+++ /dev/null
- /* Tree-dependent-iteration */
- /* Devide to segments */
-
-#include "mltaln.h"
-
-extern char **seq_g;
-extern char **res_g;
-
-static int intop;
-static int intree;
-
-void arguments( int argc, char *argv[] )
-{
- int c;
- char *argkey;
-
- outnumber = 0;
- nthread = 1;
- randomseed = 0;
- scoreout = 0;
- parallelizationstrategy = BAATARI1;
- intop = 0;
- intree = 0;
- inputfile = NULL;
- rnakozo = 0;
- rnaprediction = 'm';
- nevermemsave = 0;
- score_check = 1;
- fftkeika = 1;
- constraint = 0;
- fmodel = 0;
- kobetsubunkatsu = 1;
- bunkatsu = 1;
- nblosum = 62;
- niter = 100;
- calledByXced = 0;
- devide = 1;
- divWinSize = 20; /* 70 */
- divThreshold = 65;
- fftscore = 1;
- fftRepeatStop = 0;
- fftNoAnchStop = 0;
- scmtd = 5;
- cooling = 1;
- weight = 4;
- utree = 1;
- refine = 1;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 1;
- use_fft = 0; // CHUUI dochira demo mafft.tmpl deha F
- force_fft = 0;
- alg = 'A'; /* chuui */
- mix = 0;
- checkC = 0;
- tbitr = 0;
- treemethod = 'X';
- scoremtx = 1;
- dorp = NOTSPECIFIED;
- ppenalty = NOTSPECIFIED;
- ppenalty_ex = NOTSPECIFIED;
- poffset = NOTSPECIFIED;
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- geta2 = GETA2;
- fftWinSize = NOTSPECIFIED;
- fftThreshold = NOTSPECIFIED;
- RNAppenalty = NOTSPECIFIED;
- RNAppenalty_ex = NOTSPECIFIED;
- RNApthr = NOTSPECIFIED;
- TMorJTT = JTT;
- consweight_multi = 1.0;
- consweight_rna = 0.0;
-
- 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':
- niter = atoi( *++argv );
- fprintf( stderr, "niter = %d\n", niter );
- --argc;
- goto nextoption;
- case 'e':
- RNApthr = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'o':
- RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
- --argc;
- goto nextoption;
- case 'f':
- ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
-// fprintf( stderr, "ppenalty = %d\n", ppenalty );
- --argc;
- goto nextoption;
- case 'g':
- ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
-// fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
- --argc;
- goto nextoption;
- case 'h':
- poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
- fprintf( stderr, "poffset = %d\n", poffset );
- --argc;
- goto nextoption;
- case 'k':
- kimuraR = atoi( *++argv );
- fprintf( stderr, "kappa = %d\n", kimuraR );
- --argc;
- goto nextoption;
- case 'b':
- nblosum = atoi( *++argv );
- scoremtx = 1;
- fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
- --argc;
- goto nextoption;
- case 'j':
- pamN = atoi( *++argv );
- scoremtx = 0;
- TMorJTT = JTT;
- fprintf( stderr, "jtt/kimura %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 'l':
- fastathreshold = atof( *++argv );
- constraint = 2;
- --argc;
- goto nextoption;
- case 'r':
- consweight_rna = atof( *++argv );
- rnakozo = 1;
- --argc;
- goto nextoption;
- case 'c':
- consweight_multi = atof( *++argv );
- --argc;
- goto nextoption;
- case 'C':
- nthread = atoi( *++argv );
- fprintf( stderr, "nthread = %d\n", nthread );
- --argc;
- goto nextoption;
- case 't':
- randomseed = atoi( *++argv );
- fprintf( stderr, "randomseed = %d\n", randomseed );
- --argc;
- goto nextoption;
- case 'p':
- argkey = *++argv;
- if( !strcmp( argkey, "BESTFIRST" ) ) parallelizationstrategy = BESTFIRST;
- else if( !strcmp( argkey, "BAATARI0" ) ) parallelizationstrategy = BAATARI0;
- else if( !strcmp( argkey, "BAATARI1" ) ) parallelizationstrategy = BAATARI1;
- else if( !strcmp( argkey, "BAATARI2" ) ) parallelizationstrategy = BAATARI2;
- else
- {
- fprintf( stderr, "Unknown parallelization strategy, %s\n", argkey );
