--- /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