+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-static int nadd;
-static int treein;
-static int topin;
-static int treeout;
-static int distout;
-static int noalign;
-
-typedef struct _jobtable
-{
- int i;
- int j;
-} Jobtable;
-
-#ifdef enablemultithread
-typedef struct _distancematrixthread_arg
-{
- int njob;
- int thread_no;
- float *selfscore;
- float **iscore;
- char **seq;
- Jobtable *jobpospt;
- pthread_mutex_t *mutex;
-} distancematrixthread_arg_t;
-
-typedef struct _treebasethread_arg
-{
- int thread_no;
- int *nrunpt;
- int njob;
- int *nlen;
- int *jobpospt;
- int ***topol;
- Treedep *dep;
- char **aseq;
- double *effarr;
- int *alloclenpt;
- LocalHom **localhomtable;
- RNApair ***singlerna;
- double *effarr_kozo;
- int *fftlog;
- pthread_mutex_t *mutex;
- pthread_cond_t *treecond;
-} treebasethread_arg_t;
-#endif
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- nthread = 1;
- outnumber = 0;
- scoreout = 0;
- treein = 0;
- topin = 0;
- rnaprediction = 'm';
- rnakozo = 0;
- nevermemsave = 0;
- inputfile = NULL;
- addfile = NULL;
- addprofile = 1;
- fftkeika = 0;
- constraint = 0;
- nblosum = 62;
- fmodel = 0;
- calledByXced = 0;
- devide = 0;
- use_fft = 0; // chuui
- force_fft = 0;
- fftscore = 1;
- fftRepeatStop = 0;
- fftNoAnchStop = 0;
- weight = 3;
- utree = 1;
- tbutree = 1;
- refine = 0;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 1;
- alg = 'A';
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- treemethod = 'X';
- contin = 0;
- scoremtx = 1;
- kobetsubunkatsu = 0;
- 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':
- nadd = atoi( *++argv );
- fprintf( stderr, "nadd = %d\n", nadd );
- --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 'R':
- rnaprediction = 'r';
- break;
- case 's':
- RNAscoremtx = 'r';
- break;
-#if 1
- case 'a':
- fmodel = 1;
- break;
-#endif
- case 'K':
- addprofile = 0;
- break;
- case 'y':
- distout = 1;
- break;
- case 't':
- treeout = 1;
- break;
- case 'T':
- noalign = 1;
- break;
- case 'D':
- dorp = 'd';
- break;
- case 'P':
- dorp = 'p';
- break;
-#if 1
- case 'O':
- outgap = 0;
- break;
-#else
- case 'O':
- fftNoAnchStop = 1;
- break;
-#endif
- case 'S':
- scoreout = 1;
- break;
-#if 0
- case 'e':
- fftscore = 0;
- break;
- case 'r':
- fmodel = -1;
- break;
- case 'R':
- fftRepeatStop = 1;
- break;
- case 's':
- treemethod = 's';
- break;
-#endif
- case 'X':
- treemethod = 'X';
- break;
- case 'E':
- treemethod = 'E';
- break;
- case 'q':
- treemethod = 'q';
- break;
- case 'n' :
- outnumber = 1;
- break;
-#if 0
- case 'a':
- alg = 'a';
- break;
-#endif
- case 'Q':
- alg = 'Q';
- break;
- case 'H':
- alg = 'H';
- break;
- case 'A':
- alg = 'A';
- break;
- case 'M':
- alg = 'M';
- break;
- case 'N':
- nevermemsave = 1;
- break;
- case 'B':
- break;
- case 'F':
- use_fft = 1;
- break;
- case 'G':
- force_fft = 1;
- use_fft = 1;
- break;
- case 'U':
- treein = 1;
- break;
- case 'V':
- topin = 1;
- break;
- case 'u':
- tbrweight = 0;
- weight = 0;
- break;
- case 'v':
- tbrweight = 3;
- break;
- case 'd':
- disp = 1;
- break;
-/* Modified 01/08/27, default: user tree */
- case 'J':
- tbutree = 0;
- break;
-/* modification end. */
- case 'z':
- fftThreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- fftWinSize = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'Z':
- checkC = 1;
- break;
- default:
- fprintf( stderr, "illegal option %c\n", c );
- argc = 0;
- break;
- }
- }
- nextoption:
- ;
- }
- if( argc == 1 )
- {
- cut = atof( (*argv) );
- argc--;
- }
- if( argc != 0 )
- {
- fprintf( stderr, "options: Check source file !\n" );
- exit( 1 );
- }
- if( tbitr == 1 && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : o, m or u\n" );
- exit( 1 );
- }
- if( alg == 'C' && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : C, o\n" );
- exit( 1 );
- }
-}
-
-#if 0
-static void *distancematrixthread2( void *arg )
-{
- distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
- int njob = targ->njob;
- int thread_no = targ->thread_no;
- float *selfscore = targ->selfscore;
- float **iscore = targ->iscore;
- char **seq = targ->seq;
- Jobtable *jobpospt = targ->jobpospt;
-
- float ssi, ssj, bunbo;
- int i, j;
-
- while( 1 )
- {
- pthread_mutex_lock( targ->mutex );
- i = jobpospt->i;
- i++;
- if( i == njob-1 )
- {
- pthread_mutex_unlock( targ->mutex );
- return( NULL );
- }
- jobpospt->i = i;
- pthread_mutex_unlock( targ->mutex );
-
- ssi = selfscore[i];
- if( i % 10 == 0 ) fprintf( stderr, "\r% 5d / %d (thread %4d)", i, njob, thread_no );
- for( j=i+1; j<njob; j++)
- {
- ssj = selfscore[j];
- bunbo = MIN( ssi, ssj );
- if( bunbo == 0.0 )
- iscore[i][j-i] = 1.0;
- else
- iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
- }
- }
-}
-#endif
-
-#ifdef enablemultithread
-static void *distancematrixthread( void *arg )
-{
- distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
- int njob = targ->njob;
- int thread_no = targ->thread_no;
- float *selfscore = targ->selfscore;
- float **iscore = targ->iscore;
- char **seq = targ->seq;
- Jobtable *jobpospt = targ->jobpospt;
-
- float ssi, ssj, bunbo;
- int i, j;
-
- while( 1 )
- {
- pthread_mutex_lock( targ->mutex );
- j = jobpospt->j;
- i = jobpospt->i;
- j++;
- if( j == njob )
- {
- i++;
- j = i + 1;
- if( i == njob-1 )
- {
- pthread_mutex_unlock( targ->mutex );
- return( NULL );
- }
- }
- jobpospt->j = j;
- jobpospt->i = i;
- pthread_mutex_unlock( targ->mutex );
-
-
- if( j==i+1 && i % 10 == 0 ) fprintf( stderr, "\r% 5d / %d (thread %4d)", i, njob, thread_no );
- ssi = selfscore[i];
- ssj = selfscore[j];
- bunbo = MIN( ssi, ssj );
- if( bunbo == 0.0 )
- iscore[i][j-i] = 1.0;
- else
- iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
- }
-}
-
-static void *treebasethread( void *arg )
-{
