--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+#define END_OF_VEC -1
+
+static int nadd;
+static int treein;
+static int topin;
+static int treeout;
+static int noalign;
+static int distout;
+static float lenfaca, lenfacb, lenfacc, lenfacd;
+#if 0
+#define PLENFACA 0.0123
+#define PLENFACB 10252
+#define PLENFACC 10822
+#define PLENFACD 0.5
+#define DLENFACA 0.01
+#define DLENFACB 2445
+#define DLENFACC 2412
+#define DLENFACD 0.1
+#else
+#define PLENFACA 0.01
+#define PLENFACB 10000
+#define PLENFACC 10000
+#define PLENFACD 0.1
+#define DLENFACA 0.01
+#define DLENFACB 2500
+#define DLENFACC 2500
+#define DLENFACD 0.1
+#endif
+
+#ifdef enablemultithread
+typedef struct _treebasethread_arg
+{
+ int thread_no;
+ int njob;
+ int *nrunpt;
+ int *nlen;
+ int *jobpospt;
+ int ***topol;
+ Treedep *dep;
+ char **aseq;
+ double *effarr;
+ int *alloclenpt;
+ int *fftlog;
+ pthread_mutex_t *mutex;
+ pthread_cond_t *treecond;
+} treebasethread_arg_t;
+
+typedef struct _distancematrixthread_arg
+{
+ int thread_no;
+ int njob;
+ int *jobpospt;
+ int **pointt;
+ float **mtx;
+ pthread_mutex_t *mutex;
+} distancematrixthread_arg_t;
+#endif
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nthread = 1;
+ outnumber = 0;
+ topin = 0;
+ treein = 0;
+ treeout = 0;
+ distout = 0;
+ noalign = 0;
+ nevermemsave = 0;
+ inputfile = NULL;
+ nadd = 0;
+ addprofile = 1;
+ fftkeika = 0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ 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 = -1530;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = -123;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ TMorJTT = JTT;
+ scoreout = 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 '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 'C':
+ nthread = atoi( *++argv );
+ fprintf( stderr, "nthread = %d\n", nthread );
+ --argc;
+ goto nextoption;
+#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 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+#if 0
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+#endif
+ case 'n' :
+ outnumber = 1;
+ break;
+ case 's':
+ treemethod = 's';
+ break;
+ case 'X':
+ treemethod = 'X'; // mix
+ break;
+ case 'E':
+ treemethod = 'E'; // upg (average)
+ break;
+ case 'q':
+ treemethod = 'q'; // minimum
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'R':
+ alg = 'R';
+ break;
+ case 'Q':
+ alg = 'Q';
+ break;
+ case 'H':
+ alg = 'H';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'N':
+ nevermemsave = 1;
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'S':
+ scoreout = 1;
+ break;
+ case 'B':
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'G':
+ use_fft = 1;
+ force_fft = 1;
+ break;
+ case 'V':
+ topin = 1;
+ break;
+ case 'U':
+ treein = 1;
+ break;
+ case 'u':
+ weight = 0;
+ tbrweight = 0;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ disp = 1;
+ break;
+#if 1
+ case 'O':
+ outgap = 0;
+ break;
+#else
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#endif
+ case 'J':
+ tbutree = 0;
+ break;
+ 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 );
+ }
+}
+
+
+
+
+static int maxl;
+static int tsize;
+
+void seq_grp_nuc( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 4 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ if( grp - grpbk < 6 )
+ {
+// fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
+// exit( 1 );
+ *grpbk = -1;
+ }
+}
+
+void seq_grp( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 6 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ if( grp - grpbk < 6 )
+ {
+// fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
+// exit( 1 );
+ *grpbk = -1;
+ }
+}
+
+void makecompositiontable_p( short *table, int *pointt )
+{
+ int point;
+
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ table[point]++;
+}
+
+int commonsextet_p( short *table, int *pointt )
+{
+ int value = 0;
+ short tmp;
+ int point;
