--- /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