- treebasethread_arg_t *targ = (treebasethread_arg_t *)arg;
- int *nrunpt = targ->nrunpt;
- int thread_no = targ->thread_no;
- int njob = targ->njob;
- int *nlen = targ->nlen;
- int *jobpospt = targ->jobpospt;
- int ***topol = targ->topol;
- Treedep *dep = targ->dep;
- char **aseq = targ->aseq;
- double *effarr = targ->effarr;
- int *alloclen = targ->alloclenpt;
- LocalHom **localhomtable = targ->localhomtable;
- RNApair ***singlerna = targ->singlerna;
- double *effarr_kozo = targ->effarr_kozo;
- int *fftlog = targ->fftlog;
-
- char **mseq1, **mseq2;
- char **localcopy;
- int i, j, l;
- int len1, len2;
- int clus1, clus2;
- float pscore;
- char *indication1, *indication2;
- double *effarr1 = NULL;
- double *effarr2 = NULL;
- double *effarr1_kozo = NULL;
- double *effarr2_kozo = NULL;
- LocalHom ***localhomshrink = NULL;
- int m1, m2;
- float dumfl = 0.0;
- int ffttry;
- RNApair ***grouprna1, ***grouprna2;
-
-
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- localcopy = calloc( njob, sizeof( char * ) );
-
- if( rnakozo && rnaprediction == 'm' )
- {
- grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- }
- else
- {
- grouprna1 = grouprna2 = NULL;
- }
-
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
-#if 0
-#else
- if( constraint )
- {
- localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
- for( i=0; i<njob; i++)
- localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
- }
-#endif
- effarr1_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
- effarr2_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
- for( i=0; i<njob; i++ ) effarr1_kozo[i] = 0.0;
- for( i=0; i<njob; i++ ) effarr2_kozo[i] = 0.0;
-
-
-#if 0
-#endif
-
-#if 0
- for( i=0; i<njob; i++ )
- fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
-#endif
-
-#if 0 //-> main thread
- if( constraint )
- calcimportance( njob, effarr, aseq, localhomtable );
-#endif
-
-
-// writePre( njob, name, nlen, aseq, 0 );
-
-
-// for( l=0; l<njob-1; l++ )
- while( 1 )
- {
-
- pthread_mutex_lock( targ->mutex );
- l = *jobpospt;
- if( l == njob-1 )
- {
- pthread_mutex_unlock( targ->mutex );
- if( commonIP ) FreeIntMtx( commonIP );
- commonIP = NULL;
- Falign( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
- A__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
- free( mseq1 );
- free( mseq2 );
- free( localcopy );
- free( effarr1 );
- free( effarr2 );
- free( effarr1_kozo );
- free( effarr2_kozo );
- free( indication1 );
- free( indication2 );
- if( constraint )
- {
- for( i=0; i<njob; i++)
- free( localhomshrink[i] );
- free( localhomshrink );
- }
- return( NULL );
- }
- *jobpospt = l+1;
-
- if( dep[l].child0 != -1 )
- {
- while( dep[dep[l].child0].done == 0 )
- pthread_cond_wait( targ->treecond, targ->mutex );
- }
- if( dep[l].child1 != -1 )
- {
- while( dep[dep[l].child1].done == 0 )
- pthread_cond_wait( targ->treecond, targ->mutex );
- }
-// while( *nrunpt >= nthread )
-// pthread_cond_wait( targ->treecond, targ->mutex );
- (*nrunpt)++;
-
-// pthread_mutex_unlock( targ->mutex );
-
-
- m1 = topol[l][0][0];
- m2 = topol[l][1][0];
-
-// pthread_mutex_lock( targ->mutex );
-
- len1 = strlen( aseq[m1] );
- len2 = strlen( aseq[m2] );
- if( *alloclen <= len1 + len2 )
- {
- fprintf( stderr, "\nReallocating (by thread %d) ..", thread_no );
- *alloclen = ( len1 + len2 ) + 1000;
- ReallocateCharMtx( aseq, njob, *alloclen + 10 );
- fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
- }
-
- for( i=0; (j=topol[l][0][i])!=-1; i++ )
- {
- localcopy[j] = calloc( *alloclen, sizeof( char ) );
- strcpy( localcopy[j], aseq[j] );
- }
- for( i=0; (j=topol[l][1][i])!=-1; i++ )
- {
- localcopy[j] = calloc( *alloclen, sizeof( char ) );
- strcpy( localcopy[j], aseq[j] );
- }
-
- pthread_mutex_unlock( targ->mutex );
-
- if( effarr_kozo )
- {
- clus1 = fastconjuction_noname_kozo( topol[l][0], localcopy, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
- clus2 = fastconjuction_noname_kozo( topol[l][1], localcopy, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
- }
- else
- {
- clus1 = fastconjuction_noname( topol[l][0], localcopy, mseq1, effarr1, effarr, indication1 );
- clus2 = fastconjuction_noname( topol[l][1], localcopy, mseq2, effarr2, effarr, indication2 );
- }
-
-
-
-#if 1
- fprintf( stderr, "\rSTEP % 5d /%d (thread %4d) ", l+1, njob-1, thread_no );
-#else
- fprintf( stderr, "STEP %d /%d (thread %d) \n", l+1, njob-1, thread_no );
- fprintf( stderr, "group1 = %.66s", indication1 );
- if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
- fprintf( stderr, ", child1 = %d\n", dep[l].child0 );
- fprintf( stderr, "group2 = %.66s", indication2 );
- if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
- fprintf( stderr, ", child2 = %d\n", dep[l].child1 );
-
- fprintf( stderr, "Group1's lengths = " );
- for( i=0; i<clus1; i++ ) fprintf( stderr, "%d ", strlen( mseq1[i] ) );
- fprintf( stderr, "\n" );
- fprintf( stderr, "Group2's lengths = " );
- for( i=0; i<clus2; i++ ) fprintf( stderr, "%d ", strlen( mseq2[i] ) );
- fprintf( stderr, "\n" );
-
-#endif
-
-
-
-// for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
-
- if( constraint )
- {
- fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
-// msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
-// fprintf( stderr, "localhomshrink =\n" );
-// outlocalhompt( localhomshrink, clus1, clus2 );
-// weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
-// fprintf( stderr, "after weight =\n" );
-// outlocalhompt( localhomshrink, clus1, clus2 );
- }
- if( rnakozo && rnaprediction == 'm' )
- {
- makegrouprna( grouprna1, singlerna, topol[l][0] );
- makegrouprna( grouprna2, singlerna, topol[l][1] );
- }
-
-
-/*
- fprintf( stderr, "before align all\n" );
- display( localcopy, njob );
- fprintf( stderr, "\n" );
