res < njob - i )
+ {
+ fprintf( stderr, "count (fasta34 -z 3) = %d\n", res );
+ exit( 1 );
+ }
+
+
+ if( i == 0 )
+ for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];
+
+
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
+ fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
+ }
+#endif
+ fprintf( stderr, "query : %4d / %5d\r", i+1, njob );
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ max = mtx[i][i];
+ if( max == 0.0 )
+ {
+ for( j=0; j<njob; j++ )
+ mtx2[i][j] = 2.0;
+ }
+ else
+ {
+ for( j=0; j<njob; j++ )
+ {
+// fprintf( stderr, "##### mtx[%d][%d] = %f\n", i, j, mtx[i][j] );
+ mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
+// fprintf( stdout, "max = %f, mtx[%d][%d] = %f -> %f\n", max, i+1, j+1, mtx[i][j], mtx2[i][j] );
+ }
+ }
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+// fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
+ mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
+ }
+
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ )
+ fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
+ }
+#endif
+
+ for( i=0; i<njob; i++ ) name[i][0] = '=';
+
+ if( disopt )
+ {
+ strcpy( b, name[0] );
+ sprintf( name[0], "=query====lgth=%04d-%04d %.*s", nlen[0], howmanyx( seq[0] ), B-30, b );
+#if 0
+ strins( b, name[0] );
+#endif
+ for( i=1; i<njob; i++ )
+ {
+ strcpy( b, name[i] );
+ sprintf( name[i], "=opt=%04d=lgth=%04d-%04d %.*s", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
+#if 0
+ strins( b, name[i] );
+#endif
+ }
+ }
+
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( hat2p, njob, name, mtx2 );
+ fclose( hat2p );
+
+#if 1
+ fprintf( stderr, "##### writing hat3\n" );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+ }
+ }
+ fclose( hat3p );
+#endif
+
+ sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
+ system( com );
+
+#if 0
+ sprintf( com, ALNDIR "/supgsdl < %s", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in spgsdl" );
+#endif
+
+ sprintf( com, "mv %s hat2", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in mv" );
+
+ SHOWVERSION;
+ exit( 0 );
+}
git://source.jalview.org / jabaws.git / blobdiff