- exit( 1 );
- }
-// exit( 1 );
- --argc;
- goto nextoption;
- case 'S' :
- scoreout = 1;
- break;
- case 's' :
- RNAscoremtx = 'r';
- break;
-#if 1
- case 'a':
- fmodel = 1;
- break;
-#endif
- case 'N':
- nevermemsave = 1;
- break;
- case 'D':
- dorp = 'd';
- break;
- case 'P':
- dorp = 'p';
- break;
- case 'Q':
- alg = 'Q';
- break;
- case 'R':
- rnaprediction = 'r';
- break;
- case 'O':
- fftNoAnchStop = 1;
- break;
-#if 0
- case 'e':
- fftscore = 0;
- break;
- case 'r':
- fmodel = -1;
- break;
- case 'R':
- fftRepeatStop = 1;
- break;
-#endif
- case 'T':
- kobetsubunkatsu = 0;
- break;
- case 'B':
- bunkatsu = 0;
- break;
-#if 0
- case 'c':
- cooling = 1;
- break;
- case 'a':
- alg = 'a';
- break;
- case 's' :
- treemethod = 's';
- break;
-#endif
- case 'H':
- alg = 'H';
- break;
- case 'A':
- alg = 'A';
- break;
- case 'M':
- alg = 'M';
- break;
- case 'F':
- use_fft = 1;
- break;
-#if 0
- case 't':
- weight = 4;
- break;
-#endif
- case 'u':
- weight = 0;
- break;
- case 'U':
- intree = 1;
- break;
- case 'V':
- intop = 1;
- break;
- case 'J':
- utree = 0;
- break;
- case 'd':
- disp = 1;
- break;
- case 'Z':
- score_check = 0;
- break;
- case 'Y':
- score_check = 2;
- break;
-#if 0
- case 'n' :
- treemethod = 'n';
- break;
-#endif
- case 'n' :
- outnumber = 1;
- break;
- case 'X' :
- treemethod = 'X';
- break;
- case 'E' :
- treemethod = 'E';
- break;
- case 'q' :
- treemethod = 'q';
- break;
- case 'z':
- fftThreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- fftWinSize = atoi( *++argv );
- --argc;
- goto nextoption;
- 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 0
- if( alg == 'A' && weight == 0 )
- ErrorExit( "ERROR : Algorithm A+ and un-weighted\n" );
-#endif
-}
-
-
-int main( int argc, char *argv[] )
-{
- int identity;
- static int nlen[M];
- static char **name, **seq, **aseq, **bseq;
- static Segment *segment = NULL;
- static int anchors[MAXSEG];
- int i, j;
- int iseg, nseg;
- int ***topol;
- double **len;
- double **eff;
- FILE *prep;
- FILE *infp;
- int alloclen;
- int returnvalue;
- char c;
- int ocut;
- char **seq_g_bk;
- LocalHom **localhomtable = NULL; // by D.Mathog
- RNApair ***singlerna;
- int nogaplen;
- static char **nogap1seq;
- static char *kozoarivec;
- int nkozo;
-
- arguments( argc, argv );
-#ifndef enablemultithread
- nthread = 0;
-#endif
-
- 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
- getnumlen( infp );
-#endif
- rewind( infp );
-
- nkozo = 0;
-
- if( njob < 2 )
- {
- fprintf( stderr, "At least 2 sequences should be input!\n"
- "Only %d sequence found.\n", njob );
- exit( 1 );
- }
-
- ocut = cut;
-
- segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
-// if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' )
- topol = AllocateIntCub( njob, 2, njob );
- len = AllocateDoubleMtx( njob, 2 );
- eff = AllocateDoubleMtx( njob, njob );
- seq = AllocateCharMtx( njob, nlenmax*9+1 );
- name = AllocateCharMtx( njob, B+1 );
- seq_g = AllocateCharMtx( njob, nlenmax*9+1 );
- res_g = AllocateCharMtx( njob, nlenmax*9+1 );
- aseq = AllocateCharMtx( njob, nlenmax*9+1 );
- bseq = AllocateCharMtx( njob, nlenmax*9+1 );
- nogap1seq = AllocateCharMtx( 1, nlenmax*1+1 );
- alloclen = nlenmax * 9;
- seq_g_bk = AllocateCharMtx( njob, 0 );
- for( i=0; i<njob; i++ ) seq_g_bk[i] = seq_g[i];
- kozoarivec = AllocateCharVec( njob );
-
- if( constraint )
- {
- 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].overlapaa = -1.0;
- localhomtable[i][j].opt = -1.0;
- localhomtable[i][j].importance = -1.0;
- localhomtable[i][j].next = NULL;
- localhomtable[i][j].nokori = 0;
- localhomtable[i][j].extended = -1;
- localhomtable[i][j].last = localhomtable[i]+j;
- localhomtable[i][j].korh = 'h';
- }
- }
- fprintf( stderr, "Loading 'hat3' ... " );
- fflush( stderr );
- prep = fopen( "hat3", "r" );
- if( prep == NULL ) ErrorExit( "Make hat3." );
- readlocalhomtable2( prep, njob, localhomtable, kozoarivec );
- fclose( prep );
-// for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
-// fprintf( stdout, "%d %d %d %d %d %d %d\n", i, j, localhomtable[i][j].opt, localhomtable[i][j].start1, localhomtable[i][j].end1, localhomtable[i][j].start2, localhomtable[i][j].end2 );
- fprintf( stderr, "done.\n" );
- fflush( stderr );
-#if 0
- fprintf( stderr, "Extending localhom ... " );
- extendlocalhom( njob, localhomtable );
- fprintf( stderr, "done.\n" );
-#endif
- nkozo = 0;
- for( i=0; i<njob; i++ ) if( kozoarivec[i] ) nkozo++;
- }
-
-
-// if( nlenmax > 30000 )
- if( nlenmax > 50000 ) // version >= 6.823
- {
-#if 0
- if( constraint )
- {
- fprintf( stderr, "\nnlenmax=%d, nagasugi!\n", nlenmax );
- exit( 1 );
- }
- if( nevermemsave )
- {
- fprintf( stderr, "\nnevermemsave=1, nlenmax=%d, nagasugi!\n", nlenmax );
- exit( 1 );
- }
-#endif
- if( !constraint && !nevermemsave && alg != 'M' )
- {
- fprintf( stderr, "\nnlenmax=%d, Switching to the memsave mode\n", nlenmax );
- alg = 'M';
- }
- }
-
-#if 0
- Read( name, nlen, seq_g );
-#else
- readData_pointer( infp, name, nlen, seq_g );
-#endif
- fclose( infp );
-
-
- for( i=0; i<njob; i++ )
- {
- res_g[i][0] = 0;
- }
-
- identity = 1;
- for( i=0; i<njob; i++ )
- {
- identity *= ( nlen[i] == nlen[0] );
- }
- if( !identity )
- {
- fprintf( stderr, "Input pre-aligned data\n" );
- exit( 1 );
- }
- constants( njob, seq_g );
-
-#if 0
- fprintf( stderr, "penalty = %d\n", penalty );
- fprintf( stderr, "penalty_ex = %d\n", penalty_ex );
- fprintf( stderr, "offset = %d\n", offset );
-#endif
-
- initSignalSM();
-
- initFiles();
-
-#if 0
- if( njob == 2 )
- {
- writePre( njob, name, nlen, seq_g, 1 );
- SHOWVERSION;
- return( 0 );
- }
-#else
- if( njob == 2 )
- {
- weight = 0;
- niter = 1;
- }
-#endif
-
- c = seqcheck( seq_g );
- if( c )
- {
- fprintf( stderr, "Illegal character %c\n", c );
- exit( 1 );
- }
- commongappick( njob, seq_g );
-
- if( rnakozo && rnaprediction == 'm' )
- {
- singlerna = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- prep = fopen( "hat4", "r" );
- if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
- fprintf( stderr, "Loading 'hat4' ... " );
- fflush( stderr );
- for( i=0; i<njob; i++ )
- {
- gappick0( nogap1seq[0], seq_g[i] );
- nogaplen = strlen( nogap1seq[0] );
- singlerna[i] = (RNApair **)calloc( nogaplen, sizeof( RNApair * ) );
- for( j=0; j<nogaplen; j++ )
- {
- singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
- singlerna[i][j][0].bestpos = -1;
- singlerna[i][j][0].bestscore = -1.0;
- }
- readmccaskill( prep, singlerna[i], nogaplen );
- }
- fclose( prep );
- fprintf( stderr, "\ndone.\n" );
- fflush( stderr );
- }
- else
- singlerna = NULL;
-
-
-
- if( utree )
- {
- prep = fopen( "hat2", "r" );
- if( !prep ) ErrorExit( "Make hat2." );
- readhat2_pointer( prep, njob, name, eff );
- fclose( prep );
-#if DEBUG
- for( i=0; i<njob-1; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- printf( " %f", eff[i][j] );
- }
- printf( "\n" );
- }
-#endif
- if( intree )
- veryfastsupg_double_loadtree( njob, eff, topol, len );
- else if( intop ) // v6.528 deha if( intop ) dattanode intree ga mukou datta.