- fprintf( stderr, "before align 1 %s \n", indication1 );
- display( mseq1, clus1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "before align 2 %s \n", indication2 );
- display( mseq2, clus2 );
- fprintf( stderr, "\n" );
-*/
-
- if( !nevermemsave && ( constraint != 2 && alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
- {
- fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
- alg = 'M';
- if( commonIP ) FreeIntMtx( commonIP );
- commonAlloc1 = 0;
- commonAlloc2 = 0;
- }
-
-
-// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
- if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
- else ffttry = 0;
-// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
-// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
-// fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
- if( constraint == 2 )
- {
- if( alg == 'M' )
- {
- fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
- exit( 1 );
- }
- fprintf( stderr, "c" );
- if( alg == 'A' )
- {
- imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- }
- else if( alg == 'H' )
- {
- imp_match_init_strictH( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
- }
- else if( alg == 'Q' )
- {
- imp_match_init_strictQ( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
- pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
- }
- else if( alg == 'R' )
- {
- imp_match_init_strictR( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
- }
- }
- else if( force_fft || ( use_fft && ffttry ) )
- {
- fprintf( stderr, "f" );
- if( alg == 'M' )
- {
- fprintf( stderr, "m" );
- pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
- }
- else
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
- }
- else
- {
- fprintf( stderr, "d" );
- fftlog[m1] = 0;
- switch( alg )
- {
- case( 'a' ):
- pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
- break;
- case( 'M' ):
- fprintf( stderr, "m" );
- pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- break;
- case( 'A' ):
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- break;
- case( 'Q' ):
- pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- break;
- case( 'R' ):
- pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- break;
- case( 'H' ):
- pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- break;
- default:
- ErrorExit( "ERROR IN SOURCE FILE" );
- }
- }
-
- nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
-
-#if SCOREOUT
- fprintf( stderr, "score = %10.2f\n", pscore );
-#endif
-
-/*
- fprintf( stderr, "after align 1 %s \n", indication1 );
- display( mseq1, clus1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "after align 2 %s \n", indication2 );
- display( mseq2, clus2 );
- fprintf( stderr, "\n" );
-*/
-
-// writePre( njob, name, nlen, localcopy, 0 );
-
- if( disp ) display( localcopy, njob );
-
- pthread_mutex_lock( targ->mutex );
- dep[l].done = 1;
- (*nrunpt)--;
- pthread_cond_broadcast( targ->treecond );
-
-// pthread_mutex_unlock( targ->mutex );
-// pthread_mutex_lock( targ->mutex );
-
- for( i=0; (j=topol[l][0][i])!=-1; i++ )
- strcpy( aseq[j], localcopy[j] );
- for( i=0; (j=topol[l][1][i])!=-1; i++ )
- strcpy( aseq[j], localcopy[j] );
- pthread_mutex_unlock( targ->mutex );
-
- for( i=0; (j=topol[l][0][i])!=-1; i++ )
- free( localcopy[j] );
- for( i=0; (j=topol[l][1][i])!=-1; i++ )
- free( localcopy[j] );
- free( topol[l][0] );
- free( topol[l][1] );
- free( topol[l] );
-
- }
-}
-#endif
-
-void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, int ***topol, double *effarr, int *alloclen, LocalHom **localhomtable, RNApair ***singlerna, double *effarr_kozo )
-{
- int i, l, m;
- int len1nocommongap, len2nocommongap;
- int len1, len2;
- int clus1, clus2;
- float pscore, tscore;
- static char *indication1, *indication2;
- static double *effarr1 = NULL;
- static double *effarr2 = NULL;
- static double *effarr1_kozo = NULL;
- static double *effarr2_kozo = NULL;
- static LocalHom ***localhomshrink = NULL;
- static int *fftlog;
- int m1, m2;
- static int *gaplen;
- static int *gapmap;
- static int *alreadyaligned;
- float dumfl = 0.0;
- int ffttry;
- RNApair ***grouprna1, ***grouprna2;
-
- if( rnakozo && rnaprediction == 'm' )
- {
- grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
- }
- else
- {
- grouprna1 = grouprna2 = NULL;
- }
-
- if( effarr1 == NULL )
- {
- fftlog = AllocateIntVec( njob );
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
- gaplen = AllocateIntVec( *alloclen+10 );
- gapmap = AllocateIntVec( *alloclen+10 );
- alreadyaligned = AllocateIntVec( njob );
-#if 0
-#else
- if( constraint )
- {
- localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
- for( i=0; i<njob; i++)
- localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
- }
-#endif
- effarr1_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
- effarr2_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
- for( i=0; i<njob; i++ ) effarr1_kozo[i] = 0.0;
- for( i=0; i<njob; i++ ) effarr2_kozo[i] = 0.0;
- }
-
- for( i=0; i<njob-nadd; i++ ) alreadyaligned[i] = 1;
- for( i=njob-nadd; i<njob; i++ ) alreadyaligned[i] = 0;
-
- for( l=0; l<njob; l++ ) fftlog[l] = 1;
-
-#if 0
- fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
-#endif
-
-#if 0
- for( i=0; i<njob; i++ )
- fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
-#endif
-
-
- if( constraint )
- calcimportance( njob, effarr, aseq, localhomtable );
-
-
-// writePre( njob, name, nlen, aseq, 0 );
-
- tscore = 0.0;
- for( l=0; l<njob-1; l++ )
- {
- if( mergeoralign[l] == 'n' )
- {
-// fprintf( stderr, "SKIP!\n" );
- free( topol[l][0] );
- free( topol[l][1] );
- free( topol[l] );
- continue;
- }
-
- m1 = topol[l][0][0];
- m2 = topol[l][1][0];
- len1 = strlen( aseq[m1] );
- len2 = strlen( aseq[m2] );
- if( *alloclen < len1 + len2 )