+ static TLS short *memo = NULL;
+ static TLS int *ct = NULL;
+ static TLS int *cp;
+
+ if( table == NULL )
+ {
+ if( memo ) free( memo );
+ if( ct ) free( ct );
+ return( 0 );
+ }
+
+ if( *pointt == -1 )
+ return( 0 );
+
+ if( !memo )
+ {
+ memo = (short *)calloc( tsize, sizeof( short ) );
+ if( !memo ) ErrorExit( "Cannot allocate memo\n" );
+ ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) );
+ if( !ct ) ErrorExit( "Cannot allocate memo\n" );
+ }
+
+ cp = ct;
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ {
+ tmp = memo[point]++;
+ if( tmp < table[point] )
+ value++;
+ if( tmp == 0 ) *cp++ = point;
+ }
+ *cp = END_OF_VEC;
+
+ cp = ct;
+ while( *cp != END_OF_VEC )
+ memo[*cp++] = 0;
+
+ return( value );
+}
+
+void makepointtable_nuc( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ if( *n == -1 )
+ {
+ *pointt = -1;
+ return;
+ }
+
+ p = n;
+ point = *n++ * 1024;
+ point += *n++ * 256;
+ point += *n++ * 64;
+ point += *n++ * 16;
+ point += *n++ * 4;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 1024;
+ point *= 4;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+void makepointtable( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ if( *n == -1 )
+ {
+ *pointt = -1;
+ return;
+ }
+
+ p = n;
+ point = *n++ * 7776;
+ point += *n++ * 1296;
+ point += *n++ * 216;
+ point += *n++ * 36;
+ point += *n++ * 6;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 7776;
+ point *= 6;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+#ifdef enablemultithread
+static void *distancematrixthread( void *arg )
+{
+ distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
+ int thread_no = targ->thread_no;
+ int njob = targ->njob;
+ int *jobpospt = targ->jobpospt;
+ int **pointt = targ->pointt;
+ float **mtx = targ->mtx;
+
+ short *table1;
+ int i, j;
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex );
+ i = *jobpospt;
+ if( i == njob )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ commonsextet_p( NULL, NULL );
+ return( NULL );
+ }
+ *jobpospt = i+1;
+ pthread_mutex_unlock( targ->mutex );
+
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "\r% 5d / %d (thread %4d)", i+1, njob, thread_no );
+ }
+ makecompositiontable_p( table1, pointt[i] );
+
+ for( j=i; j<njob; j++ )
+ {
+ mtx[i][j-i] = (float)commonsextet_p( table1, pointt[j] );
+ }
+ free( table1 );
+ }
+}
+
+
+static void *treebasethread( void *arg )
+{
+ treebasethread_arg_t *targ = (treebasethread_arg_t *)arg;
+ int thread_no = targ->thread_no;
+ int *nrunpt = targ->nrunpt;
+ 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;
+ int *fftlog = targ->fftlog;
+
+ char **mseq1, **mseq2;
+ char **localcopy;
+ int i, j, l;
+ int len1, len2;
+ int clus1, clus2;
+ float pscore, tscore;
+ char *indication1, *indication2;
+ double *effarr1 = NULL;
+ double *effarr2 = NULL;
+ float dumfl = 0.0;
+ int ffttry;
+ int m1, m2;
+#if 0
+ int i, j;
+#endif
+
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ localcopy = calloc( njob, sizeof( char * ) );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+
+
+#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
+
+// for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ 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 );
+ free( mseq1 );
+ free( mseq2 );
+ free( localcopy );
+ free( effarr1 );
+ free( effarr2 );
+ free( indication1 );
+ free( indication2 );
+ 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)++;
+
+ 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 );
+ 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 1 // CHUUI@@@@
+ clus1 = fastconjuction_noname( topol[l][0], localcopy, mseq1, effarr1, effarr, indication1 );
+ clus2 = fastconjuction_noname( topol[l][1], localcopy, mseq2, effarr2, effarr, indication2 );
+#else
+ clus1 = fastconjuction_noweight( topol[l][0], localcopy, mseq1, effarr1, indication1 );