- veryfastsupg_double_loadtop( njob, eff, topol, len );
- else if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' )
-// veryfastsupg_double_outtree( njob, eff, topol, len, name );
- fixed_musclesupg_double_treeout( njob, eff, topol, len, name );
- else if( treemethod == 'n' )
- nj( njob, eff, topol, len );
- else if( treemethod == 's' )
- spg( njob, eff, topol, len );
- else if( treemethod == 'p' )
- upg2( njob, eff, topol, len );
- else ErrorExit( "Incorrect treemethod.\n" );
- }
-#if DEBUG
- printf( "utree = %d\n", utree );
-#endif
-
-
- fprintf( stderr, "\n" );
- if( ( !utree && kobetsubunkatsu ) || constraint || !bunkatsu )
- {
- nseg = 0;
- anchors[0] =0;
- anchors[1] =strlen( seq_g[0] );
- nseg += 2;
- }
- else
- {
- nseg = searchAnchors( njob, seq_g, segment );
-#if 0
- fprintf( stderr, "### nseg = %d\n", nseg );
- fprintf( stderr, "### seq_g[0] = %s\n", seq_g[0] );
- fprintf( stderr, "### nlenmax = %d\n", nlenmax );
- fprintf( stderr, "### len = %d\n", strlen( seq_g[0] ) );
-
-#endif
-
- anchors[0] = 0;
- for( i=0; i<nseg; i++ ) anchors[i+1] = segment[i].center;
- anchors[nseg+1] = strlen( seq_g[0] );
- nseg +=2;
-
-#if 0
- for( i=0; i<nseg; i++ )
- fprintf( stderr, "anchor[%d] = %d\n", i, anchors[i] );
-#endif
- }
-
- for( i=0; i<njob; i++ ) res_g[i][0] = 0;
-
- for( iseg=0; iseg<nseg-1; iseg++ )
- {
- int tmplen = anchors[iseg+1]-anchors[iseg];
- int pos = strlen( res_g[0] );
- for( j=0; j<njob; j++ )
- {
- strncpy( seq[j], seq_g[j], tmplen );
- seq[j][tmplen]= 0;
- seq_g[j] += tmplen;
-
- }
- fprintf( stderr, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
- fflush( stderr );
- fprintf( trap_g, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
-
- cut = ocut;
- returnvalue = TreeDependentIteration( njob, name, nlen, seq, bseq, topol, len, alloclen, localhomtable, singlerna, nkozo, kozoarivec );
-
- for( i=0; i<njob; i++ )
- strcat( res_g[i], bseq[i] );
- }
- FreeCharMtx( seq_g_bk );
- FreeIntCub( topol );
- FreeDoubleMtx( len );
- FreeDoubleMtx( eff );
- if( constraint ) FreeLocalHomTable( localhomtable, njob );
-
-#if 0
- Write( stdout, njob, name, nlen, bseq );
-#endif
-
- fprintf( stderr, "done\n" );
- fprintf( trap_g, "done\n" );
- fclose( trap_g );
-
-
- devide = 0;
- writePre( njob, name, nlen, res_g, 1 );
-#if 0
- writeData( stdout, njob, name, nlen, res_g, 1 );
-#endif
-
-
- SHOWVERSION;
- return( 0 );
-}
-
-#if 0
-signed int main( int argc, char *argv[] )
-{
- int i, nlen[M];
- char b[B];
- char a[] = "=";
- int value;
-
- gets( b ); njob = atoi( b );
-
-/*
- scoremtx = 0;
- if( strstr( b, "ayhoff" ) ) scoremtx = 1;
- else if( strstr( b, "dna" ) || strstr( b, "DNA" ) ) scoremtx = -1;
- else if( strstr( b, "M-Y" ) || strstr( b, "iyata" ) ) scoremtx = 2;
- else scoremtx = 0;
-*/
- if( strstr( b, "constraint" ) ) cnst = 1;
-
- nlenmax = 0;
- i = 0;
- while( i<njob )
- {
- gets( b );
- if( !strncmp( b, a, 1 ) )
- {
- gets( b ); nlen[i] = atoi( b );
- if( nlen[i] > nlenmax ) nlenmax = nlen[i];
- i++;
- }
- }
- if( nlenmax > N || njob > M )
- {
- fprintf( stderr, "ERROR in main\n" );
- exit( 1 );
- }
- /*
- nlenmax = Na;
- */
- rewind( stdin );
- value = main1( nlen, argc, argv );
- exit( 0 );
-}
-#endif
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