- {
- fprintf( stderr, "\nReallocating.." );
- *alloclen = ( len1 + len2 ) + 1000;
- ReallocateCharMtx( aseq, njob, *alloclen + 10 );
- gaplen = realloc( gaplen, ( *alloclen + 10 ) * sizeof( int ) );
- if( gaplen == NULL )
- {
- fprintf( stderr, "Cannot realloc gaplen\n" );
- exit( 1 );
- }
- gapmap = realloc( gapmap, ( *alloclen + 10 ) * sizeof( int ) );
- if( gapmap == NULL )
- {
- fprintf( stderr, "Cannot realloc gapmap\n" );
- exit( 1 );
- }
- fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
- }
-
- if( effarr_kozo )
- {
- clus1 = fastconjuction_noname_kozo( topol[l][0], aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
- clus2 = fastconjuction_noname_kozo( topol[l][1], aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
- }
- else
- {
- clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1 );
- clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2 );
- }
-
- if( mergeoralign[l] == '1' || mergeoralign[l] == '2' )
- {
- newgapstr = "=";
- }
- else
- newgapstr = "-";
-
-
- len1nocommongap = len1;
- len2nocommongap = len2;
- if( mergeoralign[l] == '1' ) // nai
- {
- findcommongaps( clus2, mseq2, gapmap );
- commongappick( clus2, mseq2 );
- len2nocommongap = strlen( mseq2[0] );
- }
- else if( mergeoralign[l] == '2' )
- {
- findcommongaps( clus1, mseq1, gapmap );
- commongappick( clus1, mseq1 );
- len1nocommongap = strlen( mseq1[0] );
- }
-
-
- fprintf( trap_g, "\nSTEP-%d\n", l );
- fprintf( trap_g, "group1 = %s\n", indication1 );
- fprintf( trap_g, "group2 = %s\n", indication2 );
-
-#if 1
- fprintf( stderr, "\rSTEP % 5d /%d ", l+1, njob-1 );
- fflush( stderr );
-#else
- fprintf( stdout, "STEP %d /%d\n", l+1, njob-1 );
- fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
- fprintf( stderr, "group1 = %.66s", indication1 );
- if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
- fprintf( stderr, "\n" );
- fprintf( stderr, "group2 = %.66s", indication2 );
- if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
- fprintf( stderr, "\n" );
-#endif
-
-
-
-// for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
-
- if( constraint )
- {
- fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
-// msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
-// fprintf( stderr, "localhomshrink =\n" );
-// outlocalhompt( localhomshrink, clus1, clus2 );
-// weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
-// fprintf( stderr, "after weight =\n" );
-// outlocalhompt( localhomshrink, clus1, clus2 );
- }
- if( rnakozo && rnaprediction == 'm' )
- {
- makegrouprna( grouprna1, singlerna, topol[l][0] );
- makegrouprna( grouprna2, singlerna, topol[l][1] );
- }
-
-
-/*
- fprintf( stderr, "before align all\n" );
- display( aseq, njob );
- fprintf( stderr, "\n" );
- fprintf( stderr, "before align 1 %s \n", indication1 );
- display( mseq1, clus1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "before align 2 %s \n", indication2 );
- display( mseq2, clus2 );
- fprintf( stderr, "\n" );
-*/
-
- if( !nevermemsave && ( constraint != 2 && alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
- {
- fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
- alg = 'M';
- if( commonIP ) FreeIntMtx( commonIP );
- commonAlloc1 = 0;
- commonAlloc2 = 0;
- }
-
-
-// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
- if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
- else ffttry = 0;
-// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
-// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
-// fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
- if( constraint == 2 )
- {
- if( alg == 'M' )
- {
- fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
- exit( 1 );
- }
- fprintf( stderr, "c" );
- if( alg == 'A' )
- {
- imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
- if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- }
- else if( alg == 'H' )
- {
- imp_match_init_strictH( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
- }
- else if( alg == 'Q' )
- {
- imp_match_init_strictQ( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
- pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
- }
- else if( alg == 'R' )
- {
- imp_match_init_strictR( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
- pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
- }
- }
- else if( force_fft || ( use_fft && ffttry ) )
- {
- fprintf( stderr, "f" );
- if( alg == 'M' )
- {
- fprintf( stderr, "m" );
- pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
- }
- else
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
- }
- else
- {
- fprintf( stderr, "d" );
- fftlog[m1] = 0;
- switch( alg )
- {
- case( 'a' ):
- pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
- break;
- case( 'M' ):
- fprintf( stderr, "m" );
- pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- break;
- case( 'A' ):
- pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
- break;
- case( 'Q' ):
- pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- break;
- case( 'R' ):
- pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- break;
- case( 'H' ):
- pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
- break;
- default:
- ErrorExit( "ERROR IN SOURCE FILE" );
- }
- }
-
- nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
-
-#if SCOREOUT
- fprintf( stderr, "score = %10.2f\n", pscore );
-#endif
- tscore += pscore;
-/*
- fprintf( stderr, "after align 1 %s \n", indication1 );
- display( mseq1, clus1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "after align 2 %s \n", indication2 );
- display( mseq2, clus2 );
- fprintf( stderr, "\n" );
-*/
-
-// writePre( njob, name, nlen, aseq, 0 );
-
- if( disp ) display( aseq, njob );
-
- if( mergeoralign[l] == '1' ) // jissainiha nai. atarashii hairetsu ha saigo dakara.
- {
- adjustgapmap( strlen( mseq2[0] )-len2nocommongap+len2, gapmap, mseq2[0] );
- restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen );
- findnewgaps( clus2, mseq2, gaplen );
- insertnewgaps( njob, alreadyaligned, aseq, topol[l][1], topol[l][0], gaplen, gapmap, *alloclen, alg );
- for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
- for( i=0; (m=topol[l][0][i])>-1; i++ ) alreadyaligned[m] = 1;
- }
- if( mergeoralign[l] == '2' )
- {
-// fprintf( stderr, ">mseq1[0] = \n%s\n", mseq1[0] );
-// fprintf( stderr, ">mseq2[0] = \n%s\n", mseq2[0] );
- adjustgapmap( strlen( mseq1[0] )-len1nocommongap+len1, gapmap, mseq1[0] );
- restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen );
- findnewgaps( clus1, mseq1, gaplen );
- insertnewgaps( njob, alreadyaligned, aseq, topol[l][0], topol[l][1], gaplen, gapmap, *alloclen, alg );
- for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
- for( i=0; (m=topol[l][1][i])>-1; i++ ) alreadyaligned[m] = 1;
- }
-
- free( topol[l][0] );
- free( topol[l][1] );
- free( topol[l] );
- }
-#if SCOREOUT
- fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
-#endif
-}
-
-static void WriteOptions( FILE *fp )
-{
-
- if( dorp == 'd' ) fprintf( fp, "DNA\n" );
- else
- {
- if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
- else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
- else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
- }
- fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
- if( use_fft ) fprintf( fp, "FFT on\n" );
-
- fprintf( fp, "tree-base method\n" );
- if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
- else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
- if( tbitr || tbweight )
- {
- fprintf( fp, "iterate at each step\n" );
- if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
- if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
- if( tbweight ) fprintf( fp, " weighted\n" );
- fprintf( fp, "\n" );
- }
-
- fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-
- if( alg == 'a' )
- fprintf( fp, "Algorithm A\n" );
- else if( alg == 'A' )
- fprintf( fp, "Algorithm A+\n" );
- else if( alg == 'C' )
- fprintf( fp, "Apgorithm A+/C\n" );
- else
- fprintf( fp, "Unknown algorithm\n" );
-
- if( treemethod == 'X' )
- fprintf( fp, "Tree = UPGMA (mix).\n" );
- else if( treemethod == 'E' )
- fprintf( fp, "Tree = UPGMA (average).\n" );
- else if( treemethod == 'q' )
- fprintf( fp, "Tree = Minimum linkage.\n" );
- else
- fprintf( fp, "Unknown tree.\n" );
-
- if( use_fft )
- {
- fprintf( fp, "FFT on\n" );
- if( dorp == 'd' )
- fprintf( fp, "Basis : 4 nucleotides\n" );
- else
- {
- if( fftscore )
- fprintf( fp, "Basis : Polarity and Volume\n" );
- else
- fprintf( fp, "Basis : 20 amino acids\n" );
- }
- fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
- fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
- }
- else
- fprintf( fp, "FFT off\n" );
- fflush( fp );
-}
-
-
-int main( int argc, char *argv[] )
-{
- static int *nlen;
- static float *selfscore;
- int nogaplen;
- static char **name, **seq;
- static char **mseq1, **mseq2;
- static char **bseq;
- static float **iscore, **iscore_kozo;
- static double *eff, *eff_kozo, *eff_kozo_mapped = NULL;
- int i, j, ien, ik, jk;
- static int ***topol, ***topol_kozo;
- static int *addmem;
- static Treedep *dep;
- static float **len, **len_kozo;
- FILE *prep;
- FILE *infp;
- FILE *orderfp;
- FILE *hat2p;
- double unweightedspscore;
- int alignmentlength;
- char *mergeoralign;
- int foundthebranch;
-
- char c;
- int alloclen;
- LocalHom **localhomtable = NULL;
- RNApair ***singlerna;
- float ssi, ssj, bunbo;
- 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;
-
- getnumlen( infp );
- 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 );
- }
-
- seq = AllocateCharMtx( njob, nlenmax+1 );
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
-
- name = AllocateCharMtx( njob, B+1 );
- nlen = AllocateIntVec( njob );
- selfscore = AllocateFloatVec( njob );
-
- topol = AllocateIntCub( njob, 2, 0 );
- len = AllocateFloatMtx( njob, 2 );
- iscore = AllocateFloatHalfMtx( njob );
- eff = AllocateDoubleVec( njob );
- kozoarivec = AllocateCharVec( njob );
-
- mergeoralign = AllocateCharVec( njob );
-
- dep = (Treedep *)calloc( njob, sizeof( Treedep ) );
- if( nadd ) addmem = AllocateIntVec( nadd+1 );
-
- 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].korh = 'h';
- }
- }
-
- fprintf( stderr, "Loading 'hat3' ... " );
- prep = fopen( "hat3", "r" );
- if( prep == NULL ) ErrorExit( "Make hat3." );
- readlocalhomtable( prep, njob, localhomtable, kozoarivec );
- fclose( prep );
- fprintf( stderr, "\ndone.\n" );
-
-
- nkozo = 0;
- for( i=0; i<njob; i++ )
- {
-// fprintf( stderr, "kozoarivec[%d] = %d\n", i, kozoarivec[i] );
- if( kozoarivec[i] ) nkozo++;
- }
- if( nkozo )
- {
- topol_kozo = AllocateIntCub( nkozo, 2, 0 );
- len_kozo = AllocateFloatMtx( nkozo, 2 );
- iscore_kozo = AllocateFloatHalfMtx( nkozo );
- eff_kozo = AllocateDoubleVec( nkozo );
- eff_kozo_mapped = AllocateDoubleVec( njob );
- }
-
-
-// outlocalhom( localhomtable, njob );
-
-#if 0
- fprintf( stderr, "Extending localhom ... " );
- extendlocalhom2( njob, localhomtable );
- fprintf( stderr, "done.\n" );
-#endif
- }
-
-#if 0
- readData( infp, name, nlen, seq );
-#else
- readData_pointer( infp, name, nlen, seq );
- fclose( infp );
-#endif
-
- constants( njob, seq );
-
-#if 0
- fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
-#endif
-
- initSignalSM();
-
- initFiles();
-
- WriteOptions( trap_g );
-
- c = seqcheck( seq );
- if( c )
- {
- fprintf( stderr, "Illegal character %c\n", c );
- exit( 1 );
- }
-
-// writePre( njob, name, nlen, seq, 0 );
-
- if( treein )
- {
-#if 0
- if( nkozo )
- {
- fprintf( stderr, "Both structure and user tree have been given. Not yet supported!\n" );
- exit( 1 );
- }
-#endif
- fprintf( stderr, "Loading a tree ... " );
- loadtree( njob, topol, len, name, nlen, dep );
- fprintf( stderr, "\ndone.\n\n" );
- }
- else
- {
- if( tbutree == 0 )
- {
- for( i=1; i<njob; i++ )
- {
- if( nlen[i] != nlen[0] )
- {
- fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
- exit( 1 );
- }
- }
-
- fprintf( stderr, "Making a distance matrix .. \n" );
- fflush( stderr );
- ien = njob-1;
- for( i=0; i<njob; i++ )
- {
- selfscore[i] = naivepairscore11( seq[i], seq[i], penalty );
- }
-#ifdef enablemultithread
- if( nthread > 0 )
- {
- distancematrixthread_arg_t *targ;
- Jobtable jobpos;
- pthread_t *handle;
- pthread_mutex_t mutex;
-
- jobpos.i = 0;
- jobpos.j = 0;
-
- targ = calloc( nthread, sizeof( distancematrixthread_arg_t ) );
- handle = calloc( nthread, sizeof( pthread_t ) );
- pthread_mutex_init( &mutex, NULL );
-
- for( i=0; i<nthread; i++ )
- {
- targ[i].thread_no = i;
- targ[i].njob = njob;
- targ[i].selfscore = selfscore;
- targ[i].iscore = iscore;
- targ[i].seq = seq;
- targ[i].jobpospt = &jobpos;
- targ[i].mutex = &mutex;
-
- pthread_create( handle+i, NULL, distancematrixthread, (void *)(targ+i) );
- }
-
- for( i=0; i<nthread; i++ )
- {
- pthread_join( handle[i], NULL );
- }
- pthread_mutex_destroy( &mutex );
- free( handle );
- free( targ );
- }
- else
-#endif
- {
- for( i=0; i<ien; i++ )
- {
- if( i % 10 == 0 )
- {
- fprintf( stderr, "\r% 5d / %d", i, ien );
- fflush( stderr );
- }
- ssi = selfscore[i];
- for( j=i+1; j<njob; j++ )
- {
- ssj = selfscore[j];
- bunbo = MIN( ssi, ssj );
- if( bunbo == 0.0 )
- iscore[i][j-i] = 1.0;
- else
-// iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
- iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
-
-#if 0
- fprintf( stderr, "### ssj = %f\n", ssj );
- fprintf( stderr, "### selfscore[i] = %f\n", selfscore[i] );
- fprintf( stderr, "### selfscore[j] = %f\n", selfscore[j] );
- fprintf( stderr, "### rawscore = %f\n", naivepairscore11( seq[i], seq[j], penalty ) );
-#endif
- }
- }
- }
- fprintf( stderr, "\ndone.\n\n" );
- fflush( stderr );
- }
- else
- {
- fprintf( stderr, "Loading 'hat2' ... " );
- prep = fopen( "hat2", "r" );
- if( prep == NULL ) ErrorExit( "Make hat2." );
- readhat2_floathalf_pointer( prep, njob, name, iscore );
- fclose( prep );
- fprintf( stderr, "done.\n" );
- }
-#if 1
- if( distout )
- {
- hat2p = fopen( "hat2", "w" );
- WriteFloatHat2_pointer_halfmtx( hat2p, njob, name, iscore );
- fclose( hat2p );
- }
-#endif
- if( nkozo )
- {
- ien = njob-1;
- ik = 0;
- for( i=0; i<ien; i++ )
- {
- jk = ik+1;
- for( j=i+1; j<njob; j++ )
- {
- if( kozoarivec[i] && kozoarivec[j] )
- {
- iscore_kozo[ik][jk-ik] = iscore[i][j-i];
- }
- if( kozoarivec[j] ) jk++;
- }
- if( kozoarivec[i] ) ik++;
- }
- }
-
- fprintf( stderr, "Constructing a UPGMA tree ... " );
- fflush( stderr );
- if( topin )
- {
- fprintf( stderr, "Loading a topology ... " );
- loadtop( njob, iscore, topol, len );
- fprintf( stderr, "\ndone.\n\n" );
- }
- else if( treeout )
- {
- fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, iscore, topol, len, name, nlen, dep );