+ clus2 = fastconjuction_noweight( topol[l][1], localcopy, mseq2, effarr2, indication2 );
+#endif
+
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+
+// fprintf( trap_g, "\nSTEP-%d\n", l );
+// fprintf( trap_g, "group1 = %s\n", indication1 );
+// fprintf( trap_g, "group2 = %s\n", indication2 );
+
+// fprintf( stderr, "\rSTEP % 5d / %d %d-%d", l+1, njob-1, clus1, clus2 );
+ fprintf( stderr, "\rSTEP % 5d / %d (thread %4d)", l+1, njob-1, thread_no );
+
+#if 0
+ 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
+
+/*
+ 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 && ( 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 );
+
+ 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" );
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'Q' ):
+ if( clus1 == 1 && clus2 == 1 && 0 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+ 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;
+ case( 'A' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f\n", pscore );
+#endif
+ tscore += pscore;
+ nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
+
+
+ if( disp ) display( localcopy, njob );
+
+ pthread_mutex_lock( targ->mutex );
+ dep[l].done = 1;
+ (*nrunpt)--;
+ pthread_cond_broadcast( targ->treecond );
+
+ 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] );
+
+
+// fprintf( stderr, "\n" );
+ }
+#if SCOREOUT
+ fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
+#endif
+}
+#endif
+
+static void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, int ***topol, double *effarr, int *alloclen )
+{
+ int l, len1, len2, i, m;
+ int len1nocommongap, len2nocommongap;
+ int clus1, clus2;
+ float pscore, tscore;
+ static char *indication1, *indication2;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ static int *fftlog; // fixed at 2006/07/26
+ float dumfl = 0.0;
+ int ffttry;
+ int m1, m2;
+ static int *gaplen;
+ static int *gapmap;
+ static int *alreadyaligned;
+#if 0
+ int i, j;
+#endif
+
+ if( effarr1 == NULL )
+ {
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+ fftlog = AllocateIntVec( njob );
+ gaplen = AllocateIntVec( *alloclen+10 );
+ gapmap = AllocateIntVec( *alloclen+10 );
+ alreadyaligned = AllocateIntVec( njob );
+ }
+ 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
+
+// for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+
+// 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 1 // CHUUI@@@@
+ clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2 );
+#else
+ clus1 = fastconjuction_noweight( topol[l][0], aseq, mseq1, effarr1, indication1 );
+ clus2 = fastconjuction_noweight( topol[l][1], aseq, mseq2, effarr2, indication2 );
+#endif
+ 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] );
+ }
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+
+// fprintf( trap_g, "\nSTEP-%d\n", l );
+// fprintf( trap_g, "group1 = %s\n", indication1 );
+// fprintf( trap_g, "group2 = %s\n", indication2 );
+
+// fprintf( stderr, "\rSTEP % 5d / %d %d-%d", l+1, njob-1, clus1, clus2 );
+ fprintf( stderr, "\rSTEP % 5d / %d ", l+1, njob-1 );
+ fflush( stderr );
+
+#if 0
+ 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
+
+/*
+ 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 && ( 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 );
+
+ 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" );
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'Q' ):
+ if( clus1 == 1 && clus2 == 1 && 0 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+ 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;
+ case( 'A' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f\n", pscore );
+#endif
+ tscore += pscore;
+ nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ if( disp ) display( aseq, njob );
+// fprintf( stderr, "\n" );
+
+ 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' )
+ {
+ adjustgapmap( strlen( mseq1[0] )-len1nocommongap+len1, gapmap, mseq1[0] );
+// fprintf( stderr, ">STEP1 mseq1[0] = \n%s\n", mseq1[0] );
+// fprintf( stderr, ">STEP1 mseq2[0] = \n%s\n", mseq2[0] );
+ restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen );
+// fprintf( stderr, "STEP2 mseq1[0] = %s\n", mseq1[0] );
+// fprintf( stderr, "STEP2 mseq2[0] = %s\n", mseq2[0] );
+ findnewgaps( clus1, mseq1, gaplen );
+ insertnewgaps( njob, alreadyaligned, aseq, topol[l][0], topol[l][1], gaplen, gapmap, *alloclen, alg );
+// fprintf( stderr, "STEP3 mseq1[0] = %s\n", mseq1[0] );
+// fprintf( stderr, "STEP3 mseq2[0] = %s\n", mseq2[0] );
+ 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
+ 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 int *nogaplen;
+ static char **name, **seq;
+ static char **mseq1, **mseq2;
+ static char **bseq;
+ static double *eff;
+ int i, j;
+ static int ***topol;
+ static int *addmem;
+ static Treedep *dep;
+ static float **len;
+ FILE *infp;
+// FILE *adfp;
+ char c;
+ int alloclen;
+ float longer, shorter;
+ float lenfac;
+ float bunbo;
+
+ FILE *orderfp, *hat2p;
+ int *grpseq;
+ char *tmpseq;
+ int **pointt;
+ float **mtx = NULL; // by D. Mathog
+ static short *table1;
+ char b[B];
+ int ien;
+ double unweightedspscore;
+ int alignmentlength;
+ char *mergeoralign;
+ int foundthebranch;
+
+ 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 );
+
+ if( njob > 20000 )
+ {
+ fprintf( stderr, "The number of sequences must be < %d\n", 20000 );
+ fprintf( stderr, "Please try the --parttree option for such large data.\n" );
+ exit( 1 );
+ }
+
+ 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+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+
+ topol = AllocateIntCub( njob, 2, 0 );
+ len = AllocateFloatMtx( njob, 2 );
+ eff = AllocateDoubleVec( njob );
+ mergeoralign = AllocateCharVec( njob );
+
+ dep = (Treedep *)calloc( njob, sizeof( Treedep ) );
+
+ if( nadd ) addmem = AllocateIntVec( nadd+1 );
+
+#if 0
+ Read( name, nlen, seq );
+ readData( infp, name, nlen, seq );
+#else
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+ nogaplen = AllocateIntVec( njob );
+ 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 );
+ }
+
+ fprintf( stderr, "\n" );
+
+ if( !treein )
+ {
+ fprintf( stderr, "\n\nMaking a distance matrix ..\n" );
+ fflush( stderr );
+
+ tmpseq = AllocateCharVec( nlenmax+1 );
+ grpseq = AllocateIntVec( nlenmax+1 );
+ pointt = AllocateIntMtx( njob, nlenmax+1 );
+ mtx = AllocateFloatHalfMtx( njob );
+ if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
+ else tsize = (int)pow( 6, 6 );
+
+ if( dorp == 'd' )
+ {
+ lenfaca = DLENFACA;
+ lenfacb = DLENFACB;
+ lenfacc = DLENFACC;
+ lenfacd = DLENFACD;
+ }
+ else
+ {
+ lenfaca = PLENFACA;
+ lenfacb = PLENFACB;
+ lenfacc = PLENFACC;
+ lenfacd = PLENFACD;
+ }
+
+ maxl = 0;
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( tmpseq, seq[i] );
+ nogaplen[i] = strlen( tmpseq );
+ if( nogaplen[i] < 6 )
+ {
+// fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nogaplen[i] );
+// fprintf( stderr, "Please use mafft-ginsi, mafft-linsi or mafft-ginsi\n\n\n" );
+// exit( 1 );
+ }
+ if( nogaplen[i] > maxl ) maxl = nogaplen[i];
+ if( dorp == 'd' ) /* nuc */
+ {
+ seq_grp_nuc( grpseq, tmpseq );
+ makepointtable_nuc( pointt[i], grpseq );
+ }
+ else /* amino */
+ {
+ seq_grp( grpseq, tmpseq );
+ makepointtable( pointt[i], grpseq );
+ }
+ }
+#ifdef enablemultithread
+ if( nthread > 0 )
+ {
+ distancematrixthread_arg_t *targ;
+ int jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+
+ jobpos = 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].jobpospt = &jobpos;
+ targ[i].pointt = pointt;
+ targ[i].mtx = mtx;
+ 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<njob; i++ )
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "\r% 5d / %d", i+1, njob );
+ fflush( stderr );
+ }
+ makecompositiontable_p( table1, pointt[i] );
+
+ for( j=i; j<njob; j++ )
+ {
