+++ /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