- }
- else
- {
- fixed_musclesupg_float_realloc_nobk_halfmtx( njob, iscore, topol, len, dep );
- }
-// else
-// ErrorExit( "Incorrect tree\n" );
-
- if( nkozo )
- {
-// for( i=0; i<nkozo-1; i++ )
-// for( j=i+1; j<nkozo; j++ )
-// fprintf( stderr, "iscore_kozo[%d][%d] =~ %f\n", i, j, iscore_kozo[i][j-i] );
- fixed_musclesupg_float_realloc_nobk_halfmtx( nkozo, iscore_kozo, topol_kozo, len_kozo, NULL );
- }
- fprintf( stderr, "\ndone.\n\n" );
- fflush( stderr );
- }
-
-
- orderfp = fopen( "order", "w" );
- if( !orderfp )
- {
- fprintf( stderr, "Cannot open 'order'\n" );
- exit( 1 );
- }
- for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
- {
- fprintf( orderfp, "%d\n", j );
- }
- for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
- {
- fprintf( orderfp, "%d\n", j );
- }
- fclose( orderfp );
-
- if( treeout && noalign )
- {
- writeData_pointer( prep_g, njob, name, nlen, seq );
- fprintf( stderr, "\n" );
- SHOWVERSION;
- return( 0 );
- }
-
-// countnode( njob, topol, node0 );
- if( tbrweight )
- {
- weight = 3;
-#if 0
- utree = 0; counteff( njob, topol, len, eff ); utree = 1;
-#else
- counteff_simple_float( njob, topol, len, eff );
-
- if( nkozo )
- {
-// counteff_simple_float( nkozo, topol_kozo, len_kozo, eff_kozo ); // single weight nanode iranai
- for( i=0,j=0; i<njob; i++ )
- {
- if( kozoarivec[i] )
- {
-// eff_kozo_mapped[i] = eff_kozo[j]; //
- eff_kozo_mapped[i] = eff[i]; // single weight
- j++;
- }
- else
- eff_kozo_mapped[i] = 0.0;
-// fprintf( stderr, "eff_kozo_mapped[%d] = %f\n", i, eff_kozo_mapped[i] );
-// fprintf( stderr, " eff[%d] = %f\n", i, eff[i] );
- }
- }
-
-
-#endif
- }
- else
- {
- for( i=0; i<njob; i++ ) eff[i] = 1.0;
- if( nkozo )
- {
- for( i=0; i<njob; i++ )
- {
- if( kozoarivec[i] )
- eff_kozo_mapped[i] = 1.0;
- else
- eff_kozo_mapped[i] = 0.0;
- }
- }
- }
-
- FreeFloatHalfMtx( iscore, njob );
- FreeFloatMtx( len );
-
- alloclen = nlenmax*2+1; //chuui!
- bseq = AllocateCharMtx( njob, alloclen );
-
- if( nadd )
- {
- alignmentlength = strlen( seq[0] );
- for( i=0; i<njob-nadd; i++ )
- {
- if( alignmentlength != strlen( seq[i] ) )
- {
- fprintf( stderr, "#################################################################################\n" );
- fprintf( stderr, "# ERROR! #\n" );
- fprintf( stderr, "# The original%4d sequences must be aligned #\n", njob-nadd );
- fprintf( stderr, "#################################################################################\n" );
- exit( 1 );
- }
- }
- if( addprofile )
- {
- alignmentlength = strlen( seq[njob-nadd] );
- for( i=njob-nadd; i<njob; i++ )
- {
- if( alignmentlength != strlen( seq[i] ) )
- {
- fprintf( stderr, "###############################################################################\n" );
- fprintf( stderr, "# ERROR! #\n" );
- fprintf( stderr, "# The%4d additional sequences must be aligned #\n", nadd );
- fprintf( stderr, "# Otherwise, try the '--add' option, instead of '--addprofile' option. #\n" );
- fprintf( stderr, "###############################################################################\n" );
- exit( 1 );
- }
- }
- for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
- addmem[nadd] = -1;
- foundthebranch = 0;
- for( i=0; i<njob-1; i++ )
- {
- if( samemember( topol[i][0], addmem ) ) // jissainiha nai
- {
- mergeoralign[i] = '1';
- foundthebranch = 1;
- }
- else if( samemember( topol[i][1], addmem ) )
- {
- mergeoralign[i] = '2';
- foundthebranch = 1;
- }
- else
- {
- mergeoralign[i] = 'n';
- }
- }
- if( !foundthebranch )
- {
- fprintf( stderr, "###############################################################################\n" );
- fprintf( stderr, "# ERROR! #\n" );
- fprintf( stderr, "# There is no appropriate position to add the%4d sequences in the guide tree.#\n", nadd );
- fprintf( stderr, "# Check whether the%4d sequences form a monophyletic cluster. #\n", nadd );
- fprintf( stderr, "# If not, try the '--add' option, instead of the '--addprofile' option. #\n" );
- fprintf( stderr, "############################################################################### \n" );
- exit( 1 );
- }
- commongappick( nadd, seq+njob-nadd );
- for( i=njob-nadd; i<njob; i++ ) strcpy( bseq[i], seq[i] );
- }
- else
- {
- for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'n';
- for( j=njob-nadd; j<njob; j++ )
- {
- addmem[0] = j;
- addmem[1] = -1;
- for( i=0; i<njob-1; i++ )
- {
- if( samemember( topol[i][0], addmem ) ) // arieru
- {
-// fprintf( stderr, "HIT!\n" );
- if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
- else mergeoralign[i] = '1';
- }
- else if( samemember( topol[i][1], addmem ) )
- {
-// fprintf( stderr, "HIT!\n" );
- if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
- else mergeoralign[i] = '2';
- }
- }
- }
-
- for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
- addmem[nadd] = -1;
- for( i=0; i<njob-1; i++ )
- {
- if( includemember( topol[i][0], addmem ) && includemember( topol[i][1], addmem ) )
- {
- mergeoralign[i] = 'w';
- }
- else if( includemember( topol[i][0], addmem ) )
- {
- mergeoralign[i] = '1';
- }
- else if( includemember( topol[i][1], addmem ) )
- {
- mergeoralign[i] = '2';
- }
- }
-#if 0
- for( i=0; i<njob-1; i++ )
- {
- fprintf( stderr, "mem0 = " );
- for( j=0; topol[i][0][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][0][j] );
- fprintf( stderr, "\n" );
- fprintf( stderr, "mem1 = " );
- for( j=0; topol[i][1][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][1][j] );
- fprintf( stderr, "\n" );
- fprintf( stderr, "i=%d, mergeoralign[] = %c\n", i, mergeoralign[i] );
- }
-#endif
- for( i=njob-nadd; i<njob; i++ ) gappick0( bseq[i], seq[i] );
- }
-
- commongappick( njob-nadd, seq );
- for( i=0; i<njob-nadd; i++ ) strcpy( bseq[i], seq[i] );
- }
- else
- {
- for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
- for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'a';
- }
-
- 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' ... " );
- for( i=0; i<njob; i++ )
- {
- nogaplen = strlen( bseq[i] );
- 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" );
- }
- else
- singlerna = NULL;
-
-
- fprintf( stderr, "Progressive alignment ... \n" );
-
-#ifdef enablemultithread
- if( nthread > 0 && nadd == 0 )
- {
- treebasethread_arg_t *targ;
- int jobpos;
- pthread_t *handle;
- pthread_mutex_t mutex;
- pthread_cond_t treecond;
- int *fftlog;
- int nrun;
- int nthread_yoyu;
-
- nthread_yoyu = nthread * 1;
- nrun = 0;
- jobpos = 0;
- targ = calloc( nthread_yoyu, sizeof( treebasethread_arg_t ) );
- fftlog = AllocateIntVec( njob );
- handle = calloc( nthread_yoyu, sizeof( pthread_t ) );
- pthread_mutex_init( &mutex, NULL );
- pthread_cond_init( &treecond, NULL );
-
- for( i=0; i<njob; i++ ) dep[i].done = 0;
- for( i=0; i<njob; i++ ) fftlog[i] = 1;
-
- if( constraint )
- calcimportance( njob, eff, bseq, localhomtable );
-
- for( i=0; i<nthread_yoyu; i++ )
- {
- targ[i].thread_no = i;
- targ[i].nrunpt = &nrun;
- targ[i].njob = njob;
- targ[i].nlen = nlen;
- targ[i].jobpospt = &jobpos;
- targ[i].topol = topol;
- targ[i].dep = dep;
- targ[i].aseq = bseq;
- targ[i].effarr = eff;
- targ[i].alloclenpt = &alloclen;
- targ[i].localhomtable = localhomtable;
- targ[i].singlerna = singlerna;
- targ[i].effarr_kozo = eff_kozo_mapped;
- targ[i].fftlog = fftlog;
- targ[i].mutex = &mutex;
- targ[i].treecond = &treecond;
-
- pthread_create( handle+i, NULL, treebasethread, (void *)(targ+i) );
- }
-
- for( i=0; i<nthread_yoyu; i++ )
- {
- pthread_join( handle[i], NULL );
- }
- pthread_mutex_destroy( &mutex );
- pthread_cond_destroy( &treecond );
- free( handle );
- free( targ );
- free( fftlog );
- }
- else
-#endif
- treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, eff, &alloclen, localhomtable, singlerna, eff_kozo_mapped );
- fprintf( stderr, "\ndone.\n" );
- if( scoreout )
- {
- unweightedspscore = plainscore( njob, bseq );
- fprintf( stderr, "\nSCORE %s = %.0f, ", "(treebase)", unweightedspscore );
- fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
- fprintf( stderr, "\n\n" );
- }
-
-#if 0
- if( constraint )
- {
- LocalHom *tmppt1, *tmppt2;
- for( i=0; i<njob; i++)
- {
- for( j=0; j<njob; j++)
- {
- tmppt1 = localhomtable[i]+j;
- while( tmppt2 = tmppt1->next )
- {
- free( (void *)tmppt1 );
- tmppt1 = tmppt2;
- }
- free( (void *)tmppt1 );
- }
- free( (void *)(localhomtable[i]+j) );
- }
- free( (void *)localhomtable );
- }
-#endif
-
- fprintf( trap_g, "done.\n" );
- fclose( trap_g );
- free( mergeoralign );
-
- writeData_pointer( prep_g, njob, name, nlen, bseq );
-#if 0
- writeData( stdout, njob, name, nlen, bseq );
- writePre( njob, name, nlen, bseq, !contin );
- writeData_pointer( prep_g, njob, name, nlen, aseq );
-#endif
-#if IODEBUG
- fprintf( stderr, "OSHIMAI\n" );
-#endif
-
- if( constraint ) FreeLocalHomTable( localhomtable, njob );
-
- SHOWVERSION;
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff