+++ /dev/null
-
-/*
- tree-dependent iteration
- algorithm A+ when group-to-group, C when group-to-singleSeqence
- OR
- algorithm A+
-*/
-
-#include "mltaln.h"
-
-
-#define DEBUG 0
-#define RECORD 0
-
-extern char **seq_g;
-extern char **res_g;
-
-static int nwa;
-
-#ifdef enablemultithread
-typedef struct _threadarg
-{
- int thread_no;
- int *jobposintpt;
- int *ndonept;
- int *ntrypt;
- int *collectingpt;
- int njob;
- int nbranch;
- int maxiter;
- int nkozo;
- int *subgenerationpt;
- float *basegainpt;
- float *gainlist;
- float *tscorelist;
- int *generationofinput;
- char *kozoarivec;
- char **mastercopy;
- char ***candidates;
- int *generationofmastercopypt;
- int *branchtable;
- RNApair ***singlerna;
- LocalHom **localhomtable;
- int alloclen;
- Node *stopol;
- int ***topol;
-// double **len;
- float **tscorehistory_detail;
- int *finishpt;
- pthread_mutex_t *mutex;
- pthread_cond_t *collection_end;
- pthread_cond_t *collection_start;
-} threadarg_t;
-#endif
-
-#if 1
-static void shuffle( int *arr, int n )
-{
- int i;
- int x;
- int b;
-
- for( i=1; i<n; i++ )
- {
- x = rand() % (i+1);
- if( x != i )
- {
- b = arr[i];
- arr[i] = arr[x];
- arr[x] = b;
- }
- }
-}
-#endif
-
-static void Writeoption2( FILE *fp, int cycle, double cut )
-{
- fprintf( fp, "%dth cycle\n", cycle );
- fprintf( fp, "marginal score to search : current score * (100-%d) / 100\n", (int)cut );
-}
-
-static void Writeoptions( FILE *fp )
-{
- fprintf( fp, "Tree-dependent-iteration\n" );
- if( scoremtx == 1 )
- fprintf( fp, "Blosum %d\n", nblosum );
- else if( scoremtx == -1 )
- fprintf( fp, "DNA\n" );
- else if( scoremtx == 2 )
- fprintf( fp, "Miyata-Yasunaga\n" );
- else
- fprintf( fp, "JTT %dPAM\n", pamN );
-
- if( scoremtx == 0 || scoremtx == 1 )
- fprintf( fp, "Gap Penalty = %+5.3f, %5.2f, %+5.3f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
- else
- fprintf( fp, "Gap Penalty = %+5.3f\n", (double)penalty/1000 );
-
-
- if( scmtd == 3 )
- fprintf( fp, "score of rnd or sco\n" );
- else if( scmtd == 4 )
- fprintf( fp, "score = sigma( score for a pair of homologous amino acids ) / ( number of amino acids pairs )\n" );
- else if( scmtd == 5 )
- fprintf( fp, "score : SP\n" );
- if( mix )
- fprintf( fp, "?\n" );
- else
- {
- if( weight == 2 )
- fprintf( fp, "weighted rationale-1, geta2 = %f\n", geta2 );
- else if( weight == 3 )
- fprintf( fp, "weighted like ClustalW," );
- else if( weight == 4 )
- fprintf( fp, "weighted rationale-2, geta2 = %f\n", geta2 );
- else
- fprintf( fp, "unweighted\n" );
- }
- if( weight && utree )
- fprintf( fp, "using tree defined by the file hat2.\n" );
- if( weight && !utree )
- fprintf( fp, "using temporary tree.\n" );
-
- if( treemethod == 'n' )
- fprintf( fp, "Tree is calculated with Neighbor-Joining Method.\n" );
- else if( treemethod == 'q' )
- fprintf( fp, "Tree is calculated with Minimum linkage.\n" );
- else if( treemethod == 'X' )
- fprintf( fp, "Tree is calculated with simplified UPG Method and UPG Method.\n" );
- else if( treemethod == 'E' )
- fprintf( fp, "Tree is calculated with UPG Method.\n" );
- else
- fprintf( fp, "Tree is calculated with unknown Method.\n" );
-
- if( alg == 'C' )
- fprintf( fp, "Algorithm A+ / C\n" );
- else if( alg == 'A' )
- fprintf( fp, "Algorithm A+ \n" );
- else if( alg == 'a' )
- fprintf( fp, "Algorithm A \n" );
- else
- fprintf( fp, "Algorithm ? \n" );
-
- if( use_fft )
- {
- if( scoremtx == -1 )
- {
- 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 );
- }
-}
-
-#ifdef enablemultithread
-
-static void freelocalarrays(
- float *tscorehistory,
- RNApair ***grouprna1, RNApair ***grouprna2,
- RNApair *rnapairboth,
- char *indication1, char *indication2,
- double *effarr, double *effarrforlocalhom, double *effarr1, double *effarr2,
- char **mseq1, char **mseq2,
- char **localcopy,
- int *gapmap1, int *gapmap2,
- double *effarr1_kozo, double *effarr2_kozo, double *effarr_kozo,
- char **pair,
- LocalHom *** localhomshrink
-)
-{
-// fprintf( stderr, "Skipping freelocalarrays\n" );
-// return;
- int i;
- if( commonIP ) FreeIntMtx( commonIP );
- commonIP = NULL;
- Falign( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
- Falign_localhom( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL,NULL, 0, NULL );
- if( rnakozo && rnaprediction == 'm' )
- {
- free( grouprna1 ); // nakamimo?
- free( grouprna2 ); // nakamimo?
- }
-
- free( tscorehistory );
- free( indication1 );
- free( indication2 );
- free( effarr );
- free( effarrforlocalhom );
- free( effarr1 );
- free( effarr2 );
- free( mseq1 );
- free( mseq2 );
- FreeCharMtx( localcopy );
- free( gapmap1 );
- free( gapmap2 );
-
- free( effarr1_kozo );
- free( effarr2_kozo );
- free( effarr_kozo );
-
- FreeCharMtx( pair );
-
- if( rnakozo ) free( rnapairboth );
-
- if( constraint )
- {
- for( i=0; i<njob; i++)
- {
- free( localhomshrink[i] ); // nakamimo??
- }
- free( localhomshrink );
- }
-}
-
-
-static void *athread( void *arg )
-{
-
- threadarg_t *targ = (threadarg_t *)arg;
- int thread_no = targ->thread_no;
- int njob = targ->njob;
- int nbranch = targ->nbranch;
- int maxiter = targ->maxiter;
- int *ndonept = targ->ndonept;
- int *ntrypt = targ->ntrypt;
- int *collectingpt = targ->collectingpt;
- int *jobposintpt = targ->jobposintpt;
- int nkozo = targ->nkozo;
- float *gainlist = targ->gainlist;
- float *tscorelist = targ->tscorelist;
- int *generationofinput = targ->generationofinput;
- int *subgenerationpt = targ->subgenerationpt;
- float *basegainpt = targ->basegainpt;
- char *kozoarivec = targ->kozoarivec;
- char **mastercopy = targ->mastercopy;
- char ***candidates = targ->candidates;
- int *generationofmastercopypt = targ->generationofmastercopypt;
- int *branchtable = targ->branchtable;
- RNApair ***singlerna = targ->singlerna;
- LocalHom **localhomtable = targ->localhomtable;
- int alloclen = targ->alloclen;
- Node * stopol = targ->stopol;
- int ***topol = targ->topol;
-// double **len = targ->len;
- float **tscorehistory_detail = targ->tscorehistory_detail;
- int *finishpt = targ->finishpt;
-
- int i, j, k, l, ii;
- float gain;
- int iterate;
- char **pair;
- int locnjob;
- int s1, s2;
- int clus1, clus2;
- char **localcopy;
- char **mseq1, **mseq2;
- double *effarr, *effarr_kozo; // re-calc
- double *effarr1, *effarr2, *effarr1_kozo, *effarr2_kozo;
- char *indication1, *indication2;
- int length;
- RNApair ***grouprna1, ***grouprna2;
- RNApair *rnapairboth;
- LocalHom ***localhomshrink;
- int *gapmap1, *gapmap2;
- float tscore, mscore, oimpmatch, impmatch;
- int identity;
- double tmpdouble;
- float naivescore0 = 0, naivescore1;
- double *effarrforlocalhom;
- float *tscorehistory;
- int intdum;
-#if 0
- int oscillating;
- int lin, ldf;
-#endif
- float maxgain;
- int bestthread;
- int branchpos;
- int subgenerationatfirst;
- double unweightedspscore;
- int myjob;
- int converged2 = 0;
- int chudanres;
-
-
- locnjob = njob;
-
- if( utree == 0 )
- {
- fprintf( stderr, "Dynamic tree is not supported in the multithread version.\n" );
- exit( 1 );
- }
- if( score_check == 2 )
- {
- fprintf( stderr, "Score_check 2 is not supported in the multithread version.\n" );
- exit( 1 );
- }
-
- if( weight == 2 )
- {
- fprintf( stderr, "Weight 2 is not supported in the multithread version.\n" );
- exit( 1 );
- }
- if( cooling && cut > 0.0 )
- {
- fprintf( stderr, "Cooling is not supported in the multithread version.\n" );
- exit( 1 );
- }
-
- tscorehistory = calloc( maxiter, sizeof( float ) );
-
- if( rnakozo && rnaprediction == 'm' )
- {
- grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- }
- else
- {
- grouprna1 = grouprna2 = NULL;
- }
-
- indication1 = AllocateCharVec( njob*3+50 );
- indication2 = AllocateCharVec( njob*3+50 );
- effarr = AllocateDoubleVec( locnjob );
- effarrforlocalhom = AllocateDoubleVec( locnjob );
- effarr1 = AllocateDoubleVec( locnjob );
- effarr2 = AllocateDoubleVec( locnjob );
- mseq1 = AllocateCharMtx( locnjob, 0 );
- mseq2 = AllocateCharMtx( locnjob, 0 );
- localcopy = AllocateCharMtx( locnjob, alloclen );
- gapmap1 = AllocateIntVec( alloclen );
- gapmap2 = AllocateIntVec( alloclen );
-
- effarr1_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
- effarr2_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
- effarr_kozo = AllocateDoubleVec( locnjob );
- for( i=0; i<locnjob; i++ )
- effarr_kozo[i] = effarr1_kozo[i] = effarr2_kozo[i] = 0.0;
-
- pair = AllocateCharMtx( locnjob, locnjob );
-
-
- if( rnakozo ) rnapairboth = (RNApair *)calloc( alloclen, sizeof( RNApair ) );
-
- if( constraint )
- {
- localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
- for( i=0; i<njob; i++)
- {
- localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom * ) );
- }
- }
-
-
- if( thread_no == 0 )
- {
- *ntrypt = 0;
- srand( randomseed );
- *finishpt = 0;
- for( iterate=0; iterate<maxiter; iterate++ )
- {
- pthread_mutex_lock( targ->mutex );
-
- if( *collectingpt == 1 )
- {
- *collectingpt = 0;
- *generationofmastercopypt = iterate;
- *subgenerationpt = 0;
- *basegainpt = 0.0;
- *ndonept = 0;
- *jobposintpt = 0;
- for( i=0; i<nwa; i++ ) gainlist[i] = 0;
- for( i=0; i<nwa; i++ ) tscorelist[i] = 0.0;
- for( i=0; i<nbranch; i++ ) generationofinput[i] = -1;
- if( parallelizationstrategy != BESTFIRST && randomseed != 0 ) shuffle( branchtable, nbranch );
- pthread_cond_broadcast( targ->collection_end );
- pthread_mutex_unlock( targ->mutex );
- }
- else
- {
- pthread_cond_broadcast( targ->collection_end );
- pthread_mutex_unlock( targ->mutex );
- freelocalarrays
- (
- tscorehistory,
- grouprna1, grouprna2,
- rnapairboth,
- indication1, indication2,
- effarr, effarrforlocalhom, effarr1, effarr2,
- mseq1, mseq2,
- localcopy,
- gapmap1, gapmap2,
- effarr1_kozo, effarr2_kozo, effarr_kozo,
- pair,
- localhomshrink
- );
-// return( NULL );
- pthread_exit( NULL );
- }
-
- pthread_mutex_lock( targ->mutex );
- while( *ndonept < nbranch )
- pthread_cond_wait( targ->collection_start, targ->mutex );
- pthread_mutex_unlock( targ->mutex );
-// fprintf( stderr, "Thread 0 got a signal, *collectionpt = %d\n", *collectingpt );
-
-/*
- Hoka no thread ga keisan
-*/
-
- pthread_mutex_lock( targ->mutex );
- *collectingpt = 1; // chofuku
-
-#if 0
- for( i=0; i<nbranch; i++ )
- {
- if( generationofinput[i] != iterate )
- {
- fprintf( stderr, "Error! generationofinput[%d] = %d, but iterate=%d\n", i, generationofinput[i], iterate );
- exit( 1 );
-
- }
- }
-#endif
-
- maxgain = gainlist[1];
- bestthread = 1;
- for( i=2; i<nwa; i++ )
- {
- if( gainlist[i] > maxgain )
- {
- maxgain = gainlist[i];
- bestthread = i;
- }
- }
-
- if( maxgain > 0.0 )
- {
-// fprintf( stderr, "\nGain = %f\n", maxgain );
-// fprintf( stderr, "best gain = %f by thread %d\n", gainlist[bestthread], bestthread );
-// fprintf( stderr, "tscorelist[best] = %f by thread %d\n", tscorelist[bestthread], bestthread );
- if( parallelizationstrategy == BESTFIRST )
- {
- for( i=0; i<locnjob; i++ ) strcpy( mastercopy[i], candidates[bestthread][i] );
- if( scoreout )
- {
- unweightedspscore = plainscore( locnjob, mastercopy );
- fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * nbranch, unweightedspscore );
- fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( locnjob * strlen( mastercopy[0] ) ) );
- if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
- fprintf( stderr, "\n" );
- }
- }
-#if 1
-// fprintf( stderr, "gain(%d, by %d) = %f\n", iterate, bestthread, maxgain );
- for( i=iterate-1; i>0; i-- )
- {
-// if( iterate-i < 15 ) fprintf( stderr, "hist[%d] = %f\n", i, tscorehistory[i] );
- if( tscorehistory[i] == tscorelist[bestthread] )
- {
- fprintf( stderr, "\nOscillating? %f == %f\n", tscorehistory[i], tscorelist[bestthread] );
- *collectingpt = -1;
- break;
- }
- }
- tscorehistory[iterate] = tscorelist[bestthread];
-#endif
- }
- else
- {
- fprintf( stderr, "\nConverged.\n" );
- *collectingpt = -1;
-// pthread_cond_broadcast( targ->collection_end );
-// pthread_mutex_unlock( targ->mutex );
-// freelocalarrays();
-// return( NULL );
-// pthread_exit( NULL );
- }
-
-#if 1
- if( *finishpt )
- {
- fprintf( stderr, "\nConverged2.\n" );
- *collectingpt = -1;
- }
-#endif
-
- pthread_mutex_unlock( targ->mutex );
- }
- pthread_mutex_lock( targ->mutex );
- fprintf( stderr, "\nReached %d\n", maxiter );
- *collectingpt = -1;
- pthread_cond_broadcast( targ->collection_end );
- pthread_mutex_unlock( targ->mutex );
- freelocalarrays
- (
- tscorehistory,
- grouprna1, grouprna2,
- rnapairboth,
- indication1, indication2,
- effarr, effarrforlocalhom, effarr1, effarr2,
- mseq1, mseq2,
- localcopy,
- gapmap1, gapmap2,
- effarr1_kozo, effarr2_kozo, effarr_kozo,
- pair,
- localhomshrink
- );
- return( NULL );
- pthread_exit( NULL );
- }
- else
- {
- while( 1 )
- {
-#if 0
- if( iterate % 2 == 0 )
- {
- lin = 0; ldf = +1;
- }
- else
- {
- lin = locnjob - 2; ldf = -1;
- }
- for( l=lin; l < locnjob-1 && l >= 0 ; l+=ldf )
- for( k=0; k<2; k++ )
-#endif
-
- pthread_mutex_lock( targ->mutex );
- while( *collectingpt > 0 )
- pthread_cond_wait( targ->collection_end, targ->mutex );
- if( *collectingpt == -1 )
- {
- pthread_mutex_unlock( targ->mutex );
- freelocalarrays
- (
- tscorehistory,
- grouprna1, grouprna2,
- rnapairboth,
- indication1, indication2,
- effarr, effarrforlocalhom, effarr1, effarr2,
- mseq1, mseq2,
- localcopy,
- gapmap1, gapmap2,
- effarr1_kozo, effarr2_kozo, effarr_kozo,
- pair,
- localhomshrink
- );
- return( NULL );
- pthread_exit( NULL );
- }
-// pthread_mutex_unlock( targ->mutex );
-
-
-// pthread_mutex_lock( targ->mutex );
- if( *jobposintpt == nbranch )
- {
- if( *collectingpt != -1 ) *collectingpt = 1; // chofuku
- pthread_mutex_unlock( targ->mutex );
- continue;
- }
-// fprintf( stderr, "JOB jobposintpt=%d\n", *jobposintpt );
- myjob = branchtable[*jobposintpt];
- l = myjob / 2;
- if( l == locnjob-2 ) k = 1;
- else k = myjob - l * 2;
-// fprintf( stderr, "JOB l=%d, k=%d\n", l, k );
- branchpos = myjob;
- (*jobposintpt)++;
- iterate = *generationofmastercopypt;
- (*ntrypt)++;
- pthread_mutex_unlock( targ->mutex );
-
-
-
-// fprintf( stderr, "branchpos = %d (thread %d)\n", branchpos, thread_no );
-
-// fprintf( stderr, "iterate=%d, l=%d, k=%d (thread %d)\n", iterate, l, k, thread_no );
-
-#if 0
- fprintf( stderr, "STEP %03d-%03d-%d (Thread %d) ", iterate+1, l+1, k, thread_no );
- fprintf( stderr, "STEP %03d-%03d-%d (thread %d) %s ", iterate+1, l+1, k, thread_no, use_fft?"\n":"\n" );
-#endif
- for( i=0; i<locnjob; i++ ) for( j=0; j<locnjob; j++ ) pair[i][j] = 0;
-
- OneClusterAndTheOther( locnjob, pair, &s1, &s2, topol, l, k );
-#if 0
- fprintf( stderr, "STEP%d-%d\n", l, k );
- for( i=0; i<locnjob; i++ )
- {
- for( j=0; j<locnjob; j++ )
- {
- fprintf( stderr, "%#3d", pair[i][j] );
- }
- fprintf( stderr, "\n" );
- }
-#endif
- if( !weight )
- {
- for( i=0; i<locnjob; i++ ) effarr[i] = 1.0;
- if( nkozo )
- {
- for( i=0; i<locnjob; i++ )
- {
- if( kozoarivec[i] )
- effarr_kozo[i] = 1.0;
- else
- effarr_kozo[i] = 0.0;
- }
- }
- }
- else if( weight == 4 )
- {
- weightFromABranch( locnjob, effarr, stopol, topol, l, k );
- if( nkozo ) // hitomadu single weight.
- {
- for( i=0; i<locnjob; i++ )
- {
- if( kozoarivec[i] ) effarr_kozo[i] = effarr[i];
- else effarr_kozo[i] = 0.0;
- }
- }
- }
- else
- {
- fprintf( stderr, "weight error!\n" );
- exit( 1 );
- }
-
- yarinaoshi:
-
- pthread_mutex_lock( targ->mutex );
- for( i=0; i<locnjob; i++ ) strcpy( localcopy[i], mastercopy[i] );
- subgenerationatfirst = *subgenerationpt;
- pthread_mutex_unlock( targ->mutex );
- length = strlen( localcopy[0] );
-
- if( nkozo )
- {
- double tmptmptmp;
- tmptmptmp = 0.0;
- clus1 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s1, localcopy, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
- for( i=0; i<clus1; i++ ) effarr1_kozo[i] *= 1.0; // 0.5 ga sairyo ?
- tmptmptmp = 0.0;
- clus2 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s2, localcopy, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
- for( i=0; i<clus2; i++ ) effarr2_kozo[i] *= 1.0; // 0.5 ga sairyo ?
-
-#if 0
- fprintf( stderr, "\ngroup1 = %s\n", indication1 );
- for( i=0; i<clus1; i++ ) fprintf( stderr, "effarr1_kozo[%d], effarr1[] = %f, %f\n", i, effarr1_kozo[i], effarr1[i] );
- fprintf( stderr, "\ngroup2 = %s\n", indication2 );
- for( i=0; i<clus2; i++ ) fprintf( stderr, "effarr2_kozo[%d], effarr2[] = %f, %f\n", i, effarr2_kozo[i], effarr2[i] );
-#endif
- }
- else
- {
- clus1 = conjuctionfortbfast( pair, s1, localcopy, mseq1, effarr1, effarr, indication1 );
- clus2 = conjuctionfortbfast( pair, s2, localcopy, mseq2, effarr2, effarr, indication2 );
- }
-
- if( rnakozo && rnaprediction == 'm' )
- {
- makegrouprnait( grouprna1, singlerna, pair, s1 );
- makegrouprnait( grouprna2, singlerna, pair, s2 );
- }
-
- if( score_check == 2 )
- {
- fprintf( stderr, "Score_check 2 is not supported in the multithread version.\n" );
- exit( 1 );
- }
- else if( score_check )
- {
- if( RNAscoremtx == 'r' )
- intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
- else
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
-
- if( constraint )
- {
- shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
-// weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink ); // >>>
- oimpmatch = 0.0;
- if( use_fft )
- {
- if( alg == 'Q' )
- {
- part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += part_imp_match_out_scQ( i, i );
-// fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
- else
- {
- part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += part_imp_match_out_sc( i, i );
-// fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
-// fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
- }
- else
- {
- if( alg == 'Q' )
- {
- imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
-
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += imp_match_out_scQ( i, i );
-// fprintf( stderr, "#### i=%d, initial impmatch = %f\n", i, oimpmatch );
- }
- }
- else
- {
- imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
-
- fprintf( stderr, "not supported\n" );
- exit( 1 );
-
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += imp_match_out_sc( i, i );
-// fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
-// fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
- }
-// fprintf( stderr, "#### initial impmatch = %f\n", oimpmatch );
- }
- else
- {
- oimpmatch = 0.0;
- }
-
-
-// fprintf( stderr, "#### tmpdouble = %f\n", tmpdouble );
- mscore = (double)oimpmatch + tmpdouble;
- }
- else
- {
- fprintf( stderr, "score_check = %d\n", score_check );
- fprintf( stderr, "Not supported\n" );
- exit( 1 );
- }
-
-
-// if( rnakozo ) foldalignedrna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, rnapairboth );
-
-// if( !use_fft && !rnakozo )
- if( !use_fft )
- {
- commongappick_record( clus1, mseq1, gapmap1 );
- commongappick_record( clus2, mseq2, gapmap2 );
- }
-
-#if 0
- fprintf( stderr, "##### mscore = %f\n", mscore );
-#endif
-
-#if DEBUG
- if( !devide )
- {
- fprintf( trap_g, "\n%d-%d-%d\n", iterate+1, l+1, k );
- fprintf( trap_g, "group1 = %s\n", indication1 );
- fprintf( trap_g, "group2 = %s\n", indication2 );
- fflush( trap_g );
- }
-
-#endif
-#if 0
- printf( "STEP %d-%d-%d\n", iterate, l, k );
- for( i=0; i<clus2; i++ ) printf( "%f ", effarr2[i] );
- printf( "\n" );
-#endif
- if( constraint == 2 )
- {
- if( use_fft )
- {
-// if( alg == 'Q' )
-// part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
-// else
-// part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- chudanres = 0;
- Falign_localhom( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2, subgenerationpt, subgenerationatfirst, &chudanres );
-// fprintf( stderr, "##### impmatch = %f\n", impmatch );
- if( chudanres && parallelizationstrategy == BAATARI2 )
- {
-// fprintf( stderr, "#### yarinaoshi!!! INS-i\n" );
- goto yarinaoshi;
- }
- }
- else
- {
- if( alg == 'Q' )
- {
- float wm;
-// imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap wo tsukuttakara iranai.
-// if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, gapmap1, gapmap2, rnapairboth );
-
- wm = Q__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL, gapmap1, gapmap2 );
- fprintf( stderr, "wm = %f\n", wm );
-#if 0
- fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
- naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
- fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-#if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
-// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
-// rewind( stdout );
-// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
-// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
-// exit( 1 );
- }
-#endif
-#endif
- }
- else if( alg == 'R' )
- {
- float wm;
- imp_match_init_strictR( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
- wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
-// fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
- naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
-// fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: %f->%f UP!\n", clus1, clus2, naivescore0, naivescore1 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-#if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
-// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
- rewind( stdout );
- for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- exit( 1 );
- }
-#endif
- }
- else if( alg == 'H' )
- {
- float wm;
- imp_match_init_strictH( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
- wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
- fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
- naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
- fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-#if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
-// fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
-// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
-// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
-// exit( 1 );
- }
-#endif
- }
- else
- {
-// imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- A__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2 );
- fprintf( stderr, "A__align_gapmap\n" );
-// fprintf( stderr, "##### impmatch = %f\n", impmatch );
- }
- }
- }
- else if( use_fft )
- {
- float totalwm;
- chudanres = 0;
- totalwm = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, subgenerationpt, subgenerationatfirst, &chudanres );
- if( chudanres && parallelizationstrategy == BAATARI2 )
- {
-// fprintf( stderr, "#### yarinaoshi!!! FFT-NS-i\n" );
- goto yarinaoshi;
- }
-
-// fprintf( stderr, "totalwm = %f\n", totalwm );
-#if 0
- if( alg == 'Q' )
- {
- fprintf( stderr, "totalwm = %f\n", totalwm );
- naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-#if 1 // chuui
- if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
- {
-// fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
-// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
-// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
-// exit( 1 );
- }
-#endif
- }
-#endif
- if( alg == 'R' )
- {
- fprintf( stderr, "totalwm = %f\n", totalwm );
- naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-#if 1 // chuui
- if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
- {
-// fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
-// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
-// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
-// exit( 1 );
- }
- }
-#endif
- }
- else
- {
- if( alg == 'M' )
- {
- chudanres = 0;
- MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, subgenerationpt, subgenerationatfirst, &chudanres, outgap, outgap );
- if( chudanres && parallelizationstrategy == BAATARI2 )
- {
-// fprintf( stderr, "#### yarinaoshi!!! NW-NS-i\n" );
- goto yarinaoshi;
- }
- }
- else if( alg == 'A' )
- {
- A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap==1
- }
- else if( alg == 'Q' )
- {
- float wm;
- wm = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
- fprintf( stderr, "wm = %f\n", wm );
- fprintf( stderr, "impmatch = %f\n", impmatch );
- naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-#if 1 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
-// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
-// rewind( stderr );
-// rewind( stdout );
-// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
-// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
-// exit( 1 );
- }
-#endif
- }
- else if( alg == 'R' )
- {
- float wm;
- wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
- naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-#if 1 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
-// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
-// rewind( stderr );
-// rewind( stdout );
-// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
-// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
-// exit( 1 );
- }
-#endif
- }
- else if( alg == 'H' )
- {
- float wm;
- wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
- naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- {
- fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
- }
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-
-#if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
- rewind( stdout );
- for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- exit( 1 );
- }
-#endif
- }
- else if( alg == 'a' )
- {
- Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- }
- else ErrorExit( "Sorry!" );
- }
-// fprintf( stderr, "## impmatch = %f\n", impmatch );
-
-#if 1
- if( parallelizationstrategy == BAATARI2 && *subgenerationpt != subgenerationatfirst )
- {
-// fprintf( stderr, "\nYarinaoshi2!! (Thread %d)\n", thread_no );
- goto yarinaoshi;
- }
-#endif
-
- identity = !strcmp( localcopy[s1], mastercopy[s1] );
- identity *= !strcmp( localcopy[s2], mastercopy[s2] );
-
-
-/* Bug? : idnetitcal but score change when scoreing mtx != JTT */
-
- length = strlen( mseq1[0] );
-
- if( identity )
- {
- tscore = mscore;
-// if( !devide ) fprintf( trap_g, "tscore = %f identical.\n", tscore );
-// fprintf( stderr, " identical." );
- fprintf( stderr, "%03d-%04d-%d (thread %4d) identical \r", iterate+1, *ndonept, k, thread_no );
- }
- else
- {
- if( score_check )
- {
- if( constraint == 2 )
- {
-#if 1
- if( RNAscoremtx == 'r' )
- intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
- else
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
-#else
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
-#endif
-
- tscore = impmatch + tmpdouble;
-
-// fprintf( stderr, "tmpdouble=%f, impmatch = %f -> %f, tscore = %f\n", tmpdouble, oimpmatch, impmatch, tscore );
- }
- else
- {
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
- tscore = tmpdouble;
- }
-// fprintf( stderr, "#######ii=%d, iterate=%d score = %f -> %f \n", ii, iterate , mscore, tscore );
- #if 0
- for( i=0; i<1; i++ )
- fprintf( stderr, "%s\n", mseq1[i] );
- fprintf( stderr, "+++++++\n" );
- for( i=0; i<1; i++ )
- fprintf( stderr, "%s\n", mseq2[i] );
- #endif
-
- }
- else
- {
- tscore = mscore + 1.0;
-// tscore = 0.0;
-// fprintf( stderr, "in line 705, tscore=%f\n", tscore );
-// for( i=0; i<length; i++ )
-// tscore = tscore + (double)mseq1[0][i];
-// mscore = tscore - 1.0;
- }
-
- if( isnan( mscore ) )
- {
- fprintf( stderr, "\n\nmscore became NaN\n" );
- exit( 1 );
- }
- if( isnan( tscore ) )
- {
- fprintf( stderr, "\n\ntscore became NaN\n" );
- exit( 1 );
- }
-
-
-
-// fprintf( stderr, "@@@@@ mscore,tscore = %f,%f\n", mscore, tscore );
-
-#if 1
- if( parallelizationstrategy == BAATARI1 && *subgenerationpt != subgenerationatfirst )
- {
-// fprintf( stderr, "\nYarinaoshi1!! (Thread %d)\n", thread_no );
- goto yarinaoshi;
- }
-#endif
- gain = tscore - ( mscore - cut/100.0*mscore );
- if( gain > 0 )
- {
- if( parallelizationstrategy == BESTFIRST )
- {
- if( gain > gainlist[thread_no] )
- {
- gainlist[thread_no] = gain;
- for( i=0; i<locnjob; i++ ) strcpy( candidates[thread_no][i], localcopy[i] );
- tscorelist[thread_no] = tscore;
-// if( iterate == 0 ) fprintf( stderr, "hist %d-%d-%d, gain=%f (Thread %d)\n", iterate, l, k, gain, thread_no );
- }
- }
- else
- {
- pthread_mutex_lock( targ->mutex );
- for( i=0; i<locnjob; i++ ) strcpy( mastercopy[i], localcopy[i] );
- *subgenerationpt += 1;
- gainlist[thread_no] = *basegainpt + gain;
- *basegainpt += gain;
-
- if( scoreout )
- {
- unweightedspscore = plainscore( locnjob, localcopy );
- fprintf( stderr, "\nSCORE %d = %.0f, ", *ntrypt, unweightedspscore );
- fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( locnjob * strlen( mastercopy[0] ) ) );
- if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
- fprintf( stderr, "\n" );
- }
-
- pthread_mutex_unlock( targ->mutex );
- tscorelist[thread_no] = tscore;
- }
-#if 0
- fprintf( stderr, "tscore = %f mscore = %f accepted.\n", tscore, mscore );
- fprintf( stderr, "\nbetter! gain = %f (thread %d)\r", gain, thread_no );
-#else
- fprintf( stderr, "%03d-%04d-%d (thread %4d) better \r", iterate+1, *ndonept, k, thread_no );
-#endif
-
- }
- else
- {
-#if 0
- fprintf( stderr, "tscore = %f mscore = %f rejected.\r", tscore, mscore );
- fprintf( stderr, "worse! gain = %f", gain );
-#else
- fprintf( stderr, "%03d-%04d-%d (thread %4d) worse \r", iterate+1, *ndonept, k, thread_no );
-#endif
- tscore = mscore;
- }
- }
- converged2 = 0;
- for( ii=iterate-2; ii>=0; ii-=1 )
- {
-// fprintf( stderr, "Checking tscorehistory %f ?= %f\n", tscore, tscorehistory_detail[ii][branchpos] );
- if( tscore == tscorehistory_detail[ii][branchpos] )
- {
- converged2 = 1;
- break;
- }
- }
- if( parallelizationstrategy != BESTFIRST && converged2 )
- {
-// fprintf( stderr, "\nFINISH!\n" );
- pthread_mutex_lock( targ->mutex );
- *finishpt = 1;
- pthread_mutex_unlock( targ->mutex );
- }
-
- tscorehistory_detail[iterate][branchpos] = tscore;
- fprintf( stderr, "\r" );
-
- pthread_mutex_lock( targ->mutex );
- (*ndonept)++;
-// fprintf( stderr, "*ndonept = %d, nbranch = %d (thread %d) iterate=%d\n", *ndonept, nbranch, thread_no, iterate );
- generationofinput[branchpos] = iterate;
- if( *ndonept == nbranch )
- {
- if( *collectingpt != -1 ) *collectingpt = 1; // chofuku
-// fprintf( stderr, "Thread %d sends a signal, *ndonept = %d\n", thread_no, *ndonept );
- pthread_cond_signal( targ->collection_start );
- }
- pthread_mutex_unlock( targ->mutex );
- } /* while( 1 ) */
-
- } /* for( iterate ) */
-// return( NULL );
-}
-#endif
-
-
-int TreeDependentIteration( int locnjob, char **name, int nlen[M],
- char **aseq, char **bseq, int ***topol, double **len,
- int alloclen, LocalHom **localhomtable,
- RNApair ***singlerna,
- int nkozo, char *kozoarivec )
-{
- int i, j, k, l, iterate, ii, iu, ju;
- int lin, ldf, length;
- int clus1, clus2;
- int s1, s2;
- static double **imanoten;
- static Node *stopol;
- static double *effarrforlocalhom = NULL;
- static double *effarr = NULL;
- static double *effarr1 = NULL;
- static double *effarr2 = NULL;
- static double *effarr_kozo = NULL;
- static double *effarr1_kozo = NULL;
- static double *effarr2_kozo = NULL;
- static double **mtx = NULL;
- static int **node = NULL;
- static int *branchnode = NULL;
- static double **branchWeight = NULL;
- static char **mseq1, **mseq2;
- static float ***history;
- FILE *trap;
- double tscore, mscore;
- int identity;
- int converged;
- int oscillating;
- float naivescore0 = 0.0; // by D.Mathog, a guess
- float naivescore1;
-#if 0
- char pair[njob][njob];
-#else
- static char **pair;
-#endif
-#if DEBUG + RECORD
- double score_for_check0, score_for_check1;
- static double **effmtx = NULL;
- extern double score_calc0();
-#endif
- static char *indication1, *indication2;
- static LocalHom ***localhomshrink = NULL;
- float impmatch = 0.0, oimpmatch = 0.0;
- static int *gapmap1;
- static int *gapmap2;
- double tmpdouble;
- int intdum;
- static RNApair *rnapairboth;
- RNApair ***grouprna1, ***grouprna2;
- double unweightedspscore;
-
- if( rnakozo && rnaprediction == 'm' )
- {
- grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- }
- else
- {
- grouprna1 = grouprna2 = NULL;
- }
-
- Writeoptions( trap_g );
- fflush( trap_g );
-
- if( effarr == NULL ) /* locnjob == njob ni kagiru */
- {
- indication1 = AllocateCharVec( njob*3+50 );
- indication2 = AllocateCharVec( njob*3+50 );
- effarr = AllocateDoubleVec( locnjob );
- effarrforlocalhom = AllocateDoubleVec( locnjob );
- effarr1 = AllocateDoubleVec( locnjob );
- effarr2 = AllocateDoubleVec( locnjob );
- mseq1 = AllocateCharMtx( locnjob, 0 );
- mseq2 = AllocateCharMtx( locnjob, 0 );
- mtx = AllocateDoubleMtx( locnjob, locnjob );
- node = AllocateIntMtx( locnjob, locnjob );
- branchnode = AllocateIntVec( locnjob );
- branchWeight = AllocateDoubleMtx( locnjob, 2 );
- history = AllocateFloatCub( niter, locnjob, 2 );
- stopol = (Node *)calloc( locnjob * 2, sizeof( Node ) );
- gapmap1 = AllocateIntVec( alloclen );
- gapmap2 = AllocateIntVec( alloclen );
- if( score_check == 2 ) imanoten = AllocateDoubleMtx( njob, njob );
-
- effarr1_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
- effarr2_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
- effarr_kozo = AllocateDoubleVec( locnjob );
- for( i=0; i<locnjob; i++ )
- effarr_kozo[i] = effarr1_kozo[i] = effarr2_kozo[i] = 0.0;
-
-#if 0
-#else
- pair = AllocateCharMtx( locnjob, locnjob );
- if( rnakozo ) rnapairboth = (RNApair *)calloc( alloclen, sizeof( RNApair ) );
-
- if( constraint )
- {
- localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
- for( i=0; i<njob; i++)
- {
- localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom * ) );
- }
- }
-#endif
- }
-#if DEBUG + RECORD
- if( !effmtx ) effmtx = AllocateDoubleMtx( locnjob, locnjob );
- for( i=0; i<locnjob; i++ ) for( j=0; j<locnjob; j++ ) effmtx[i][j] = 1.0;
-#endif
-
- for( i=0; i<locnjob; i++ ) strcpy( bseq[i], aseq[i] );
-
- writePre( locnjob, name, nlen, aseq, 0 );
-
- if( utree )
- {
- if( constraint )
- {
- counteff_simple( locnjob, topol, len, effarrforlocalhom );
- calcimportance( locnjob, effarrforlocalhom, aseq, localhomtable );
- }
-
- if( weight == 2 )
- {
- countnode_int( locnjob, topol, node );
- if( nkozo )
- {
- fprintf( stderr, "Not supported, weight=%d nkozo=%d.\n", weight, nkozo );
- }
- }
- else if( weight == 4 )
- {
- treeCnv( stopol, locnjob, topol, len, branchWeight );
- calcBranchWeight( branchWeight, locnjob, stopol, topol, len );
- }
- }
-
-#ifdef enablemultithread
- if( nthread > 0 )
- {
- threadarg_t *targ;
- pthread_t *handle;
- pthread_mutex_t mutex;
- pthread_cond_t collection_end;
- pthread_cond_t collection_start;
- int jobposint;
- int generationofmastercopy;
- int subgeneration;
- float basegain;
- int *generationofinput;
- float *gainlist;
- float *tscorelist;
- int ndone;
- int ntry;
- int collecting;
- int nbranch;
- int maxiter;
- char ***candidates;
- int *branchtable;
- float **tscorehistory_detail;
- int finish;
-
- nwa = nthread + 1;
- nbranch = (njob-1) * 2 - 1;
- maxiter = niter;
-
- targ = calloc( nwa, sizeof( threadarg_t ) );
- handle = calloc( nwa, sizeof( pthread_t ) );
- pthread_mutex_init( &mutex, NULL );
- pthread_cond_init( &collection_end, NULL );
- pthread_cond_init( &collection_start, NULL );
-
- gainlist = calloc( nwa, sizeof( float ) );
- tscorelist = calloc( nwa, sizeof( float ) );
- branchtable = calloc( nbranch, sizeof( int ) );
- generationofinput = calloc( nbranch, sizeof( int ) );
- if( parallelizationstrategy == BESTFIRST )
- candidates = AllocateCharCub( nwa, locnjob, alloclen );
- for( i=0; i<nbranch; i++ ) branchtable[i] = i;
- tscorehistory_detail = AllocateFloatMtx( maxiter, nbranch );
-
- collecting = 1;
-
- for( i=0; i<nwa; i++ )
- {
- targ[i].thread_no = i;
- targ[i].njob = njob;
- targ[i].nbranch = nbranch;
- targ[i].maxiter = maxiter;
- targ[i].ndonept = &ndone;
- targ[i].ntrypt = &ntry;
- targ[i].collectingpt = &collecting;
- targ[i].jobposintpt = &jobposint;
- targ[i].gainlist = gainlist;
- targ[i].tscorelist = tscorelist;
- targ[i].nkozo = nkozo;
- targ[i].kozoarivec = kozoarivec;
- targ[i].mastercopy = bseq;
- targ[i].candidates = candidates;
- targ[i].subgenerationpt = &subgeneration;
- targ[i].basegainpt = &basegain;
- targ[i].generationofmastercopypt = &generationofmastercopy;
- targ[i].generationofinput = generationofinput;
- targ[i].branchtable = branchtable;
- targ[i].singlerna = singlerna;
- targ[i].localhomtable = localhomtable;
- targ[i].alloclen = alloclen;
- targ[i].stopol = stopol;
- targ[i].topol = topol;
-// targ[i].len = len;
- targ[i].mutex = &mutex;
- targ[i].collection_end = &collection_end;
- targ[i].collection_start = &collection_start;
- targ[i].tscorehistory_detail = tscorehistory_detail;
- targ[i].finishpt = &finish;
-
- pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
- }
-
- for( i=0; i<nwa; i++ )
- {
- pthread_join( handle[i], NULL );
- }
-
- pthread_mutex_destroy( &mutex );
- pthread_cond_destroy( &collection_end );
- pthread_cond_destroy( &collection_start );
-
- free( targ );
- free( handle );
- free( gainlist );
- free( tscorelist );
- free( branchtable );
- free( generationofinput );
- if( parallelizationstrategy == BESTFIRST )
- FreeCharCub( candidates );
- FreeFloatMtx( tscorehistory_detail );
- }
- else
-#endif
- {
-#if 0
- int *branchtable;
- int jobpos;
- int myjob;
-
- int nbranch;
- nbranch = (njob-1) * 2 - 1;
-
- branchtable = calloc( nbranch, sizeof( int ) );
- for( i=0; i<nbranch; i++ ) branchtable[i] = i;
-
- srand( randomseed );
-#endif
-
- if( parallelizationstrategy == BESTFIRST )
- {
- fprintf( stderr, "Not implemented. Try --thread 1 --bestfirst\n" );
- exit( 1 );
- }
- converged = 0;
- if( cooling ) cut *= 2.0;
- for( iterate = 0; iterate<niter; iterate++ )
- {
- if( cooling ) cut *= 0.5; /* ... */
-
-#if 0
- if( randomseed != 0 ) shuffle( branchtable, nbranch );
-#endif
-
- fprintf( trap_g, "\n" );
- Writeoption2( trap_g, iterate, cut );
- fprintf( trap_g, "\n" );
-
-
- if( utree == 0 )
- {
- if( nkozo )
- {
- fprintf( stderr, "The combination of dynamic tree and kozo is not supported.\n" );
- exit( 1 );
- }
- if( devide )
- {
- static char *buff1 = NULL;
- static char *buff2 = NULL;
- if( !buff1 )
- {
- buff1 = AllocateCharVec( alloclen );
- buff2 = AllocateCharVec( alloclen );
- }
-
- for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ )
- {
- buff1[0] = buff2[0] = 0;
- strcat( buff1, res_g[i] ); strcat( buff2, res_g[j] );
- strcat( buff1, bseq[i] ); strcat( buff2, bseq[j] );
- strcat( buff1, seq_g[i] ); strcat( buff2, seq_g[j] );
-
- mtx[i][j] = (double)substitution_hosei( buff1, buff2 );
- }
- }
- else
- {
- for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ )
- mtx[i][j] = (double)substitution_hosei( bseq[i], bseq[j] );
- }
-
- if ( treemethod == 'n' )
- nj( locnjob, mtx, topol, len );
- else if( treemethod == 's' )
- spg( locnjob, mtx, topol, len );
- else if( treemethod == 'X' )
- supg( locnjob, mtx, topol, len );
- else if( treemethod == 'p' )
- upg2( locnjob, mtx, topol, len );
- /* veryfastsupg\e$B$O!":#$N$H$3$m;H$($^$;$s!#\e(B*/
- /* \e$B=gHV$NLdBj$,$"$k$N$G\e(B */
-
- if( weight == 2 )
- countnode_int( locnjob, topol, node );
- else if( weight == 4 )
- {
- treeCnv( stopol, locnjob, topol, len, branchWeight );
- calcBranchWeight( branchWeight, locnjob, stopol, topol, len );
- }
- trap = fopen( "hat2", "w" );
- if( !trap ) ErrorExit( "Cannot open hat2." );
- WriteHat2_pointer( trap, locnjob, name, mtx );
- fclose( trap );
- if( constraint )
- {
- counteff_simple( locnjob, topol, len, effarrforlocalhom );
- calcimportance( locnjob, effarrforlocalhom, aseq, localhomtable );
- }
- }
-
- if( iterate % 2 == 0 )
- {
- lin = 0; ldf = +1;
- }
- else
- {
- lin = locnjob - 2; ldf = -1;
- }
-
- if( score_check == 2 )
- {
- effarr1[0] = 1.0;
- effarr2[0] = 1.0;
- length = strlen( bseq[0] );
- for( i=0; i<locnjob-1; i++ )
- for( j=i+1; j<locnjob; j++ )
- intergroup_score( bseq+i, bseq+j, effarr1, effarr2, 1, 1, length, imanoten[i]+j );
- }
-
-#if 1
- for( l=lin; l < locnjob-1 && l >= 0 ; l+=ldf )
- {
-
-
- for( k=0; k<2; k++ )
- {
- if( l == locnjob-2 ) k = 1;
-#else
-
- for( jobpos=0; jobpos<nbranch; jobpos++)
- {
- {
- myjob = branchtable[jobpos];
- l = myjob / 2;
- if( l == locnjob-2 ) k = 1;
- else k = myjob - l * 2;
-#endif
- #if 1
- fprintf( stderr, "STEP %03d-%03d-%d ", iterate+1, l+1, k );
- fflush( stderr );
- #else
- fprintf( stderr, "STEP %03d-%03d-%d %s", iterate+1, l+1, k, use_fft?"\n":"\n" );
- #endif
- for( i=0; i<locnjob; i++ ) for( j=0; j<locnjob; j++ ) pair[i][j] = 0;
-
- OneClusterAndTheOther( locnjob, pair, &s1, &s2, topol, l, k );
- #if 0
- fprintf( stderr, "STEP%d-%d\n", l, k );
- for( i=0; i<locnjob; i++ )
- {
- for( j=0; j<locnjob; j++ )
- {
- fprintf( stderr, "%#3d", pair[i][j] );
- }
- fprintf( stderr, "\n" );
- }
- #endif
- if( !weight )
- {
- for( i=0; i<locnjob; i++ ) effarr[i] = 1.0;
- if( nkozo )
- {
- for( i=0; i<locnjob; i++ )
- {
- if( kozoarivec[i] )
- effarr_kozo[i] = 1.0;
- else
- effarr_kozo[i] = 0.0;
- }
- }
- }
- else if( weight == 2 )
- {
- nodeFromABranch( locnjob, branchnode, node, topol, len, l, k );
- node_eff( locnjob, effarr, branchnode );
- }
- else if( weight == 4 )
- {
- weightFromABranch( locnjob, effarr, stopol, topol, l, k );
- #if 0
- if( nkozo )
- {
- assignstrweight( locnjob, effarr_kozo, stopol, topol, l, k, kozoarivec, effarr );
- }
-
- #else
- if( nkozo ) // hitomadu single weight.
- for( i=0; i<locnjob; i++ )
- {
- if( kozoarivec[i] ) effarr_kozo[i] = effarr[i];
- else effarr_kozo[i] = 0.0;
- }
- #endif
- #if 0
- fprintf( stderr, "\n" );
- fprintf( stderr, "effarr_kozo = \n" );
- for( i=0; i<locnjob; i++ ) fprintf( stderr, "%5.3f ", effarr_kozo[i] );
- fprintf( stderr, "\n" );
- fprintf( stderr, "effarr = \n" );
- for( i=0; i<locnjob; i++ ) fprintf( stderr, "%5.3f ", effarr[i] );
- fprintf( stderr, "\n\n" );
- #endif
- }
-
- for( i=0; i<locnjob; i++ ) strcpy( aseq[i], bseq[i] );
- length = strlen( aseq[0] );
-
- if( nkozo )
- {
- #if 1
- double tmptmptmp;
- tmptmptmp = 0.0;
- clus1 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s1, aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
- for( i=0; i<clus1; i++ ) effarr1_kozo[i] *= 1.0; // 0.5 ga sairyo ?
- tmptmptmp = 0.0;
- clus2 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s2, aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
- for( i=0; i<clus2; i++ ) effarr2_kozo[i] *= 1.0; // 0.5 ga sairyo ?
-
- #if 0
- fprintf( stderr, "\ngroup1 = %s\n", indication1 );
- for( i=0; i<clus1; i++ ) fprintf( stderr, "effarr1_kozo[%d], effarr1[] = %f, %f\n", i, effarr1_kozo[i], effarr1[i] );
- fprintf( stderr, "\ngroup2 = %s\n", indication2 );
- for( i=0; i<clus2; i++ ) fprintf( stderr, "effarr2_kozo[%d], effarr2[] = %f, %f\n", i, effarr2_kozo[i], effarr2[i] );
- #endif
-
-
-
-
-
- #else
- clus1 = conjuctionfortbfast_kozo_BUG( pair, s1, aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
- clus2 = conjuctionfortbfast_kozo_BUG( pair, s2, aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
- #endif
- }
- else
- {
- clus1 = conjuctionfortbfast( pair, s1, aseq, mseq1, effarr1, effarr, indication1 );
- clus2 = conjuctionfortbfast( pair, s2, aseq, mseq2, effarr2, effarr, indication2 );
- }
-
-
-
- if( rnakozo && rnaprediction == 'm' )
- {
- makegrouprnait( grouprna1, singlerna, pair, s1 );
- makegrouprnait( grouprna2, singlerna, pair, s2 );
- }
-
- if( score_check == 2 )
- {
- if( constraint )
- {
- // msshrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
- shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
- oimpmatch = 0.0;
- if( use_fft )
- {
- if( alg == 'Q' )
- {
- part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- for( i=length-1; i>=0; i-- ) oimpmatch += part_imp_match_out_scQ( i, i );
- }
- else
- {
- part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- for( i=length-1; i>=0; i-- ) oimpmatch += part_imp_match_out_sc( i, i );
- }
- }
- else
- {
- if( alg == 'Q' )
- {
- imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- for( i=length-1; i>=0; i-- ) oimpmatch += imp_match_out_scQ( i, i );
- }
- else
- {
- imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- fprintf( stderr, "not supported\n" );
- exit( 1 );
- }
- }
- // fprintf( stderr, "### oimpmatch = %f\n", oimpmatch );
- }
- else
- {
- oimpmatch = 0.0;
- }
- tmpdouble = 0.0;
- iu=0;
- for( i=s1; i<locnjob; i++ )
- {
- if( !pair[s1][i] ) continue;
- ju=0;
- for( j=s2; j<locnjob; j++ )
- {
- if( !pair[s2][j] ) continue;
- // fprintf( stderr, "i = %d, j = %d, effarr1=%f, effarr2=%f\n", i, j, effarr1[iu], effarr2[ju] );
- tmpdouble += effarr1[iu] * effarr2[ju] * imanoten[MIN(i,j)][MAX(i,j)];
- ju++;
- }
- iu++;
- }
- mscore = oimpmatch + tmpdouble;
- }
- else if( score_check )
- {
- #if 1
- if( RNAscoremtx == 'r' )
- intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
- else
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
- #else
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
- #endif
-
- if( constraint )
- {
- shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
- // weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink ); // >>>
- oimpmatch = 0.0;
- if( use_fft )
- {
- if( alg == 'Q' )
- {
- part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += part_imp_match_out_scQ( i, i );
- // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
- else
- {
- part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += part_imp_match_out_sc( i, i );
- // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
- // fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
- }
- else
- {
- if( alg == 'Q' )
- {
- imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
-
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += imp_match_out_scQ( i, i );
- // fprintf( stderr, "#### i=%d, initial impmatch = %f\n", i, oimpmatch );
- }
- }
- else
- {
- imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
-
- fprintf( stderr, "not supported\n" );
- exit( 1 );
-
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += imp_match_out_sc( i, i );
- // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
- // fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
- }
- // fprintf( stderr, "#### initial impmatch = %f\n", oimpmatch );
- }
- else
- {
- oimpmatch = 0.0;
- }
-
-
- // fprintf( stderr, "#### tmpdouble = %f\n", tmpdouble );
- mscore = (double)oimpmatch + tmpdouble;
- }
- else
- {
- // fprintf( stderr, "score_check = %d\n", score_check );
- /* atode kousokuka */
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
- mscore = tmpdouble;
- /* atode kousokuka */
-
- if( constraint )
- {
- oimpmatch = 0.0;
- shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
- if( use_fft )
- {
- if( alg == 'Q' )
- {
- part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- }
- else
- {
- part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- }
- }
- else
- {
- if( alg == 'Q' )
- {
- imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
- }
- else
- {
- imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- fprintf( stderr, "Not supported\n" );
- exit( 1 );
- }
- }
- }
- }
-
- // oimpmatch = 0.0;
- if( constraint )
- {
- #if 0 // iranai
- if( alg == 'Q' )
- {
- imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += imp_match_out_scQ( i, i );
- // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
- else
- {
- imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- for( i=length-1; i>=0; i-- )
- {
- oimpmatch += imp_match_out_sc( i, i );
- // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
- }
- }
- #endif
- }
- #if 0
- if( alg == 'H' )
- naivescore0 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + oimpmatch;
- else if( alg == 'Q' )
- naivescore0 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + oimpmatch;
- else if( alg == 'R' )
- naivescore0 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + oimpmatch;
- #endif
-
- // if( rnakozo ) foldalignedrna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, rnapairboth );
-
- // if( !use_fft && !rnakozo )
- if( !use_fft )
- {
- commongappick_record( clus1, mseq1, gapmap1 );
- commongappick_record( clus2, mseq2, gapmap2 );
- }
-
- #if 0
- fprintf( stderr, "##### mscore = %f\n", mscore );
- #endif
-
- #if DEBUG
- if( !devide )
- {
- fprintf( trap_g, "\nSTEP%d-%d-%d\n", iterate+1, l+1, k );
- fprintf( trap_g, "group1 = %s\n", indication1 );
- fprintf( trap_g, "group2 = %s\n", indication2 );
- fflush( trap_g );
- }
-
- #endif
- #if 0
- printf( "STEP %d-%d-%d\n", iterate, l, k );
- for( i=0; i<clus2; i++ ) printf( "%f ", effarr2[i] );
- printf( "\n" );
- #endif
- if( constraint == 2 )
- {
- if( use_fft )
- {
- // if( alg == 'Q' )
- // part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- // else
- // part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- Falign_localhom( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2, NULL, 0, NULL );
- // fprintf( stderr, "##### impmatch = %f\n", impmatch );
- }
- else
- {
- if( alg == 'Q' )
- {
- float wm;
- // imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap wo tsukuttakara iranai.
- // if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, gapmap1, gapmap2, rnapairboth );
-
- wm = Q__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL, gapmap1, gapmap2 );
- fprintf( stderr, "wm = %f\n", wm );
- #if 0
- fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
- naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
- fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
- #if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
- // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
- // rewind( stdout );
- // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- // exit( 1 );
- }
- #endif
- #endif
- }
- else if( alg == 'R' )
- {
- float wm;
- imp_match_init_strictR( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
- wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
- // fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
- naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
- // fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: %f->%f UP!\n", clus1, clus2, naivescore0, naivescore1 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
- #if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
- // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
- rewind( stdout );
- for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- exit( 1 );
- }
- #endif
- }
- else if( alg == 'H' )
- {
- float wm;
- imp_match_init_strictH( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
- wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
- fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
- naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
- fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
- #if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
- // fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
- // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- // exit( 1 );
- }
- #endif
- }
- else
- {
- // imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- A__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2 );
- // fprintf( stderr, "##### impmatch = %f\n", impmatch );
- }
- }
- }
- else if( use_fft )
- {
- float totalwm;
- totalwm = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
-
- // fprintf( stderr, "totalwm = %f\n", totalwm );
- #if 0
- if( alg == 'Q' )
- {
- fprintf( stderr, "totalwm = %f\n", totalwm );
- naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
- #if 1 // chuui
- if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
- {
- // fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
- // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- // exit( 1 );
- }
- #endif
- }
- #endif
- if( alg == 'R' )
- {
- fprintf( stderr, "totalwm = %f\n", totalwm );
- naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
- #if 1 // chuui
- if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
- {
- // fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
- // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- // exit( 1 );
- }
- }
- #endif
- }
- else
- {
- if( alg == 'M' )
- {
- MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- }
- else if( alg == 'A' )
- {
- A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); // outgap==1
- }
- else if( alg == 'Q' )
- {
- float wm;
- wm = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
- fprintf( stderr, "wm = %f\n", wm );
- fprintf( stderr, "impmatch = %f\n", impmatch );
- naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
- #if 1 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
- // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
- // rewind( stderr );
- // rewind( stdout );
- // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- // exit( 1 );
- }
- #endif
- }
- else if( alg == 'R' )
- {
- float wm;
- wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
- naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
- #if 1 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
- // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
- // rewind( stderr );
- // rewind( stdout );
- // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- // exit( 1 );
- }
- #endif
- }
- else if( alg == 'H' )
- {
- float wm;
- wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
- naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
-
- if( naivescore1 > naivescore0 )
- fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
- else if( naivescore1 < naivescore0 )
- {
- fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
- }
- else
- fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
-
- #if 0 // chuui
- if( abs( wm - naivescore1 ) > 100 )
- {
- rewind( stdout );
- for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
- for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
- exit( 1 );
- }
- #endif
- }
- else if( alg == 'a' )
- {
- Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- }
- else ErrorExit( "Sorry!" );
- }
- // fprintf( stderr, "## impmatch = %f\n", impmatch );
-
- if( checkC )
- {
- extern double DSPscore();
- extern double SSPscore();
- static double cur;
- static double pre;
-
- /*
- pre = SSPscore( locnjob, bseq );
- cur = SSPscore( locnjob, aseq );
- */
- pre = DSPscore( locnjob, bseq );
- cur = DSPscore( locnjob, aseq );
-
- fprintf( stderr, "Previous Sscore = %f\n", pre );
- fprintf( stderr, "Currnet Sscore = %f\n\n", cur );
- }
-
- // fprintf( stderr, "## impmatch = %f\n", impmatch );
- identity = !strcmp( aseq[s1], bseq[s1] );
- identity *= !strcmp( aseq[s2], bseq[s2] );
-
-
- /* Bug? : idnetitcal but score change when scoreing mtx != JTT */
-
- length = strlen( mseq1[0] );
-
- if( identity )
- {
- tscore = mscore;
- if( !devide ) fprintf( trap_g, "tscore = %f identical.\n", tscore );
- fprintf( stderr, " identical." );
- converged++;
- }
- else
- {
- if( score_check )
- {
- if( constraint == 2 )
- {
- #if 1
- if( RNAscoremtx == 'r' )
- intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
- else
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
- #else
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
- #endif
-
- tscore = impmatch + tmpdouble;
-
- // fprintf( stderr, "tmpdouble=%f, impmatch = %f -> %f, tscore = %f\n", tmpdouble, oimpmatch, impmatch, tscore );
- }
- else
- {
- intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
- tscore = tmpdouble;
- }
- // fprintf( stderr, "#######ii=%d, iterate=%d score = %f -> %f \n", ii, iterate , mscore, tscore );
- #if 0
- for( i=0; i<1; i++ )
- fprintf( stderr, "%s\n", mseq1[i] );
- fprintf( stderr, "+++++++\n" );
- for( i=0; i<1; i++ )
- fprintf( stderr, "%s\n", mseq2[i] );
- #endif
-
- }
- else
- {
- tscore = mscore + 1.0;
- // tscore = 0.0;
- // fprintf( stderr, "in line 705, tscore=%f\n", tscore );
- // for( i=0; i<length; i++ )
- // tscore = tscore + (double)mseq1[0][i];
- // mscore = tscore - 1.0;
- }
-
- if( isnan( mscore ) )
- {
- fprintf( stderr, "\n\nmscore became NaN\n" );
- exit( 1 );
- }
- if( isnan( tscore ) )
- {
- fprintf( stderr, "\n\ntscore became NaN\n" );
- exit( 1 );
- }
-
-
-
- // fprintf( stderr, "@@@@@ mscore,tscore = %f,%f\n", mscore, tscore );
-
- if( tscore > mscore - cut/100.0*mscore )
- {
- writePre( locnjob, name, nlen, aseq, 0 );
- for( i=0; i<locnjob; i++ ) strcpy( bseq[i], aseq[i] );
- if( score_check == 2 )
- {
- effarr1[0] = 1.0;
- effarr2[0] = 1.0;
- for( i=0; i<locnjob-1; i++ )
- for( j=i+1; j<locnjob; j++ )
- intergroup_score( bseq+i, bseq+j, effarr1, effarr2, 1, 1, length, imanoten[i]+j );
- }
-
- #if 0
- fprintf( stderr, "tscore = %f mscore = %f accepted.\n", tscore, mscore );
- #endif
- fprintf( stderr, " accepted." );
- converged = 0;
-
- }
- else
- {
- #if 0
- fprintf( stderr, "tscore = %f mscore = %f rejected.\n", tscore, mscore );
- #endif
- fprintf( stderr, " rejected." );
- tscore = mscore;
- converged++;
- }
- }
- fprintf( stderr, "\r" );
-
-
- history[iterate][l][k] = (float)tscore;
-
- // fprintf( stderr, "tscore = %f\n", tscore );
-
- if( converged >= locnjob * 2 )
- {
- fprintf( trap_g, "Converged.\n\n" );
- fprintf( stderr, "\nConverged.\n\n" );
- if( scoreout )
- {
- unweightedspscore = plainscore( njob, bseq );
- fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * ( (njob-1)*2-1 ), unweightedspscore );
- fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
- if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
- fprintf( stderr, "\n\n" );
- }
- return( 0 );
- }
- if( iterate >= 1 )
- {
- /* oscillation check */
- oscillating = 0;
- for( ii=iterate-2; ii>=0; ii-=2 )
- {
- if( (float)tscore == history[ii][l][k] )
- {
- oscillating = 1;
- break;
- }
- }
- if( ( oscillating && !cooling ) || ( oscillating && cut < 0.001 && cooling ) )
- {
- fprintf( trap_g, "Oscillating.\n" );
- fprintf( stderr, "\nOscillating.\n\n" );
- if( scoreout )
- {
- unweightedspscore = plainscore( njob, bseq );
- fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * ( (njob-1)*2-1 ), unweightedspscore );
- fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
- if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
- fprintf( stderr, "\n\n" );
- }
- #if 1 /* hujuubun */
- return( -1 );
- #endif
- }
- } /* if( iterate ) */
- } /* for( k ) */
- } /* for( l ) */
- if( scoreout )
- {
- unweightedspscore = plainscore( njob, bseq );
- fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * ( (njob-1)*2-1 ), unweightedspscore );
- fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
- if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
- fprintf( stderr, "\n\n" );
- }
- } /* for( iterate ) */
- }
- return( 2 );
-} /* int Tree... */
git://source.jalview.org / jabaws.git / blobdiff