+ mtx[i][j-i] = (float)commonsextet_p( table1, pointt[j] );
+ }
+ free( table1 );
+ }
+ }
+ fprintf( stderr, "\ndone.\n\n" );
+ fflush( stderr );
+ ien = njob-1;
+
+ for( i=0; i<ien; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ if( nogaplen[i] > nogaplen[j] )
+ {
+ longer=(float)nogaplen[i];
+ shorter=(float)nogaplen[j];
+ }
+ else
+ {
+ longer=(float)nogaplen[j];
+ shorter=(float)nogaplen[i];
+ }
+// lenfac = 3.0 / ( LENFACA + LENFACB / ( longer + LENFACC ) + shorter / longer * LENFACD );
+ lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
+// lenfac = 1.0;
+// fprintf( stderr, "lenfac = %f (%.0f,%.0f)\n", lenfac, longer, shorter );
+ bunbo = MIN( mtx[i][0], mtx[j][0] );
+ if( bunbo == 0.0 )
+ mtx[i][j-i] = 1.0;
+ else
+ mtx[i][j-i] = ( 1.0 - mtx[i][j-i] / bunbo ) * lenfac;
+// fprintf( stdout, "##### mtx = %f, mtx[i][0]=%f, mtx[j][0]=%f, bunbo=%f\n", mtx[i][j-i], mtx[i][0], mtx[j][0], bunbo );
+ }
+ }
+ if( disopt )
+ {
+ for( i=0; i<njob; i++ )
+ {
+ sprintf( b, "=lgth = %04d", nogaplen[i] );
+ strins( b, name[i] );
+ }
+ }
+ free( grpseq );
+ free( tmpseq );
+ FreeIntMtx( pointt );
+
+#if 1 // writehat2 wo kakinaosu
+ if( distout )
+ {
+ hat2p = fopen( "hat2", "w" );
+ WriteFloatHat2_pointer_halfmtx( hat2p, njob, name, mtx );
+ fclose( hat2p );
+ }
+#endif
+
+ }
+ else {
+#if 0 // readhat2 wo kakinaosu
+ fprintf( stderr, "Loading 'hat2' ... " );
+ prep = fopen( "hat2", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat2." );
+ readhat2_float( prep, njob, name, mtx ); // name chuui
+ fclose( prep );
+ fprintf( stderr, "done.\n" );
+#endif
+ }
+
+ if( treein )
+ {
+ fprintf( stderr, "Loading a tree ... " );
+ loadtree( njob, topol, len, name, nogaplen, dep );
+ }
+ else if( topin )
+ {
+ fprintf( stderr, "Loading a topology ... " );
+ loadtop( njob, mtx, topol, len );
+ FreeFloatHalfMtx( mtx, njob );
+ }
+ else if( treeout )
+ {
+ fprintf( stderr, "Constructing a UPGMA tree ... " );
+
+ fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, mtx, topol, len, name, nogaplen, dep );
+// veryfastsupg_float_realloc_nobk_halfmtx_treeout( njob, mtx, topol, len, name, nogaplen );
+
+
+ FreeFloatHalfMtx( mtx, njob );
+ }
+ else
+ {
+ fprintf( stderr, "Constructing a UPGMA tree ... " );
+ fixed_musclesupg_float_realloc_nobk_halfmtx( njob, mtx, topol, len, dep );
+ FreeFloatHalfMtx( mtx, njob );
+ }
+// else
+// ErrorExit( "Incorrect tree\n" );
+ 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 || distout ) && noalign )
+ {
+ writeData_pointer( stdout, njob, name, nlen, seq );
+ fprintf( stderr, "\n" );
+ SHOWVERSION;
+ return( 0 );
+ }
+
+
+ if( tbrweight )
+ {
+ weight = 3;
+#if 0
+ utree = 0; counteff( njob, topol, len, eff ); utree = 1;
+#else
+ counteff_simple_float( njob, topol, len, eff );
+#endif
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+ }
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stdout, "eff[%d] = %20.16f\n", i, eff[i] );
+ exit( 1 );
+#endif
+
+
+ FreeFloatMtx( len );
+
+ bseq = AllocateCharMtx( njob, nlenmax*2+1 );
+ alloclen = nlenmax*2+1;
+
+
+ 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';
+ }
+
+ 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;
+
+ for( i=0; i<nthread_yoyu; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].nrunpt = &nrun;
+ 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].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 );
+ }
+ fprintf( stderr, "\ndone.\n\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+ 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" );
+ }
+
+ free( mergeoralign );
+// writePre( njob, name, nlen, aseq, !contin );
+#if DEBUG
+ fprintf( stderr, "writing alignment to stdout\n" );
+#endif
+ writeData_pointer( stdout, njob, name, nlen, bseq );
+#if 0
+ writeData( stdout, njob, name, nlen, bseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
+
git://source.jalview.org / jabaws.git / blobdiff