+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-static int usecache;
-static char *whereispairalign;
-static double scale;
-static int *alreadyoutput;
-static int equivthreshold;
-static int equivwinsize;
-static int equivshortestlen;
-
-static void cutpath( char *s )
-{
- char *pos;
- pos = s + strlen( s );
-
- while( --pos >= s )
- {
- if( *pos == '/' ) break;
- }
-
- strcpy( s, pos+1 );
-}
-
-static char getchainid( char *s )
-{
- s += strlen( s ) - 2;
- if( isspace( s[0] ) && isalnum( s[1] ) )
- return( s[1] );
- else
- return( 'A' );
-}
-
-static void extractfirstword( char *s )
-{
- while( *s )
- {
- if( isspace( *s ) ) break;
- s++;
- }
- *s = 0;
-}
-
-static char *strip( char *s )
-{
- char *v;
-
- while( *s )
- {
- if( !isspace( *s ) ) break;
- s++;
- }
- v = s;
-
- s += strlen( v ) - 1;
- while( s>=v )
- {
- if( !isspace( *s ) )
- {
- *(s+1) = 0;
- break;
- }
- s--;
- }
-
- return( v );
-}
-
-#if 0
-static void makeequivdouble( double *d, char *c )
-{
- while( *c )
- {
- *d++ = (double)( *c++ - '0' );
- }
-}
-
-static void maskequiv( double *d, int n )
-{
- int halfwin;
- int ok;
- int i, j;
-
- halfwin = (int)( equivwinsize / 2 );
-
- for( i=0; i<n; i++ )
- {
- ok = 1;
- for( j = i-halfwin; j<i+halfwin; j++ )
- {
- if( j<0 || n=<j ) continue;
- if( d[j] <= 0.0 )
- {
- ok = 0;
- break;
- }
- }
- if( ok == 0 ) d[i] = 0.0;
- }
-}
-#else
-static void maskequiv( double *d, int n )
-{
- int i, len;
- int count;
- len = 0;
- double *dbk, *dori, *dbkori;
-
- dbk = calloc( n, sizeof( double ) );
-
- dbkori = dbk;
- dori = d;
- count = n;
- while( count-- )
- {
- *dbk++ = *d++;
- }
-
- dbk = dbkori;
- d = dori;
- len = 0;
-
-
- for( i=0; i<n; i++ )
- {
- if( d[i] > 0.0 )
- {
- len += 1;
- d[i] = 0.0;
- }
- else
- {
- d[i] = 0.0;
- if( len >= equivshortestlen )
- {
- len++;
- while( len-- ) d[i-len] = dbk[i-len];
- }
- len = 0;
- }
- }
-
- if( len >= equivshortestlen )
- {
- len++;
- while( len-- ) d[n-len] = dbk[n-len];
- }
-
- free( dbk );
-}
-#endif
-
-static void makeequivdouble_tmalign( double *d, char *c, int n )
-{
- double tmpd;
- double *dbk;
- int tmpi;
- char s;
- dbk = d;
- while( *c )
- {
- if( ( s=*c++ ) == ':' )
- tmpi = 9;
- else if( s == '.' )
- tmpi = 4;
- else
- tmpi = 0;
-// tmpd = (double)( tmpi + 1 - equivthreshold ) / ( 10 - equivthreshold ) * 9.0;
-// if( tmpd < 0.0 ) tmpd = 0.0;
- tmpd = (double)( tmpi );
-// *d++ = (int)tmpd;
- *d++ = tmpd;
- }
-
- d = dbk;
-// maskequiv( d, n );
-}
-
-static void makeequivdouble_threshold( double *d, char *c, int n )
-{
- double tmpd;
- double *dbk;
- int tmpi;
- dbk = d;
- while( *c )
- {
- tmpi = (int)( *c++ - '0' );
- tmpd = (double)( tmpi + 1 - equivthreshold ) / ( 10 - equivthreshold ) * 9.0;
- if( tmpd < 0.0 ) tmpd = 0.0;
-// *d++ = (int)tmpd;
- *d++ = tmpd;
- }
-
- d = dbk;
- maskequiv( d, n );
-}
-
-static void readtmalign( FILE *fp, char *seq1, char *seq2, double *equiv )
-{
- static char *line = NULL;
- static char *equivchar = NULL;
- int n;
-
-
- if( equivchar == NULL )
- {
- equivchar = calloc( nlenmax * 2 + 1, sizeof( char ) );
- line = calloc( nlenmax * 2 + 1, sizeof( char ) );
- }
- seq1[0] = 0;
- seq2[0] = 0;
- equivchar[0] = 0;
-
-
-// system( "vi _tmalignout" );
- while( 1 )
- {
- if( feof( fp ) )
- {
- fprintf( stderr, "Error in TMalign\n" );
- exit( 1 );
- }
- fgets( line, 999, fp );
-// fprintf( stdout, "line = :%s:\n", line );
- if( !strncmp( line+5, "denotes the residue pairs", 20 ) ) break;
- }
- fgets( line, nlenmax*2, fp );
- strcat( seq1, strip( line ) );
-
- fgets( line, nlenmax*2, fp );
- strcat( equivchar, strip( line ) );
-
- fgets( line, nlenmax*2, fp );
- strcat( seq2, strip( line ) );
-
-#if 0
- printf( "seq1=%s\n", seq1 );
- printf( "seq2=%s\n", seq2 );
- printf( "equi=%s\n", equivchar );
-exit( 1 );
-#endif
- n = strlen( seq1 );
- makeequivdouble_tmalign( equiv, equivchar, n );
-
-#if 0
- fprintf( stdout, "\n" );
- for( i=0; i<n; i++ )
- {
- fprintf( stdout, "%1.0f", equiv[i] );
- }
- fprintf( stdout, "\n" );
- exit( 1 );
-#endif
-}
-static void readrash( FILE *fp, char *seq1, char *seq2, double *equiv )
-{
- char line[1000];
- static char *equivchar = NULL;
- int n;
-
-
- if( equivchar == NULL )
- {
- equivchar = calloc( nlenmax * 2, sizeof( char ) );
- }
- seq1[0] = 0;
- seq2[0] = 0;
- equivchar[0] = 0;
-
- while( 1 )
- {
- fgets( line, 999, fp );
-// fprintf( stdout, "line = :%s:\n", line );
- if( !strncmp( line, "Query ", 6 ) ) break;
- if( feof( fp ) ) break;
- if( !strncmp( line, "QUERY ", 6 ) )
- {
- strcat( seq1, strip( line+5 ) );
- fgets( line, 999, fp );
- }
- if( !strncmp( line, "TEMPL ", 6 ) )
- {
- strcat( seq2, strip( line+5 ) );
- fgets( line, 999, fp );
- }
- if( !strncmp( line, "Equiva", 6 ) )
- {
- strcat( equivchar, strip( line+11 ) );
- fgets( line, 999, fp );
- }
- }
-#if 0
- printf( "seq1=:%s:\n", seq1 );
- printf( "seq2=:%s:\n", seq2 );
- printf( "equi=:%s:\n", equivchar );
-exit( 1 );
-#endif
- n = strlen( seq1 );
- makeequivdouble_threshold( equiv, equivchar, n );
-
-#if 0
- fprintf( stdout, "\n" );
- for( i=0; i<n; i++ )
- {
- fprintf( stdout, "%1.0f", equiv[i] );
- }
- fprintf( stdout, "\n" );
-#endif
-}
-
-static int checkcbeta( FILE *fp )
-{
- char linec[1000];
- while( 1 )
- {
- fgets( linec, 999, fp );
- if( feof( fp ) ) break;
- if( !strncmp( "ATOM ", linec, 5 ) )
- {
- if( !strncmp( "CB ", linec+13, 3 ) ) return( 0 );
- }
- }
- return( 1 );
-}
-
-
-static float calltmalign( char **mseq1, char **mseq2, double *equiv, char *fname1, char *chain1, char *fname2, char *chain2, int alloclen )
-{
- FILE *fp;
- int res;
- static char com[10000];
- float value;
- char cachedir[10000];
- char cachefile[10000];
- int runnow;
-
-
- if( usecache )
- {
- sprintf( cachedir, "%s/.tmalignoutcache", getenv( "HOME" ) );
- sprintf( com, "mkdir -p %s", cachedir );
- system( com );
-
- sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
-
- runnow = 0;
- fp = fopen( cachefile, "r" );
- if( fp == NULL ) runnow = 1;
- else
- {
- fgets( com, 100, fp );
- if( strncmp( com, "successful", 10 ) ) runnow = 1;
- fclose( fp );
- }
- }
- else
- {
- runnow = 1;
- }
-
- if( runnow )
- {
-#if 0
- sprintf( com, "ln -s %s %s.pdb 2>_dum", fname1, fname1 );
- res = system( com );
- sprintf( com, "ln -s %s %s.pdb 2>_dum", fname2, fname2 );
- res = system( com );
-#endif
- sprintf( com, "\"%s/TMalign\" %s.pdb %s.pdb > _tmalignout 2>_dum", whereispairalign, fname1, fname2 );
- fprintf( stderr, "command = %s\n", com );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in TMalign\n" );
- exit( 1 );
- }
-
- }
- else
- {
- fprintf( stderr, "Cache is not supported!\n" );
- exit( 1 );
- }
-
- fp = fopen( "_tmalignout", "r" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _tmalignout\n" );
- exit( 1 );
- }
-
- readtmalign( fp, *mseq1, *mseq2, equiv );
-
- fclose( fp );
-
-// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
-// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
-
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
-
- return( value );
-}
-
-static float callrash( int mem1, int mem2, char **mseq1, char **mseq2, double *equiv, char *fname1, char *chain1, char *fname2, char *chain2, int alloclen )
-{
- FILE *fp;
- int res;
- static char com[10000];
- float value;
- char cachedir[10000];
- char cachefile[10000];
- int runnow;
- char pairid[1000];
-
- sprintf( pairid, "%d-%d", mem1, mem2 );
-// fprintf( stderr, "pairid = %s\n", pairid );
-
- if( usecache )
- {
- sprintf( cachedir, "%s/.rashoutcache", getenv( "HOME" ) );
- sprintf( com, "mkdir -p %s", cachedir );
- system( com );
-
- sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
-
- runnow = 0;
- fp = fopen( cachefile, "r" );
- if( fp == NULL ) runnow = 1;
- else
- {
- fgets( com, 100, fp );
- if( strncmp( com, "successful", 10 ) ) runnow = 1;
- fclose( fp );
- }
- }
- else
- {
- runnow = 1;
- }
-
- if( runnow )
- {
-#if 0
- sprintf( com, "ln -s %s %s.pdb 2>_dum", fname1, fname1 );
- res = system( com );
- sprintf( com, "ln -s %s %s.pdb 2>_dum", fname2, fname2 );
- res = system( com );
-#endif
-#if 0 // 091127, pdp nai!
- sprintf( com, "env PATH=%s PDP_ASH.pl --qf %s.pdb --qc %s --tf %s.pdb --tc %s > _rashout 2>_dum", whereispairalign, fname1, chain1, fname2, chain2 );
-#else
- sprintf( com, "\"%s/rash\" --qf %s.pdb --qc %s --tf %s.pdb --tc %s --of %s.pdbpair > %s.rashout 2>%s.dum", whereispairalign, fname1, chain1, fname2, chain2, pairid, pairid, pairid );
-#endif
- fprintf( stderr, "command = %s\n", com );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in structural alignment\n" );
- exit( 1 );
- }
- sprintf( com, "awk '/^REMARK/,/^TER/' %s.pdbpair > %s.%s-x-%s.%s.pdbpair", pairid, fname1, chain1, fname2, chain2 );
- res = system( com );
-
- sprintf( com, "awk '/^REMARK/,/^TER/{next} 1' %s.pdbpair > %s.%s-x-%s.%s.pdbpair", pairid, fname2, chain2, fname1, chain1 );
- res = system( com );
-
- sprintf( com, "rm %s.pdbpair", pairid );
- res = system( com );
-
-
- }
- else
- {
- fprintf( stderr, "Use cache!\n" );
- sprintf( com, "grep -v successful %s > %s.rashout", cachefile, pairid );
- system( com );
- }
-
- if( usecache && runnow )
- {
- sprintf( com, "echo successful > %s", cachefile );
- system( com );
- sprintf( com, "cat %s.rashout >> %s", pairid, cachefile );
- system( com );
- }
-
- sprintf( com, "%s.rashout", pairid );
- fp = fopen( com, "r" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open %s\n", com );
- exit( 1 );
- }
-
- readrash( fp, *mseq1, *mseq2, equiv );
-
- fclose( fp );
-
-// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
-// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
-
-
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
-
- return( value );
-}
-
-static void preparetmalign( FILE *fp, char ***strfiles, char ***chainids, char ***seqpt, char ***mseq1pt, char ***mseq2pt, double **equivpt, int *alloclenpt )
-{
- int i, res;
- char *dumseq;
- char line[1000];
- char fname[1000];
- char command[1000];
- int linenum, istr, nstr;
- FILE *checkfp;
- char *sline;
- int use[1000];
- linenum = 0;
- nstr = 0;
- while( 1 )
- {
- fgets( line, 999, fp );
- if( feof( fp ) ) break;
- sline = strip( line );
- use[linenum] = 1;
- if( sline[0] == '#' || strlen( sline ) < 2 )
- {
- use[linenum] = 0;
- linenum++;
- continue;
- }
- extractfirstword( sline );
- checkfp = fopen( sline, "r" );
- if( checkfp == NULL )
- {
- fprintf( stderr, "Cannot open %s.\n", sline );
- exit( 1 );
- }
-#if 0
- fgets( linec, 999, checkfp );
- if( strncmp( "HEADER ", linec, 7 ) )
- {
- fprintf( stderr, "Check the format of %s.\n", sline );
- exit( 1 );
- }
-#endif
- if( checkcbeta( checkfp ) )
- {
- fprintf( stderr, "%s has no C-beta atoms.\n", sline );
- exit( 1 );
- }
- else
- nstr++;
- fclose( checkfp );
- linenum++;
- }
- njob = nstr;
- fprintf( stderr, "nstr = %d\n", nstr );
-
- *strfiles = AllocateCharMtx( nstr, 1000 );
- *chainids = AllocateCharMtx( nstr, 2 );
-
- rewind( fp );
- istr = 0;
- linenum = 0;
- while( 1 )
- {
- fgets( line, 999, fp );
- if( feof( fp ) ) break;
- sline = strip( line );
- if( use[linenum++] )
- {
- (*chainids)[istr][0] = getchainid( sline );
- (*chainids)[istr][1] = 0;
- extractfirstword( sline );
- sprintf( fname, "%s", sline );
- cutpath( fname );
- sprintf( command, "cp %s %s.pdb", sline, fname );
- system( command );
- sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
- res = system( command );
- if( res )
- {
- fprintf( stderr, "error: Install clean.pl\n" );
- exit( 1 );
- }
- strcpy( (*strfiles)[istr++], fname );
- }
- }
-
- *seqpt = AllocateCharMtx( njob, nlenmax*2+1 );
- *mseq1pt = AllocateCharMtx( njob, 0 );
- *mseq2pt = AllocateCharMtx( njob, 0 );
- *equivpt = AllocateDoubleVec( nlenmax*2+1 );
- *alloclenpt = nlenmax*2;
- dumseq = AllocateCharVec( nlenmax*2+1 );
- alreadyoutput = AllocateIntVec( njob );
- for( i=0; i<njob; i++ ) alreadyoutput[i] = 0;
-
- for( i=0; i<istr; i++ )
- {
- fprintf( stderr, "i=%d\n", i );
- (*seqpt)[i][0] = 0;
-
- (*mseq1pt)[0] = (*seqpt)[i];
- (*mseq2pt)[0] = dumseq;
-
- calltmalign( *mseq1pt, *mseq2pt, *equivpt, (*strfiles)[i], (*chainids)[i], (*strfiles)[i], (*chainids)[i], *alloclenpt );
- fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, (*strfiles)[i], (*chainids)[i], (*seqpt)[i] );
- alreadyoutput[i] = 1;
- }
-}
-
-static void prepareash( FILE *fp, char ***strfiles, char ***chainids, char ***seqpt, char ***mseq1pt, char ***mseq2pt, double **equivpt, int *alloclenpt )
-{
- int i, res;
- char *dumseq;
- char line[1000];
- char fname[1000];
- char command[1000];
- int linenum, istr, nstr;
- FILE *checkfp;
- char *sline;
- int use[1000];
- linenum = 0;
- nstr = 0;
- while( 1 )
- {
- fgets( line, 999, fp );
- if( feof( fp ) ) break;
- sline = strip( line );
- use[linenum] = 1;
- if( sline[0] == '#' || strlen( sline ) < 2 )
- {
- use[linenum] = 0;
- linenum++;
- continue;
- }
- extractfirstword( sline );
- checkfp = fopen( sline, "r" );
- if( checkfp == NULL )
- {
- fprintf( stderr, "Cannot open %s.\n", sline );
- exit( 1 );
- }
-#if 0
- fgets( linec, 999, checkfp );
- if( strncmp( "HEADER ", linec, 7 ) )
- {
- fprintf( stderr, "Check the format of %s.\n", sline );
- exit( 1 );
- }
-#endif
- if( checkcbeta( checkfp ) )
- {
- fprintf( stderr, "%s has no C-beta atoms.\n", sline );
- exit( 1 );
- }
- else
- nstr++;
- fclose( checkfp );
- linenum++;
- }
- njob = nstr;
- fprintf( stderr, "nstr = %d\n", nstr );
-
- *strfiles = AllocateCharMtx( nstr, 1000 );
- *chainids = AllocateCharMtx( nstr, 2 );
-
- rewind( fp );
- istr = 0;
- linenum = 0;
- while( 1 )
- {
- fgets( line, 999, fp );
- if( feof( fp ) ) break;
- sline = strip( line );
- if( use[linenum++] )
- {
- (*chainids)[istr][0] = getchainid( sline );
- (*chainids)[istr][1] = 0;
- extractfirstword( sline );
- sprintf( fname, "%s", sline );
- cutpath( fname );
- sprintf( command, "cp %s %s.pdb", sline, fname );
- system( command );
- sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
- res = system( command );
- if( res )
- {
- fprintf( stderr, "error: Install clean.pl\n" );
- exit( 1 );
- }
- strcpy( (*strfiles)[istr++], fname );
- }
- }
-
- *seqpt = AllocateCharMtx( njob, nlenmax*2+1 );
- *mseq1pt = AllocateCharMtx( njob, 0 );
- *mseq2pt = AllocateCharMtx( njob, 0 );
- *equivpt = AllocateDoubleVec( nlenmax*2+1 );
- *alloclenpt = nlenmax*2;
- dumseq = AllocateCharVec( nlenmax*2+1 );
- alreadyoutput = AllocateIntVec( njob );
- for( i=0; i<njob; i++ ) alreadyoutput[i] = 0;
-
- for( i=0; i<istr; i++ )
- {
- fprintf( stderr, "i=%d\n", i );
- (*seqpt)[i][0] = 0;
-
- (*mseq1pt)[0] = (*seqpt)[i];
- (*mseq2pt)[0] = dumseq;
-
- callrash( i, i, *mseq1pt, *mseq2pt, *equivpt, (*strfiles)[i], (*chainids)[i], (*strfiles)[i], (*chainids)[i], *alloclenpt );
- fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, (*strfiles)[i], (*chainids)[i], (*seqpt)[i] );
- alreadyoutput[i] = 1;
- }
-}
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- usecache = 0;
- scale = 1.0;
- equivthreshold = 5;
- equivwinsize = 5;
- equivshortestlen = 1;
- inputfile = NULL;
- fftkeika = 0;
- pslocal = -1000.0;
- constraint = 0;
- nblosum = 62;
- fmodel = 0;
- calledByXced = 0;
- devide = 0;
- use_fft = 0;
- fftscore = 1;
- fftRepeatStop = 0;
- fftNoAnchStop = 0;
- weight = 3;
- utree = 1;
- tbutree = 1;
- refine = 0;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 1;
- alg = 'R';
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- treemethod = 'x';
- contin = 0;
- scoremtx = 1;
- kobetsubunkatsu = 0;
- divpairscore = 0;
- dorp = NOTSPECIFIED;
- ppenalty = NOTSPECIFIED;
- ppenalty_OP = NOTSPECIFIED;
- ppenalty_ex = NOTSPECIFIED;
- ppenalty_EX = NOTSPECIFIED;
- poffset = NOTSPECIFIED;
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- geta2 = GETA2;
- fftWinSize = NOTSPECIFIED;
- fftThreshold = NOTSPECIFIED;
- RNAppenalty = NOTSPECIFIED;
- RNApthr = 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 'f':
- ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'g':
- ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'O':
- ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'E':
- ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'h':
- poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'k':
- kimuraR = atoi( *++argv );
-// fprintf( stderr, "kimuraR = %d\n", kimuraR );
- --argc;
- goto nextoption;
- case 'b':
- nblosum = atoi( *++argv );
- scoremtx = 1;
-// fprintf( stderr, "blosum %d\n", nblosum );
- --argc;
- goto nextoption;
- case 'j':
- pamN = atoi( *++argv );
- scoremtx = 0;
- TMorJTT = JTT;
- fprintf( stderr, "jtt %d\n", pamN );
- --argc;
- goto nextoption;
- case 'm':
- pamN = atoi( *++argv );
- scoremtx = 0;
- TMorJTT = TM;
- fprintf( stderr, "TM %d\n", pamN );
- --argc;
- goto nextoption;
- case 'd':
- whereispairalign = *++argv;
- fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
- --argc;
- goto nextoption;
- case 't':
- equivthreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- equivwinsize = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'l':
- equivshortestlen = atoi( *++argv );
- --argc;
- goto nextoption;
- case 's':
- scale = atof( *++argv );
- --argc;
- goto nextoption;
- case 'c':
- usecache = 1;
- break;
-#if 1
- case 'a':
- fmodel = 1;
- break;
-#endif
- case 'r':
- fmodel = -1;
- break;
- case 'D':
- dorp = 'd';
- break;
- case 'P':
- dorp = 'p';
- break;
- case 'e':
- fftscore = 0;
- break;
-#if 0
- case 'O':
- fftNoAnchStop = 1;
- break;
-#endif
- case 'Q':
- calledByXced = 1;
- break;
- case 'x':
- disp = 1;
- break;
-#if 0
- case 'a':
- alg = 'a';
- break;
-#endif
- case 'S':
- alg = 'S';
- break;
- case 'L':
- alg = 'L';
- break;
- case 'B':
- alg = 'B';
- break;
- case 'T':
- alg = 'T';
- break;
- case 'H':
- alg = 'H';
- break;
- case 'M':
- alg = 'M';
- break;
- case 'R':
- alg = 'R';
- break;
- case 'N':
- alg = 'N';
- break;
- case 'K':
- alg = 'K';
- break;
- case 'A':
- alg = 'A';
- break;
- case 'V':
- alg = 'V';
- break;
- case 'C':
- alg = 'C';
- break;
- case 'F':
- use_fft = 1;
- break;
- case 'v':
- tbrweight = 3;
- break;
- case 'y':
- divpairscore = 1;
- break;
-/* Modified 01/08/27, default: user tree */
- case 'J':
- tbutree = 0;
- break;
-/* modification end. */
-#if 0
- case 'z':
- fftThreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- fftWinSize = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'Z':
- checkC = 1;
- break;
-#endif
- default:
- fprintf( stderr, "illegal option %c\n", c );
- argc = 0;
- break;
- }
- }
- nextoption:
- ;
- }
- if( argc == 1 )
- {
- cut = atof( (*argv) );
- argc--;
- }
- if( argc != 0 )
- {
- fprintf( stderr, "options: Check source file !\n" );
- exit( 1 );
- }
- if( tbitr == 1 && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : o, m or u\n" );
- exit( 1 );
- }
- if( alg == 'C' && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : C, o\n" );
- exit( 1 );
- }
-}
-
-int countamino( char *s, int end )
-{
- int val = 0;
- while( end-- )
- if( *s++ != '-' ) val++;
- return( val );
-}
-
-static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *equiv, double *effarr, char **strfiles, char **chainids, int alloclen )
-{
- int i, j, ilim;
- int clus1, clus2;
- int off1, off2;
- float pscore = 0.0; // by D.Mathog
- static char *indication1, *indication2;
- FILE *hat2p, *hat3p;
- static double **distancemtx;
- static double *effarr1 = NULL;
- static double *effarr2 = NULL;
- char *pt;
- char *hat2file = "hat2";
- LocalHom **localhomtable, *tmpptr;
- static char **pair;
-// int intdum;
- double bunbo;
- char **checkseq;
-
-
- 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;
- localhomtable[i][j].nokori = 0;
- }
- }
-
- if( effarr1 == NULL )
- {
- distancemtx = AllocateDoubleMtx( njob, njob );
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
- checkseq = AllocateCharMtx( njob, alloclen );
-#if 0
-#else
- pair = AllocateCharMtx( njob, njob );
-#endif
- }
-
-#if 0
- fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
-#endif
-
-#if 0
- for( i=0; i<njob; i++ )
- fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
-#endif
-
-
-// writePre( njob, name, nlen, aseq, 0 );
-
- for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
- for( i=0; i<njob; i++ ) pair[i][i] = 1;
-
- for( i=0; i<njob; i++ )
- {
- strcpy( checkseq[i], seq[i] );
-// fprintf( stderr, "checkseq[%d] = %s\n", i, checkseq[i] );
- }
-
-
- ilim = njob - 1;
- for( i=0; i<ilim; i++ )
- {
- fprintf( stderr, "% 5d / %d\r", i, njob );
-
-
- for( j=i+1; j<njob; j++ )
- {
-
-
-#if 0
- if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
- {
- distancemtx[i][j] = pscore;
- continue;
- }
-#endif
-
- strcpy( aseq[i], seq[i] );
- strcpy( aseq[j], seq[j] );
- clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
- clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
- // fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
- // fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
-
-#if 0
- fprintf( stderr, "group1 = %.66s", indication1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "group2 = %.66s", indication2 );
- fprintf( stderr, "\n" );
-#endif
-// for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
-
-#if 1
- {
- switch( alg )
- {
- case( 'T' ):
- fprintf( stderr, " Calling tmalign %d-%d/%d \r", i+1, j+1, njob );
- pscore = calltmalign( mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen );
- off1 = off2 = 0;
- break;
- case( 'R' ):
- fprintf( stderr, " Calling PDP_ASH.pl %d-%d/%d \r", i+1, j+1, njob );
- pscore = callrash( i, j, mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen );
- off1 = off2 = 0;
- break;
- ErrorExit( "ERROR IN SOURCE FILE" );
- }
- }
-#endif
- distancemtx[i][j] = pscore;
-#if SCOREOUT
- fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
-#endif
-
- putlocalhom_str( mseq1[0], mseq2[0], equiv, scale, localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
-#if 1
-
- if( alreadyoutput[i] == 0 )
- {
- alreadyoutput[i] = 1;
- gappick0( seq[i], mseq1[0] );
- fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, strfiles[i], chainids[i], seq[i] );
- strcpy( checkseq[i], seq[i] );
- }
- else
- {
- gappick0( seq[i], mseq1[0] );
- fprintf( stderr, "checking seq%d\n", i );
-
-// fprintf( stderr, " seq=%s\n", seq[i] );
-// fprintf( stderr, "checkseq=%s\n", checkseq[i] );
-
- if( strcmp( checkseq[i], seq[i] ) )
- {
- fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
- fprintf( stderr, "i=%d\n", i );
- fprintf( stderr, " seq=%s\n", seq[i] );
- fprintf( stderr, "checkseq=%s\n", checkseq[i] );
- exit( 1 );
- }
- }
- if( alreadyoutput[j] == 0 )
- {
- alreadyoutput[j] = 1;
- gappick0( seq[j], mseq2[0] );
- fprintf( stdout, ">%d_%s-%s\n%s\n", j+1, strfiles[j], chainids[j], seq[j] );
- strcpy( checkseq[j], seq[j] );
- }
- else
- {
- gappick0( seq[j], mseq2[0] );
- fprintf( stderr, "checking seq%d\n", j );
- if( strcmp( checkseq[j], seq[j] ) )
- {
- fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
- fprintf( stderr, "j=%d\n", j );
- fprintf( stderr, " seq=%s\n", seq[j] );
- fprintf( stderr, "checkseq=%s\n", checkseq[j] );
- exit( 1 );
- }
- }
-#endif
- }
- }
- for( i=0; i<njob; i++ )
- {
- pscore = 0.0;
- for( pt=seq[i]; *pt; pt++ )
- pscore += amino_dis[(int)*pt][(int)*pt];
- distancemtx[i][i] = pscore;
-
- }
-
- ilim = njob-1;
- for( i=0; i<ilim; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
- if( bunbo == 0.0 )
- distancemtx[i][j] = 2.0;
- else
- distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
- }
- }
-
- hat2p = fopen( hat2file, "w" );
- if( !hat2p ) ErrorExit( "Cannot open hat2." );
- WriteHat2( hat2p, njob, name, distancemtx );
- fclose( hat2p );
-
- fprintf( stderr, "##### writing hat3\n" );
- hat3p = fopen( "hat3", "w" );
- if( !hat3p ) ErrorExit( "Cannot open hat3." );
- ilim = njob-1;
- for( i=0; i<ilim; 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 %7.5f %d %d %d %d k\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
- }
- }
- }
- fclose( hat3p );
-#if DEBUG
- fprintf( stderr, "calling FreeLocalHomTable\n" );
-#endif
- FreeLocalHomTable( localhomtable, njob );
-#if DEBUG
- fprintf( stderr, "done. FreeLocalHomTable\n" );
-#endif
-}
-
-static void WriteOptions( FILE *fp )
-{
-
- if( dorp == 'd' ) fprintf( fp, "DNA\n" );
- else
- {
- if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
- else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
- else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
- }
- fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
- if( use_fft ) fprintf( fp, "FFT on\n" );
-
- fprintf( fp, "tree-base method\n" );
- if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
- else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
- if( tbitr || tbweight )
- {
- fprintf( fp, "iterate at each step\n" );
- if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
- if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
- if( tbweight ) fprintf( fp, " weighted\n" );
- fprintf( fp, "\n" );
- }
-
- fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-
- if( alg == 'a' )
- fprintf( fp, "Algorithm A\n" );
- else if( alg == 'A' )
- fprintf( fp, "Algorithm A+\n" );
- else if( alg == 'S' )
- fprintf( fp, "Apgorithm S\n" );
- else if( alg == 'C' )
- fprintf( fp, "Apgorithm A+/C\n" );
- else
- fprintf( fp, "Unknown algorithm\n" );
-
- if( use_fft )
- {
- fprintf( fp, "FFT on\n" );
- if( dorp == 'd' )
- fprintf( fp, "Basis : 4 nucleotides\n" );
- else
- {
- if( fftscore )
- fprintf( fp, "Basis : Polarity and Volume\n" );
- else
- fprintf( fp, "Basis : 20 amino acids\n" );
- }
- fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
- fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
- }
- else
- fprintf( fp, "FFT off\n" );
- fflush( fp );
-}
-
-
-int main( int argc, char *argv[] )
-{
- static int nlen[M];
- static char name[M][B], **seq;
- static char **mseq1, **mseq2;
- static char **aseq;
- static char **bseq;
- static double *eff;
- static double *equiv;
- char **strfiles;
- char **chainids;
- int i;
- FILE *infp;
- char c;
- int alloclen;
-
- arguments( argc, argv );
-
- if( equivthreshold < 1 || 9 < equivthreshold )
- {
- fprintf( stderr, "-t n, n must be 1..9\n" );
- exit( 1 );
- }
-
- if( ( equivwinsize + 1 ) % 2 != 0 )
- {
- fprintf( stderr, "equivwinsize = %d\n", equivwinsize );
- fprintf( stderr, "It must be an odd number.\n" );
- exit( 1 );
- }
-
- if( inputfile )
- {
- infp = fopen( inputfile, "r" );
- if( !infp )
- {
- fprintf( stderr, "Cannot open %s\n", inputfile );
- exit( 1 );
- }
- }
- else
- infp = stdin;
-
- nlenmax = 10000; // tekitou
-
- if( alg == 'R' )
- prepareash( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
- else if( alg == 'T' )
- preparetmalign( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
-
- fclose( infp );
-
- aseq = AllocateCharMtx( njob, nlenmax*2+1 );
- bseq = AllocateCharMtx( njob, nlenmax*2+1 );
- eff = AllocateDoubleVec( njob );
-
- for( i=0; i<njob; i++ )
- {
- fprintf( stderr, "str%d = %s-%s\n", i, strfiles[i], chainids[i] );
- }
-
- if( njob < 1 )
- {
- fprintf( stderr, "No structure found.\n" );
- exit( 1 );
- }
- if( njob < 2 )
- {
- fprintf( stderr, "Only %d structure found.\n", njob );
- exit( 0 );
- }
- if( njob > M )
- {
- fprintf( stderr, "The number of structures must be < %d\n", M );
- fprintf( stderr, "Please try sequence-based methods for such large data.\n" );
- exit( 1 );
- }
-
-
-
-#if 0
- readData( infp, name, nlen, seq );
-#endif
-
- constants( njob, seq );
-
-#if 0
- fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
-#endif
-
- initSignalSM();
-
- initFiles();
-
- WriteOptions( trap_g );
-
- c = seqcheck( seq );
- if( c )
- {
- fprintf( stderr, "Illegal character %c\n", c );
- exit( 1 );
- }
-
-// writePre( njob, name, nlen, seq, 0 );
-
- for( i=0; i<njob; i++ ) eff[i] = 1.0;
-
-
- for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
- pairalign( name, nlen, bseq, aseq, mseq1, mseq2, equiv, eff, strfiles, chainids, alloclen );
-
- fprintf( trap_g, "done.\n" );
-#if DEBUG
- fprintf( stderr, "closing trap_g\n" );
-#endif
- fclose( trap_g );
-
-// writePre( njob, name, nlen, aseq, !contin );
-#if 0
- writeData( stdout, njob, name, nlen, aseq );
-#endif
-#if IODEBUG
- fprintf( stderr, "OSHIMAI\n" );
-#endif
- SHOWVERSION;
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff