static int usecache;
static char *whereispairalign;
+static char *odir;
+static char *pdir;
static double scale;
static int *alreadyoutput;
static int equivthreshold;
}
-static float calltmalign( char **mseq1, char **mseq2, double *equiv, char *fname1, char *chain1, char *fname2, char *chain2, int alloclen )
+static double 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;
+ double value;
char cachedir[10000];
char cachefile[10000];
int runnow;
// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+ value = (double)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 )
+static double callrash( int mem1, int mem2, char **mseq1, char **mseq2, double *equiv, char *fname1, char *fname2, int alloclen )
{
FILE *fp;
- int res;
+// int res;
static char com[10000];
- float value;
+ double value;
char cachedir[10000];
char cachefile[10000];
int runnow;
if( usecache )
{
- sprintf( cachedir, "%s/.rashoutcache", getenv( "HOME" ) );
- sprintf( com, "mkdir -p %s", cachedir );
- system( com );
+// sprintf( cachedir, "tmp" );
+ sprintf( cachedir, "%s", pdir );
- sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
+ sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 );
runnow = 0;
fp = fopen( cachefile, "r" );
- if( fp == NULL ) runnow = 1;
+ if( fp == NULL )
+ {
+ fprintf( stderr, "Cannot open %s\n", cachefile );
+ exit( 1 );
+ }
else
{
- fgets( com, 100, fp );
- if( strncmp( com, "successful", 10 ) ) runnow = 1;
fclose( fp );
}
}
else
{
- runnow = 1;
+ fprintf( stderr, "Not supported!\n" );
+ exit( 1 );
}
- if( runnow )
+#if 0
+ if( 0 )
{
#if 0
sprintf( com, "ln -s %s %s.pdb 2>_dum", fname1, fname1 );
}
else
+#endif
{
- fprintf( stderr, "Use cache!\n" );
- sprintf( com, "grep -v successful %s > %s.rashout", cachefile, pairid );
+ fprintf( stderr, "Use cache! cachefile = %s\n", cachefile );
+ sprintf( com, "cat %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 );
+ fprintf( stderr, "Okashii! usechache=%d, runnow=%d\n", usecache, runnow );
+ exit( 1 );
}
sprintf( com, "%s.rashout", pairid );
// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+ value = (double)naivepairscore11( *mseq1, *mseq2, penalty );
return( value );
}
int linenum, istr, nstr;
FILE *checkfp;
char *sline;
- int use[1000];
+ int use[10000];
linenum = 0;
nstr = 0;
while( 1 )
}
}
-static void prepareash( FILE *fp, char ***strfiles, char ***chainids, char ***seqpt, char ***mseq1pt, char ***mseq2pt, double **equivpt, int *alloclenpt )
+static void prepareash( FILE *fp, char *inputfile, char ***strfiles, char ***chainids, char ***seqpt, char ***mseq1pt, char ***mseq2pt, double **equivpt, int *alloclenpt )
{
int i, res;
char *dumseq;
char fname[1000];
char command[1000];
int linenum, istr, nstr;
- FILE *checkfp;
+// FILE *checkfp;
char *sline;
- int use[1000];
+ int use[10000];
linenum = 0;
nstr = 0;
+
+ fprintf( stderr, "inputfile = %s\n", inputfile );
while( 1 )
{
fgets( line, 999, fp );
continue;
}
extractfirstword( sline );
+#if 0
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 );
else
nstr++;
fclose( checkfp );
+#else
+ nstr++;
+#endif
linenum++;
}
njob = nstr;
fgets( line, 999, fp );
if( feof( fp ) ) break;
sline = strip( line );
+ fprintf( stderr, "sline = %s\n", sline );
if( use[linenum++] )
{
(*chainids)[istr][0] = getchainid( sline );
extractfirstword( sline );
sprintf( fname, "%s", sline );
cutpath( fname );
+#if 0
sprintf( command, "cp %s %s.pdb", sline, fname );
system( command );
sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
fprintf( stderr, "error: Install clean.pl\n" );
exit( 1 );
}
+#endif
strcpy( (*strfiles)[istr++], fname );
}
}
alreadyoutput = AllocateIntVec( njob );
for( i=0; i<njob; i++ ) alreadyoutput[i] = 0;
+ fprintf( stderr, "Running pdp_ash_batch.pl..\n" );
+// sprintf( command, "/opt/protein/share/domains/code/pdp_ash/pdp_ash_batch.pl -f %s -d tmp -i %d", inputfile, wheretooutput );
+ sprintf( command, "/opt/protein/share/mafftash/pdp_ash/pdp_ash_batch.pl -f %s -d %s -i %s", inputfile, pdir, odir );
+ res = system( command );
+ if( res )
+ {
+ fprintf( stderr, "Ask KM!\n" );
+ exit( 1 );
+ }
+ fprintf( stderr, "done\n" );
+
+
for( i=0; i<istr; i++ )
{
fprintf( stderr, "i=%d\n", i );
(*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] );
+ callrash( i, i, *mseq1pt, *mseq2pt, *equivpt, (*strfiles)[i], (*strfiles)[i], *alloclenpt );
+ fprintf( stdout, ">%d_%s\n%s\n", i+1, (*strfiles)[i], (*seqpt)[i] );
alreadyoutput[i] = 1;
}
}
fftThreshold = NOTSPECIFIED;
RNAppenalty = NOTSPECIFIED;
RNApthr = NOTSPECIFIED;
+ odir = "";
+ pdir = "";
while( --argc > 0 && (*++argv)[0] == '-' )
{
--argc;
goto nextoption;
case 'k':
- kimuraR = atoi( *++argv );
+ kimuraR = myatoi( *++argv );
// fprintf( stderr, "kimuraR = %d\n", kimuraR );
--argc;
goto nextoption;
case 'b':
- nblosum = atoi( *++argv );
+ nblosum = myatoi( *++argv );
scoremtx = 1;
// fprintf( stderr, "blosum %d\n", nblosum );
--argc;
goto nextoption;
case 'j':
- pamN = atoi( *++argv );
+ pamN = myatoi( *++argv );
scoremtx = 0;
TMorJTT = JTT;
fprintf( stderr, "jtt %d\n", pamN );
--argc;
goto nextoption;
case 'm':
- pamN = atoi( *++argv );
+ pamN = myatoi( *++argv );
scoremtx = 0;
TMorJTT = TM;
fprintf( stderr, "TM %d\n", pamN );
fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
--argc;
goto nextoption;
+ case 'o':
+ odir = *++argv;
+ fprintf( stderr, "odir = %s\n", odir );
+ --argc;
+ goto nextoption;
+ case 'p':
+ pdir = *++argv;
+ fprintf( stderr, "pdir = %s\n", pdir );
+ --argc;
+ goto nextoption;
case 't':
- equivthreshold = atoi( *++argv );
+ equivthreshold = myatoi( *++argv );
--argc;
goto nextoption;
case 'w':
- equivwinsize = atoi( *++argv );
+ equivwinsize = myatoi( *++argv );
--argc;
goto nextoption;
case 'l':
- equivshortestlen = atoi( *++argv );
+ equivshortestlen = myatoi( *++argv );
--argc;
goto nextoption;
case 's':
/* modification end. */
#if 0
case 'z':
- fftThreshold = atoi( *++argv );
+ fftThreshold = myatoi( *++argv );
--argc;
goto nextoption;
case 'w':
- fftWinSize = atoi( *++argv );
+ fftWinSize = myatoi( *++argv );
--argc;
goto nextoption;
case 'Z':
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 )
+static void pairalign( char **name, 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
+ double pscore = 0.0; // by D.Mathog
static char *indication1, *indication2;
FILE *hat2p, *hat3p;
static double **distancemtx;
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 );
+ clus1 = conjuctionfortbfast_old( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast_old( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
// fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
// fprintf( stderr, "mseq2 = %s\n", mseq2[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 );
+ pscore = callrash( i, j, mseq1, mseq2, equiv, strfiles[i], strfiles[j], alloclen );
off1 = off2 = 0;
break;
ErrorExit( "ERROR IN SOURCE FILE" );
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] ) );
+ putlocalhom_str( mseq1[0], mseq2[0], equiv, scale, localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ), 'k' );
#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] );
+ fprintf( stdout, ">%d_%s\n%s\n", i+1, strfiles[i], seq[i] );
strcpy( checkseq[i], seq[i] );
}
else
hat2p = fopen( hat2file, "w" );
if( !hat2p ) ErrorExit( "Cannot open hat2." );
- WriteHat2( hat2p, njob, name, distancemtx );
+ WriteHat2_pointer( hat2p, njob, name, distancemtx );
fclose( hat2p );
fprintf( stderr, "##### writing hat3\n" );
int main( int argc, char *argv[] )
{
static int nlen[M];
- static char name[M][B], **seq;
+ static char **name, **seq;
static char **mseq1, **mseq2;
static char **aseq;
static char **bseq;
nlenmax = 10000; // tekitou
if( alg == 'R' )
- prepareash( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
+ prepareash( infp, inputfile, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
else if( alg == 'T' )
preparetmalign( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
fclose( infp );
+ name = AllocateCharMtx( njob, B+1 );
aseq = AllocateCharMtx( njob, nlenmax*2+1 );
bseq = AllocateCharMtx( njob, nlenmax*2+1 );
eff = AllocateDoubleVec( njob );
git://source.jalview.org / jabaws.git / blobdiff