4 #define PICKSIZE 50 // must be >= 3
9 // kouzoutai ni sasareru pointer ha static
17 //static int doalign = 'f';
27 static int maxdepth = 0;
29 static double lenfaca, lenfacb, lenfacc, lenfacd;
31 #define PLENFACB 10000
32 #define PLENFACC 10000
39 static char datafile[1000];
40 static char queryfile[1000];
41 static char resultfile[1000];
43 typedef struct _scores
51 // char *seq; // reallo
56 int intcompare( const int *a, const int *b )
61 int dcompare( const Scores *a, const Scores *b )
63 if( a->score > b->score ) return 1;
64 else if( a->score < b->score ) return -1;
67 if( a->selfscore < b->selfscore ) return 1;
68 else if( a->selfscore > b->selfscore ) return -1;
71 if( a->orilen < b->orilen ) return 1;
72 else if( a->orilen > b->orilen ) return -1;
78 static void gappickandx0( char *out, char *in )
85 if( (c=*in++) == '-' )
89 else if( amino_n[c] < 4 && amino_n[c] > -1 )
99 if( (c=*in++) == '-' )
101 else if( amino_n[c] < 20 && amino_n[c] > -1 )
110 static int getkouho( int *pickkouho, double prob, int nin, Scores *scores, char **seq ) // 0 < prob < 1
114 int *iptr = pickkouho;
115 for( i=1; i<nin; i++ )
117 if( ( nkouho==0 || rnd() < prob ) && ( scores[i].shimon != scores->shimon || strcmp( seq[scores->numinseq], seq[scores[i].numinseq] ) ) )
120 for( j=0; j<nkouho; j++ )
122 if( scores[i].shimon == scores[pickkouho[j]].shimon || !strcmp( seq[scores[pickkouho[j]].numinseq], seq[scores[i].numinseq] ) )
130 // fprintf( stderr, "ok! nkouho=%d\n", nkouho );
136 // fprintf( stderr, "no! %d-%d\n", 0, scores[i].numinseq );
139 fprintf( stderr, "\ndone\n\n" );
143 static void getblastscoremtx( int **tmpaminodis )
154 static char *tmpname;
159 tmpaminodis['a']['a'] = 1;
160 tmpaminodis['g']['g'] = 1;
161 tmpaminodis['c']['c'] = 1;
162 tmpaminodis['t']['t'] = 1;
168 tmpseq = calloc( 2000, sizeof( char ) );
169 tmpname = calloc( B, sizeof( char ) );
170 resvec = calloc( 1, sizeof( double ) );
172 // fprintf( stderr, "xformatting .. " );
173 dfp = fopen( datafile, "w" );
174 if( !dfp ) ErrorExit( "Cannot open datafile." );
175 sprintf( tmpname, "\0", i );
176 strcpy( tmpseq, "AAAAAAXXXXXX" );
177 strcat( tmpseq, "CCCCCCXXXXXX" );
178 strcat( tmpseq, "DDDDDDXXXXXX" );
179 strcat( tmpseq, "EEEEEEXXXXXX" );
180 strcat( tmpseq, "FFFFFFXXXXXX" );
181 strcat( tmpseq, "GGGGGGXXXXXX" );
182 strcat( tmpseq, "HHHHHHXXXXXX" );
183 strcat( tmpseq, "IIIIIIXXXXXX" );
184 strcat( tmpseq, "KKKKKKXXXXXX" );
185 strcat( tmpseq, "LLLLLLXXXXXX" );
186 strcat( tmpseq, "MMMMMMXXXXXX" );
187 strcat( tmpseq, "NNNNNNXXXXXX" );
188 strcat( tmpseq, "PPPPPPXXXXXX" );
189 strcat( tmpseq, "QQQQQQXXXXXX" );
190 strcat( tmpseq, "RRRRRRXXXXXX" );
191 strcat( tmpseq, "SSSSSSXXXXXX" );
192 strcat( tmpseq, "TTTTTTXXXXXX" );
193 strcat( tmpseq, "VVVVVVXXXXXX" );
194 strcat( tmpseq, "WWWWWWXXXXXX" );
195 strcat( tmpseq, "YYYYYYXXXXXX" );
196 slen = strlen( tmpseq );
197 writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
200 sprintf( com, "formatdb -p f -i %s -o F", datafile );
202 sprintf( com, "formatdb -i %s -o F", datafile );
204 fprintf( stderr, "done.\n" );
206 for( i=0; i<20; i++ )
209 fprintf( stderr, "checking %c\n", aa );
212 sprintf( tmpseq+strlen( tmpseq ), "%c", aa );
213 qfp = fopen( queryfile, "w" );
214 if( !qfp ) ErrorExit( "Cannot open queryfile." );
215 writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
218 sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7 -i %s -d %s > %s\0", 1, queryfile, datafile, resultfile );
220 if( res ) ErrorExit( "error in blast" );
222 rfp = fopen( resultfile, "r" );
224 ErrorExit( "file 'fasta.$$' does not exist\n" );
225 res = ReadBlastm7_scoreonly( rfp, resvec, 1 );
226 fprintf( stdout, "%c: %f\n", 'A'+i, *resvec/6 );
228 if( ( (int)*resvec % 6 ) > 0.0 )
230 fprintf( stderr, "Error in blast, *resvec=%f\n", *resvec );
231 fprintf( stderr, "Error in blast, *resvec/6=%f\n", *resvec/6 );
234 tmpaminodis[aa][aa] = (int)( *resvec / 6 );
236 tmpaminodis['X']['X'] = 0;
243 static double *callfasta( char **seq, Scores *scores, int nin, int query, int rewritedata )
251 static char datafile[1000];
252 static char queryfile[1000];
253 static char resultfile[1000];
256 static char *tmpname;
260 static Scores *scoresbk = NULL;
261 static int ninbk = 0;
266 sprintf( datafile, "/tmp/data-%d\0", pid );
267 sprintf( queryfile, "/tmp/query-%d\0", pid );
268 sprintf( resultfile, "/tmp/fasta-%d\0", pid );
270 tmpseq = calloc( nlenmax+1, sizeof( char ) );
271 tmpname = calloc( B+1, sizeof( char ) );
274 val = calloc( nin, sizeof( double ) );
275 // fprintf( stderr, "nin=%d, q=%d\n", nin, query );
281 fprintf( stderr, "\nformatting .. " );
282 dfp = fopen( datafile, "w" );
283 if( !dfp ) ErrorExit( "Cannot open datafile." );
284 for( i=0; i<nin; i++ )
286 // fprintf( stderr, "i=%d / %d / %d\n", i, nin, njob );
287 // fprintf( stderr, "nlenmax = %d\n", nlenmax );
288 // fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
289 // fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
290 gappick0( tmpseq, seq[scores[i].numinseq] );
291 sprintf( tmpname, "+===========+%d \0", i );
292 slen = scores[i].orilen;
293 writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
299 gappick0( tmpseq, seq[scores[query].numinseq] );
300 sprintf( tmpname, "+==========+%d \0", 0 );
301 slen = scores[query].orilen;
302 qfp = fopen( queryfile, "w" );
303 if( !qfp ) ErrorExit( "Cannot open queryfile." );
304 writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
306 // fprintf( stderr, "q=%s\n", tmpseq );
309 sprintf( com, "fasta34 -z3 -m10 -n -Q -b%d -E%d -d%d %s %s %d > %s\0", M, M, M, queryfile, datafile, 1, resultfile );
311 sprintf( com, "fastea34 -z3 -m10 -Q -b%d -E%d -d%d %s %s %d > %s\0", M, M, M, queryfile, datafile, 6, resultfile );
313 if( res ) ErrorExit( "error in fasta" );
317 rfp = fopen( resultfile, "r" );
319 ErrorExit( "file 'fasta.$$' does not exist\n" );
320 res = ReadBlastm7_scoreonly( rfp, val, nin );
324 for( i=0; i<nin; i++ )
325 fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
330 static double *callblast( char **seq, Scores *scores, int nin, int query, int rewritedata )
338 static char datafile[1000];
339 static char queryfile[1000];
340 static char resultfile[1000];
343 static char *tmpname;
347 static Scores *scoresbk = NULL;
348 static int ninbk = 0;
353 sprintf( datafile, "/tmp/data-%d\0", pid );
354 sprintf( queryfile, "/tmp/query-%d\0", pid );
355 sprintf( resultfile, "/tmp/fasta-%d\0", pid );
357 tmpseq = calloc( nlenmax+1, sizeof( char ) );
358 tmpname = calloc( B+1, sizeof( char ) );
361 val = calloc( nin, sizeof( double ) );
362 // fprintf( stderr, "nin=%d, q=%d\n", nin, query );
368 fprintf( stderr, "\nformatting .. " );
369 dfp = fopen( datafile, "w" );
370 if( !dfp ) ErrorExit( "Cannot open datafile." );
371 for( i=0; i<nin; i++ )
373 // fprintf( stderr, "i=%d / %d / %d\n", i, nin, njob );
374 // fprintf( stderr, "nlenmax = %d\n", nlenmax );
375 // fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
376 // fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
377 gappick0( tmpseq, seq[scores[i].numinseq] );
378 sprintf( tmpname, "+===========+%d \0", i );
379 slen = scores[i].orilen;
380 writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
385 sprintf( com, "formatdb -p f -i %s -o F", datafile );
387 sprintf( com, "formatdb -i %s -o F", datafile );
389 // fprintf( stderr, "done.\n" );
393 gappick0( tmpseq, seq[scores[query].numinseq] );
394 sprintf( tmpname, "+==========+%d \0", 0 );
395 slen = scores[query].orilen;
396 qfp = fopen( queryfile, "w" );
397 if( !qfp ) ErrorExit( "Cannot open queryfile." );
398 writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
400 // fprintf( stderr, "q=%s\n", tmpseq );
402 fprintf( stderr, "\ncalling blast .. \n" );
404 sprintf( com, "blastall -b %d -e 1e10 -p blastn -m 7 -i %s -d %s > %s\0", nin, queryfile, datafile, resultfile );
406 sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7 -i %s -d %s > %s\0", nin, queryfile, datafile, resultfile );
408 if( res ) ErrorExit( "error in blast" );
410 rfp = fopen( resultfile, "r" );
412 ErrorExit( "file 'fasta.$$' does not exist\n" );
413 res = ReadBlastm7_scoreonly( rfp, val, nin );
417 for( i=0; i<nin; i++ )
418 fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
424 static void selhead( int *ar, int n )
434 if( ( tmp = *ptr++ ) < min )
449 void arguments( int argc, char *argv[] )
491 ppenalty_ex = NOTSPECIFIED;
493 kimuraR = NOTSPECIFIED;
496 fftWinSize = NOTSPECIFIED;
497 fftThreshold = NOTSPECIFIED;
499 classsize = NOTSPECIFIED;
500 picksize = NOTSPECIFIED;
502 while( --argc > 0 && (*++argv)[0] == '-' )
504 while ( c = *++argv[0] )
509 picksize = atoi( *++argv );
510 fprintf( stderr, "picksize = %d\n", picksize );
514 classsize = atoi( *++argv );
515 fprintf( stderr, "groupsize = %d\n", classsize );
520 fprintf( stderr, "inputfile = %s\n", inputfile );
524 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
525 // fprintf( stderr, "ppenalty = %d\n", ppenalty );
529 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
530 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
534 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
535 // fprintf( stderr, "poffset = %d\n", poffset );
539 kimuraR = atoi( *++argv );
540 fprintf( stderr, "kimuraR = %d\n", kimuraR );
544 nblosum = atoi( *++argv );
546 // fprintf( stderr, "blosum %d\n", nblosum );
550 pamN = atoi( *++argv );
553 fprintf( stderr, "jtt %d\n", pamN );
557 pamN = atoi( *++argv );
560 fprintf( stderr, "tm %d\n", pamN );
641 fftThreshold = atoi( *++argv );
645 fftWinSize = atoi( *++argv );
652 fprintf( stderr, "illegal option %c\n", c );
662 cut = atof( (*argv) );
667 fprintf( stderr, "options: Check source file !\n" );
670 if( tbitr == 1 && outgap == 0 )
672 fprintf( stderr, "conflicting options : o, m or u\n" );
675 if( alg == 'C' && outgap == 0 )
677 fprintf( stderr, "conflicting options : C, o\n" );
685 void seq_grp_nuc( int *grp, char *seq )
690 tmp = amino_grp[*seq++];
694 fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
699 void seq_grp( int *grp, char *seq )
704 tmp = amino_grp[*seq++];
708 fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
713 void makecompositiontable_p( short *table, int *pointt )
717 while( ( point = *pointt++ ) != END_OF_VEC )
721 int commonsextet_p( short *table, int *pointt )
726 static short *memo = NULL;
727 static int *ct = NULL;
732 memo = (short *)calloc( tsize, sizeof( short ) );
733 if( !memo ) ErrorExit( "Cannot allocate memo\n" );
734 ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) );
735 if( !ct ) ErrorExit( "Cannot allocate memo\n" );
739 while( ( point = *pointt++ ) != END_OF_VEC )
742 if( tmp < table[point] )
744 if( tmp == 0 ) *cp++ = point;
749 while( *cp != END_OF_VEC )
755 void makepointtable_nuc( int *pointt, int *n )
769 while( *n != END_OF_VEC )
771 point -= *p++ * 1024;
776 *pointt = END_OF_VEC;
779 void makepointtable( int *pointt, int *n )
786 point += *n++ * 1296;
793 while( *n != END_OF_VEC )
795 point -= *p++ * 7776;
800 *pointt = END_OF_VEC;
804 static void pairalign( int nseq, int *nlen, char **seq, int *mem1, int *mem2, double *weight, int *alloclen )
810 float pscore, tscore;
812 static char *indication1, *indication2;
813 static double *effarr1 = NULL;
814 static double *effarr2 = NULL;
815 static char **mseq1, **mseq2;
824 if( effarr1 == NULL )
826 fftlog = AllocateIntVec( nseq );
827 effarr1 = AllocateDoubleVec( nseq );
828 effarr2 = AllocateDoubleVec( nseq );
829 indication1 = AllocateCharVec( 150 );
830 indication2 = AllocateCharVec( 150 );
831 mseq1 = AllocateCharMtx( nseq, 0 );
832 mseq2 = AllocateCharMtx( nseq, 0 );
833 for( l=0; l<nseq; l++ ) fftlog[l] = 1;
839 len1 = strlen( seq[m1] );
840 len2 = strlen( seq[m2] );
841 if( *alloclen < len1 + len2 )
843 fprintf( stderr, "\nReallocating.." );
844 *alloclen = ( len1 + len2 ) + 1000;
845 ReallocateCharMtx( seq, nseq, *alloclen + 10 );
846 fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
850 clus1 = fastconjuction_noname( mem1, seq, mseq1, effarr1, weight, indication1 );
851 clus2 = fastconjuction_noname( mem2, seq, mseq2, effarr2, weight, indication2 );
853 clus1 = fastconjuction_noweight( mem1, seq, mseq1, effarr1, indication1 );
854 clus2 = fastconjuction_noweight( mem2, seq, mseq2, effarr2, indication2 );
858 for( i=0; i<clus1; i++ )
859 fprintf( stderr, "in p seq[%d] = %s\n", mem1[i], seq[mem1[i]] );
860 for( i=0; i<clus2; i++ )
861 fprintf( stderr, "in p seq[%d] = %s\n", mem2[i], seq[mem2[i]] );
865 fprintf( stderr, "group1 = %.66s", indication1 );
866 if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
867 fprintf( stderr, "\n" );
868 fprintf( stderr, "group2 = %.66s", indication2 );
869 if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
870 fprintf( stderr, "\n" );
873 // fprintf( stdout, "mseq1 = %s\n", mseq1[0] );
874 // fprintf( stdout, "mseq2 = %s\n", mseq2[0] );
876 if( !nevermemsave && ( alg != 'M' && ( len1 > 10000 || len2 > 10000 ) ) )
878 fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode\n", len1, len2 );
880 if( commonIP ) FreeShortMtx( commonIP );
885 if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
888 if( force_fft || ( use_fft && ffttry ) )
890 fprintf( stderr, "\bf" );
893 fprintf( stderr, "\bm" );
894 // fprintf( stderr, "%d-%d", clus1, clus2 );
895 pscore = Falign_noudp( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
899 // fprintf( stderr, "%d-%d", clus1, clus2 );
900 pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
905 fprintf( stderr, "\bd" );
910 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
913 fprintf( stderr, "\bm" );
914 // fprintf( stderr, "%d-%d", clus1, clus2 );
915 pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL );
918 if( clus1 == 1 && clus2 == 1 )
920 // fprintf( stderr, "%d-%d", clus1, clus2 );
921 pscore = G__align11( mseq1, mseq2, *alloclen );
925 // fprintf( stderr, "%d-%d", clus1, clus2 );
926 pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
930 ErrorExit( "ERROR IN SOURCE FILE" );
934 fprintf( stderr, "score = %10.2f\n", pscore );
936 nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
941 static void treebase( int nseq, int *nlen, char **aseq, double *eff, int nalign, int ***topol, int *alloclen ) // topol
948 for( l=0; l<nlim; l++ )
950 fprintf( stderr, "in treebase, l = %d\n", l );
951 fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
952 fprintf( stderr, "aseq[topol[l][0][0]] = %s\n", aseq[topol[l][0][0]] );
953 pairalign( nseq, nlen, aseq, topol[l][0], topol[l][1], eff, alloclen );
959 static void WriteOptions( FILE *fp )
962 if( dorp == 'd' ) fprintf( fp, "DNA\n" );
965 if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
966 else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
967 else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
969 fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
970 if( use_fft ) fprintf( fp, "FFT on\n" );
972 fprintf( fp, "tree-base method\n" );
973 if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
974 else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
975 if( tbitr || tbweight )
977 fprintf( fp, "iterate at each step\n" );
978 if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
979 if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
980 if( tbweight ) fprintf( fp, " weighted\n" );
984 fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
987 fprintf( fp, "Algorithm A\n" );
988 else if( alg == 'A' )
989 fprintf( fp, "Algorithm A+\n" );
990 else if( alg == 'S' )
991 fprintf( fp, "Apgorithm S\n" );
992 else if( alg == 'C' )
993 fprintf( fp, "Apgorithm A+/C\n" );
995 fprintf( fp, "Unknown algorithm\n" );
997 if( treemethod == 'x' )
998 fprintf( fp, "Tree = UPGMA (3).\n" );
999 else if( treemethod == 's' )
1000 fprintf( fp, "Tree = UPGMA (2).\n" );
1001 else if( treemethod == 'p' )
1002 fprintf( fp, "Tree = UPGMA (1).\n" );
1004 fprintf( fp, "Unknown tree.\n" );
1008 fprintf( fp, "FFT on\n" );
1010 fprintf( fp, "Basis : 4 nucleotides\n" );
1014 fprintf( fp, "Basis : Polarity and Volume\n" );
1016 fprintf( fp, "Basis : 20 amino acids\n" );
1018 fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
1019 fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
1022 fprintf( fp, "FFT off\n" );
1027 static int splitseq_mq( Scores *scores, int nin, int *nlen, char **seq, char **name, char *inputfile, int uniform, char **tree, int *alloclen, int *order, int *whichgroup, double *weight, int *depthpt )
1034 static int groupid = 0;
1035 static int branchid = 0;
1036 static int uniformid = 0;
1038 int selfscore0, selfscore1;
1042 static short *table1;
1043 Scores **outs, *ptr;
1052 static int *orderpos = NULL;
1068 double *minscoreinpick;
1076 char **mseq1, **mseq2;
1077 double *blastresults;
1078 static int palloclen = 0;
1081 if( orderpos == NULL )
1083 if( palloclen == 0 )
1084 palloclen = *alloclen * 2;
1093 *tree = (char *)calloc( 1, sizeof( char ) );
1099 if( doalign && doalign != 'b' )
1101 mseq1 = AllocateCharMtx( 1, palloclen );
1102 mseq2 = AllocateCharMtx( 1, palloclen );
1109 fprintf( stderr, "checking before swap!!\n" );
1110 for( i=0; i<nin; i++ )
1112 fprintf( stderr, "scores[%d].seq (%d) = \n%s\n", i, scores[i].numinseq, scores[i].seq );
1113 if( strlen( seq[scores[i].numinseq] ) == 0 )
1116 fprintf( stderr, "OKASHII before swap!!\n" );
1123 for( i=0; i<njob; i++ )
1125 // fprintf( stderr, "seq[%d] = \n%s\n", i, seq[i] );
1126 if( strlen( seq[i] ) == 0 )
1128 fprintf( stderr, "OKASHII in seq!!\n" );
1137 selfscore0 = scores->selfscore;
1141 // fprintf( stderr, "ptr-scores=%d, selfscore = %d, score = %f\n", ptr-scores, ptr->selfscore, ptr->score );
1142 if( ptr->selfscore > selfscore0 )
1144 selfscore0 = ptr->selfscore;
1145 belongto = ptr-scores;
1152 // fprintf( stderr, "swap %d %s\n<->\n%d %s\n", 0, scores->name, belongto, (scores+belongto)->name );
1153 ptr = calloc( 1, sizeof( Scores ) );
1154 *ptr = scores[belongto];
1155 scores[belongto] = *scores;
1164 if( doalign == 'f' )
1166 blastresults = callfasta( seq, scores, nin, 0, 1 );
1167 if( scores->selfscore != blastresults[0] )
1169 fprintf( stderr, "WARNING: selfscore\n" );
1170 fprintf( stderr, "scores->numinseq = %d\n", scores->numinseq+1 );
1171 fprintf( stderr, "scores->orilen = %d\n", scores->orilen );
1172 fprintf( stderr, "scores->selfscore = %d, but blastresults[0] = %f\n", scores->selfscore, blastresults[0] );
1178 gappick0( mseq1[0], seq[scores->numinseq] );
1182 table1 = (short *)calloc( tsize, sizeof( short ) );
1183 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
1184 makecompositiontable_p( table1, scores[0].pointt );
1187 selfscore0 = scores[0].selfscore;
1188 for( i=0; i<nin; i++ )
1190 if( scores->orilen > scores[i].orilen )
1192 longer = (double)scores->orilen;
1193 shorter = (double)scores[i].orilen;
1197 longer = (double)scores[i].orilen; // nai
1198 shorter = (double)scores->orilen; //nai
1202 lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
1203 // lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
1204 // fprintf( stderr, "lenfac = %f l=%d,%d\n", lenfac,scores->orilen, scores[i].orilen );
1211 if( doalign == 'b' )
1213 scores[i].score = ( 1.0 - blastresults[i] / MIN( scores->selfscore, scores[i].selfscore ) ) * 3;
1217 fprintf( stderr, "\r%d / %d ", i, nin );
1218 gappick0( mseq2[0], seq[scores[i].numinseq] );
1219 scores[i].score = ( 1.0 - (double)L__align11_noalign( mseq1, mseq2, palloclen, &off1, &off2 ) / MIN( selfscore0, scores[i].selfscore ) ) * 3;
1220 // fprintf( stderr, "scores[i] = %f\n", scores[i].score );
1221 // fprintf( stderr, "m1=%s\n", seq[scores[0].numinseq] );
1222 // fprintf( stderr, "m2=%s\n", seq[scores[i].numinseq] );
1226 scores[i].score = ( 1.0 - (double)commonsextet_p( table1, scores[i].pointt ) / MIN( selfscore0, scores[i].selfscore ) ) * lenfac;
1227 // if( i ) fprintf( stderr, "%d-%d d %4.2f len %d %d\n", 1, i+1, scores[i].score, scores->orilen, scores[i].orilen );
1229 if( doalign == 'b' ) free( blastresults );
1230 if( doalign == 0 ) free( table1 );
1233 // fprintf( stderr, "sorting .. " );
1234 qsort( scores, nin, sizeof( Scores ), (int (*)())dcompare );
1235 // fprintf( stderr, "done.\n" );
1237 maxdist = scores[nin-1].score;
1238 fprintf( stderr, "maxdist? = %f, nin=%d\n", scores[nin-1].score, nin );
1240 if( nin < 2 || uniform == -1 ) // kokodato chotto muda
1242 fprintf( stderr, "\nLeaf %d / %d ", ++branchid, njob );
1244 outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
1245 sprintf( outputfile, "%s-%d", inputfile, branchid );
1247 sprintf( outputfile + strlen(outputfile), "u%d", uniform );
1248 fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
1249 outfp = fopen( outputfile, "w" );
1253 fprintf( stderr, "Cannot open %s\n", outputfile );
1256 for( j=0; j<nin; j++ )
1257 fprintf( outfp, ">G%d %s\n%s\n", branchid, scores[j].name+1, seq[scores[j].numinseq] );
1266 tmptree = calloc( 100, sizeof( char ) );
1267 for( j=0; j<nin; j++ )
1269 treelen += sprintf( tmptree, "%d", scores[j].numinseq+1 );
1273 *tree = (char *)calloc( treelen + nin + 5, sizeof( char ) );
1274 if( nin > 1 ) **tree = '(';
1277 for( j=0; j<nin-1; j++ )
1279 sprintf( *tree+strlen( *tree ), "%d,", scores[j].numinseq+1 );
1281 sprintf( *tree+strlen( *tree ), "%d", scores[j].numinseq+1 );
1282 if( nin > 1 ) strcat( *tree, ")" );
1283 // fprintf( stdout, "*tree = %s\n", *tree );
1287 for( j=0; j<nin; j++ )
1289 *orderpos++ = scores[j].numinseq;
1290 // fprintf( stderr, "*order = %d\n", scores[j].numinseq );
1295 picks = AllocateIntVec( nin+1 );
1296 s_p_map = AllocateIntVec( nin+1 );
1297 p_o_map = AllocateIntVec( nin+1 );
1298 pickkouho = AllocateIntVec( nin+1 );
1300 // nkouho = getkouho( pickkouho, (picksize+100)/nin, nin, scores, seq );
1301 // nkouho = getkouho( pickkouho, 1.0, nin, scores, seq ); // zenbu
1302 // fprintf( stderr, "selecting kouhos phase 2\n" );
1303 // if( nkouho == 0 )
1305 // fprintf( stderr, "selecting kouhos, phase 2\n" );
1306 // nkouho = getkouho( pickkouho, 1.0, nin, scores, seq );
1308 // fprintf( stderr, "\ndone\n\n" );
1309 for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu
1312 // fprintf( stderr, "selecting picks" );
1319 // fprintf( stderr, "pickkouho[0] = %d\n", pickkouho[0] );
1320 // fprintf( stderr, "pickkouho[nin-1] = %d\n", pickkouho[nin-1] );
1321 // fprintf( stderr, "\nMOST DISTANT kouho=%d, nin=%d, nkouho=%d\n", pickkouho[nkouho], nin, nkouho );
1322 picktmp = pickkouho[nkouho-1];
1324 if( ( scores[picktmp].shimon == scores[0].shimon ) && ( !strcmp( seq[scores[0].numinseq], seq[scores[picktmp].numinseq] ) ) )
1326 // fprintf( stderr, "known, j=%d (%d inori)\n", 0, scores[picks[0]].numinseq );
1327 // fprintf( stderr, "%s\n%s\n", seq[scores[picktmp].numinseq], seq[scores[picks[0]].numinseq] );
1334 // fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
1338 while( npick<picksize && nkouho>0 )
1344 // fprintf( stderr, "rn = %d\n", rn );
1348 rn = rnd() * (nkouho);
1350 picktmp = pickkouho[rn];
1351 // fprintf( stderr, "rn=%d/%d (%d inori), kouho=%d, nin=%d, nkouho=%d\n", rn, nkouho, scores[pickkouho[rn]].numinseq, pickkouho[rn], nin, nkouho );
1353 // fprintf( stderr, "#kouho before swap\n" );
1354 // for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ", pickkouho[i] ); fprintf( stderr, "\n" );
1357 pickkouho[rn] = pickkouho[nkouho];
1359 // fprintf( stderr, "#kouho after swap\n" );
1360 // for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ", pickkouho[i] ); fprintf( stderr, "\n" );
1361 for( j=0; j<npick; j++ )
1363 if( scores[picktmp].shimon == scores[picks[j]].shimon && !strcmp( seq[scores[picks[j]].numinseq], seq[scores[picktmp].numinseq] ) )
1369 // fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
1375 // fprintf( stderr, "known, j=%d (%d inori)\n", j, scores[picks[j]].numinseq );
1379 for( i=0; i<nin; i++ )
1381 fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, nin, i, scores[i].score, scores[i].numinseq );
1383 fprintf( stderr, "range:nin=%d scores[%d].score <= %f\n", nin, npick, scores[nin-1].score);
1384 for( i=0; i<npick; i++ )
1386 fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, npick, picks[i], scores[picks[i]].score, scores[picks[i]].numinseq );
1391 // fprintf( stderr, "\nnkouho=%d, defaultq2 = %d (%d inori)\n", nkouho, picks[npick-1], scores[picks[npick-1]].numinseq );
1393 qsort( picks, npick, sizeof( int ), (int (*)())intcompare );
1395 for( i=0; i<nin; i++ ) s_p_map[i] = -1;
1396 // fprintf( stderr, "npick = %d\n", npick );
1397 // fprintf( stderr, "picks =" );
1398 for( i=0; i<npick; i++ )
1400 s_p_map[picks[i]] = i;
1401 p_o_map[i] = scores[picks[i]].numinseq;
1402 // fprintf( stderr, " %d\n", picks[i] );
1404 // fprintf( stderr, "\n" );
1407 fprintf( stderr, "p_o_map =" );
1408 for( i=0; i<npick; i++ )
1410 fprintf( stderr, " %d", p_o_map[i] );
1412 fprintf( stderr, "\n" );
1414 // fprintf( stderr, "allocating..\n" );
1416 // fprintf( stderr, "allocating outs, npick = %d\n", npick );
1417 numin = calloc( npick+1, sizeof( int ) );
1418 outs = calloc( npick+1, sizeof( Scores * ) );
1419 for( i=0; i<npick+1; i++ ) outs[i] = NULL;
1420 topol = AllocateIntCub( npick+1, 2, 0 );
1421 treeorder = AllocateIntVec( npick+1 + 1 );
1422 len = AllocateFloatMtx( npick+1, 2 );
1423 pickmtx = AllocateFloatHalfMtx( npick+1 );
1424 minscoreinpick = AllocateDoubleVec( npick );
1425 hanni = AllocateDoubleVec( npick );
1426 saien = AllocateIntVec( npick );
1427 horyudist = AllocateDoubleVec( npick );
1431 children = calloc( npick+1, sizeof( char * ) );
1432 for( i=0; i<npick+1; i++ ) children[i] = NULL;
1435 // fprintf( stderr, "done..\n" );
1437 // fprintf( stderr, "classifying, pick=%d or %d \n", npick, npick+1 );
1440 // fprintf( stderr, "### itchi suru hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore );
1441 // fprintf( stderr, "seq[%d] = scores->seq = \n%s\n", scores->numinseq, seq[scores->numinseq] );
1444 for( j=0; j<nin; j++ )
1447 outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
1448 outs[belongto][numin[belongto]] = scores[j];
1454 dfromc = AllocateDoubleMtx( npick, nin );
1456 for( i=0; i<npick; i++ ) for( j=0; j<nin; j++ )
1457 dfromc[i][j] = -0.5;
1458 for( i=0; i<npick; i++ ) pickmtx[i][0] = 0.0;
1459 for( j=0; j<nin; j++ )
1461 dfromc[0][j] = ( scores[j].score );
1462 // fprintf( stderr, "j=%d, s_p_map[j]=%d\n", j, s_p_map[j] );
1463 if( s_p_map[j] != -1 )
1465 pickmtx[0][s_p_map[j]] = (float)dfromc[0][j];
1469 fprintf( stderr, "\n\n%dx%d distance matrix\n", npick, nin );
1472 fprintf( stderr, "picks = \n" );
1473 for( i=0; i<npick; i++ ) fprintf( stderr, "%d ", p_o_map[i] + 1 );
1474 fprintf( stderr, "\n" );
1476 fprintf( stderr, "scores = \n" );
1477 for( i=0; i<nin; i++ ) fprintf( stderr, "%d ", scores[i].numinseq + 1 );
1478 fprintf( stderr, "\n" );
1481 for( i=1; i<npick; i++ )
1483 fprintf( stderr, "%d / %d \r", i, npick );
1487 if( doalign == 'f' )
1488 blastresults = callfasta( seq, scores, nin, picks[i], 0 );
1490 gappick0( mseq1[0], seq[scores[picks[i]].numinseq] );
1494 table1 = (short *)calloc( tsize, sizeof( short ) );
1495 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
1496 makecompositiontable_p( table1, scores[picks[i]].pointt );
1499 selfscore0 = scores[picks[i]].selfscore;
1500 for( j=0; j<nin; j++ )
1502 if( scores[picks[i]].orilen > scores[j].orilen )
1504 longer = scores[picks[i]].orilen;
1505 shorter = scores[j].orilen;
1509 shorter = scores[picks[i]].orilen;
1510 longer = scores[j].orilen;
1514 // lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
1515 lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
1516 // lenfac = 1.0 / ( shorter / longer * LENFACD + LENFACB / ( longer + LENFACC ) + LENFACA );
1517 // fprintf( stderr, "lenfac = %f, l=%d, %d\n", lenfac, scores[picks[i]].orilen, scores[j].orilen );
1522 ii = s_p_map[j]; jj=s_p_map[picks[i]];
1523 if( ii != -1 && jj != -1 )
1525 if( dfromc[ii][picks[jj]] != -0.5 )
1527 dfromc[i][j] = dfromc[ii][picks[jj]];
1533 if( doalign == 'b' )
1535 dfromc[ii][picks[jj]] =
1537 ( 1.0 - blastresults[j] / MIN( scores[picks[i]].selfscore, scores[j].selfscore ) ) * 3;
1541 gappick0( mseq2[0], seq[scores[j].numinseq] );
1542 dfromc[ii][picks[jj]] =
1544 ( 1.0 - (double)L__align11_noalign( mseq1, mseq2, palloclen, &off1, &off2 ) / MIN( selfscore0, scores[j].selfscore ) ) * 3;
1549 dfromc[ii][picks[jj]] =
1551 ( 1.0 - (double)commonsextet_p( table1, scores[j].pointt ) / MIN( selfscore0, scores[j].selfscore ) ) * lenfac;
1560 if( doalign == 'b' )
1563 ( 1.0 - blastresults[j] / MIN( scores[picks[i]].selfscore, scores[j].selfscore ) ) * 3;
1567 gappick0( mseq2[0], seq[scores[j].numinseq] );
1568 dfromc[i][j] = ( 1.0 - (double)L__align11_noalign( mseq1, mseq2, palloclen, &off1, &off2 ) / MIN( selfscore0, scores[j].selfscore ) ) * 3;
1572 dfromc[i][j] = ( 1.0 - (double)commonsextet_p( table1, scores[j].pointt ) / MIN( selfscore0, scores[j].selfscore ) ) * lenfac;
1574 // fprintf( stderr, "i,j=%d,%d (%d,%d)/ %d,%d, dfromc[][]=%f \n", i, j, scores[picks[i]].numinseq, scores[j].numinseq, npick, nin, dfromc[i][j] );
1576 if( s_p_map[j] != -1 )
1578 // fprintf( stderr, "i=%d, j=%d, s_p_map[j]=%d, mtx[][]=%f\n", i, j, s_p_map[j], dfromc[i][j] );
1579 ii = i; jj=s_p_map[j];
1586 pickmtx[ii][jj-ii] = (float)dfromc[i][j];
1589 // fprintf( stdout, "&&& dfromc[%d][%d] (%d,%d) = %f\n", i, j, p_o_map[i], scores[j].numinseq, dfromc[i][j] );
1591 // fprintf( stderr, "i=%d, freeing\n", i );
1592 if( !doalign ) free( table1 );
1593 if( doalign && doalign == 'b' ) free( blastresults );
1595 fprintf( stderr, " \r" );
1597 for( i=0; i<npick; i++ ) for( j=0; j<npick-i; j++ )
1598 fprintf( stderr, "pickmtx[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j+i]+1, pickmtx[i][j] );
1600 for( i=0; i<npick; i++ )
1605 minscoreinpick[i] = 99.99;
1606 for( j=1; j<npick-i; j++ )
1608 // fprintf( stderr, "minscoreinpick[%d] ?o %f\n", p_o_map[i]+1, pickmtx[i][j] );
1609 if( minscoreinpick[i] > pickmtx[i][j] )
1610 minscoreinpick[i] = pickmtx[i][j];
1612 for( j=0; j<i; j++ )
1614 // fprintf( stderr, "minscoreinpick[%d] ?x %f\n", p_o_map[i]+1, pickmtx[j][i-j] );
1615 if( minscoreinpick[i] > pickmtx[j][i-j] )
1616 minscoreinpick[i] = pickmtx[j][i-j];
1618 minscoreinpick[i] *= 1.0;
1619 fprintf( stderr, "minscoreinpick[%d] = %f\n", p_o_map[i]+1, minscoreinpick[i] );
1624 // fprintf( stderr, "### itchi shinai hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d, len=%d,%d, nin=%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore, scores->orilen, scores[nin-1].orilen, nin );
1625 for( j=0; j<nin; j++ )
1627 belongto = s_p_map[j];
1628 if( belongto == -1 )
1630 belongto = npick; // default ha horyu
1632 for( i=0; i<npick; i++ )
1634 // fprintf( stderr, "checking %d/%d,%d/%d (%d-%d inori) minscore=%f, dfromc[0][j]=%f, dfromc[i][j]=%f\n", i, npick, j, nin, p_o_map[i], scores[j].numinseq, minscore, dfromc[0][j], dfromc[i][j] );
1635 if( scores[j].shimon == scores[picks[i]].shimon && !strcmp( seq[scores[j].numinseq], seq[p_o_map[i]] ) )
1637 // fprintf( stderr, "pick-%d (%d in ori) to score-%d (%d inori) ha kanzen itch\n", i, p_o_map[i], j, scores[j].numinseq );
1641 if( dfromc[i][j] < minscore )
1642 // if( rnd() < 0.5 ) // CHUUI !!!!!
1644 if( dfromc[i][j] > hanni[i] )
1645 hanni[i] = dfromc[i][j];
1647 fprintf( stderr, "pick-%d (%d in ori) to score-%d (%d inori) ha tikai, %f>%f\n", i, p_o_map[i]+1, j, scores[j].numinseq+1, minscore, dfromc[i][j] );
1648 minscore = dfromc[i][j];
1654 if( dfromc[belongto][j] > minscoreinpick[belongto] )
1656 fprintf( stderr, "dame, %f > %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
1660 fprintf( stderr, "ok, %f < %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
1662 fprintf( stderr, "j=%d (%d inori) -> %d (%d inori)\n", j, scores[j].numinseq+1, belongto, p_o_map[belongto]+1 );
1663 fprintf( stderr, "numin = %d\n", numin[belongto] );
1664 outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
1665 outs[belongto][numin[belongto]] = scores[j];
1671 for( i=0; i<npick; i++ )
1672 fprintf( stderr, "hanni[%d] = %f\n", p_o_map[i]+1, hanni[i] );
1673 for( i=0; i<npick-1; i++ ) for( j=i; j<npick; j++ )
1674 fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
1676 for( i=0; i<npick; i++ )
1678 fprintf( stderr, "numin[%d] = %d\n", p_o_map[i]+1, numin[i] );
1684 for( i=0; i<npick-1; i++ )
1686 if( numin[i] == 0 ) continue;
1687 for( j=i+1; j<npick; j++ )
1689 fprintf( stderr, "%d-%d (%d-%d)\n", i, j, p_o_map[i]+1, p_o_map[j]+1 );
1690 if( i==0 && j == 1 )
1692 fprintf( stderr, "continueing because i=0 and j=1\n" );
1697 fprintf( stderr, "continueing because numin[j]=0\n" );
1700 fprintf( stderr, "checking %d-%d\n", p_o_map[i]+1, p_o_map[j]+1 );
1701 fprintf( stderr, "dist[i,j] = %f, hanni[i]=%f, hanni[j]=%f\n", pickmtx[i][j-i], hanni[i], hanni[j] );
1702 // if( pickmtx[i][j-i] < abs( dfromc[i][saien[i]] - dfromc[j][saien[i]] ) )
1703 if( pickmtx[i][j-i] < maxdist * 0.7 )
1705 fprintf( stderr, "%d => %d, because %f<%f(md=%f)\n", p_o_map[j]+1, p_o_map[i]+1, pickmtx[i][j-i], maxdist*0.7, maxdist );
1707 outs[i] = realloc( outs[i], sizeof( Scores ) * ( numin[i] + numin[j] ) );
1708 for( k=0; k<numin[j]; k++ ) outs[i][numin[i]+k] = outs[j][k];
1709 free( outs[j] ); outs[j] = NULL;
1710 numin[i] += numin[j];
1714 else if( pickmtx[i][j-i] < abs( dfromc[j][saien[j]] - dfromc[i][saien[i]] ) )
1716 fprintf( stderr, "%d => %d\n", p_o_map[i]+1, p_o_map[j]+1 );
1718 outs[j] = realloc( outs[j], sizeof( Scores ) * ( numin[j] + numin[i] ) );
1719 for( k=0; k<numin[i]; k++ ) outs[j][numin[j]+k] = outs[i][k];
1720 free( outs[i] ); outs[i] = NULL;
1721 numin[j] += numin[i];
1731 for( i=0; i<npick; i++ )
1733 fprintf( stderr, "numin[%d] = %d, (%d inori)\n", i, numin[i], p_o_map[i]+1 );
1735 pickmtx2 = AllocateFloatHalfMtx( npick2 );
1736 for( ii=0,i=0; i<npick; i++ )
1740 for( jj=ii,j=i; j<npick; j++ )
1744 pickmtx2[ii][jj-ii] = pickmtx[i][j-i];
1751 FreeFloatHalfMtx( pickmtx, npick );
1753 for( ii=0,i=0; i<npick; i++ )
1758 numin[ii] = numin[i];
1759 p_o_map[ii] = p_o_map[i];
1763 for( ; ii<npick; ii++ )
1767 for( i=0; i<npick; i++ )
1769 fprintf( stderr, "numin[%d(%d)] = %d\n", i, p_o_map[i]+1, numin[i] );
1773 for( i=0; i<npick2; i++ ) for( j=i; j<npick2; j++ )
1774 fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
1778 FreeDoubleMtx( dfromc );
1780 fprintf( stderr, "##### npick = %d\n", npick );
1785 fprintf( stderr, "upgma " );
1786 // veryfastspg_float_realloc_nobk_halfmtx( npick, pickmtx, topol, len );
1787 veryfastsupg_float_realloc_nobk_halfmtx( npick, pickmtx, topol, len );
1788 fprintf( stderr, "\r \r" );
1792 topol[0][0] = (int *)realloc( topol[0][0], 2 * sizeof( int ) );
1793 topol[0][1] = (int *)realloc( topol[0][1], 2 * sizeof( int ) );
1795 topol[0][0][1] = -1;
1797 topol[0][1][1] = -1;
1798 // free( pickmtx[0] );
1803 fprintf( stderr, "npick = %d, topol[][] = \n", npick );
1804 for( j=0; j<npick; j++ )
1806 fprintf( stderr, "STEP%d \n", j );
1809 fprintf( stderr, "%d ", ( topol[j][0][i] )+0 );
1810 if( topol[j][0][i] == -1 ) break;
1812 fprintf( stderr, "\n" );
1815 fprintf( stderr, "%d ", ( topol[j][1][i] )+0 );
1816 if( topol[j][1][i] == -1 ) break;
1818 fprintf( stderr, "\n" );
1819 fprintf( stderr, "\n" );
1824 iptr = topol[npick-2][0]; while( *iptr != -1 ) *jptr++ = *iptr++;
1825 iptr = topol[npick-2][1]; while( *iptr != -1 ) *jptr++ = *iptr++;
1827 for( j=0; j<npick; j++ )
1829 // fprintf( stderr, "treeorder[%d] = %d\n", j, treeorder[j] );
1830 if( treeorder[j] == -1 ) break;
1835 for( i=0; i<npick; i++ )
1839 fprintf( stderr, "\npick%d (%d inori): # of mem=%d\n", i, p_o_map[ii], numin[ii] );
1840 for( j=0; j<numin[ii]; j++ )
1842 fprintf( stderr, "%d: %s\n", outs[ii][j].numinseq, seq[outs[ii][j].numinseq] );
1845 aligned *= splitseq_mq( outs[ii], numin[ii], nlen, seq, name, inputfile, uniform, children+ii, alloclen, order, whichgroup, weight, depthpt );
1849 for( i=0; i<npick; i++ )
1853 fprintf( stderr, "i=%d/%d, ERROR!\n", i, npick );
1854 for( j=0; j<npick; j++ )
1855 fprintf( stderr, "numin[%d] = %d (rep=%d inori)\n", j, numin[j], p_o_map[j] );
1864 for( i=0; i<npick; i++ )
1865 treelen += strlen( children[i] );
1866 *tree = calloc( treelen + nin * 3, sizeof ( char ) );
1871 if( nin >= classsize || !aligned )
1879 int mem1size, mem2size;
1884 static int *mem1 = NULL;
1885 static int *mem2 = NULL;
1891 parttree = (char **)calloc( npick, sizeof( char * ) );
1892 for( i=0; i<npick; i++ )
1894 // fprintf( stderr, "allocating parttree, size = %d\n", treelen + nin * 5 );
1895 parttree[i] = calloc( treelen + nin * 5, sizeof ( char ) );
1896 strcpy( parttree[i], children[i] );
1897 free( children[i] );
1904 mem1 = AllocateIntVec( njob+1 );
1905 mem2 = AllocateIntVec( njob+1 );
1908 // veryfastsupg_float_realloc_nobk_halfmtx( npick, pickmtx, topol, len );
1910 // counteff_simple_float( npick, topol, len, eff );
1914 for( l=0; l<nlim; l++ )
1916 mem1p = topol[l][0];
1919 while( *mem1p != -1 )
1921 // fprintf( stderr, "*mem1p = %d (%d inori), numin[]=%d\n", *mem1p, p_o_map[*mem1p], numin[*mem1p] );
1922 i = numin[*mem1p]; ptr = outs[*(mem1p++)];
1926 *mptr++ = (ptr++)->numinseq;
1931 mem2p = topol[l][1];
1934 while( *mem2p != -1 )
1936 // fprintf( stderr, "*mem2p = %d (%d inori), numin[]=%d\n", *mem2p, p_o_map[*mem2p], numin[*mem2p] );
1937 i = numin[*mem2p]; ptr = outs[*(mem2p++)];
1941 *mptr++ = (ptr++)->numinseq;
1946 qsort( mem1, mem1size, sizeof( int ), (int (*)())intcompare );
1947 qsort( mem2, mem2size, sizeof( int ), (int (*)())intcompare );
1948 // selhead( mem1, numin[0] );
1949 // selhead( mem2, numin[1] );
1953 fprintf( stderr, "\n" );
1954 fprintf( stderr, "mem1 (nin=%d) = \n", nin );
1957 fprintf( stderr, "%d ", mem1[i]+1 );
1958 if( mem1[i] == -1 ) break;
1960 fprintf( stderr, "\n" );
1961 fprintf( stderr, "mem2 (nin=%d) = \n", nin );
1964 fprintf( stderr, "%d ", mem2[i]+1 );
1965 if( mem2[i] == -1 ) break;
1967 fprintf( stderr, "\n" );
1971 fprintf( stderr, "before pairalign, l = %d, npick=%d, mem1size=%d, mem2size=%d\n", l, npick, mem1size, mem2size );
1972 fprintf( stderr, "before alignment\n" );
1973 for( j=0; j<mem1size; j++ )
1974 fprintf( stderr, "%s\n", seq[mem1[j]] );
1975 fprintf( stderr, "----\n" );
1976 for( j=0; j<mem2size; j++ )
1977 fprintf( stderr, "%s\n", seq[mem2[j]] );
1978 fprintf( stderr, "----\n\n" );
1980 fprintf( stderr, "\r Alignment %d-%d \r", mem1size, mem2size );
1985 pairalign( njob, nlen, seq, mem1, mem2, weight, alloclen );
1987 pairalign( njob, nlen, seq, mem2, mem1, weight, alloclen );
1993 v1 = topol[l][0][0];
1994 v2 = topol[l][1][0];
1996 // fprintf( stderr, "npick=%d, v1=%d, v2=%d\n", npick, v1, v2 );
2003 // fprintf( stderr, "npick=%d, v1=%d, v2=%d after sort\n", npick, v1, v2 );
2004 // fprintf( stderr, "npick=%d, v1=%d, v2=%d\n", npick, v1, v2 );
2005 // fprintf( stderr, "v1=%d, v2=%d, parttree[v1]=%s, parttree[v2]=%s\n", v1, v2, parttree[v1], parttree[v2] );
2006 sprintf( *tree, "(%s,%s)", parttree[v1], parttree[v2] );
2007 strcpy( parttree[v1], *tree );
2008 // fprintf( stderr, "parttree[%d] = %s\n", v1, parttree[v1] );
2009 // fprintf( stderr, "*tree = %s\n", *tree );
2010 free( parttree[v2] ); parttree[v2] = NULL;
2015 fprintf( stderr, "after alignment\n" );
2016 for( j=0; j<mem1size; j++ )
2017 fprintf( stderr, "%s\n", seq[mem1[j]] );
2018 fprintf( stderr, "----\n" );
2019 for( j=0; j<mem2size; j++ )
2020 fprintf( stderr, "%s\n", seq[mem2[j]] );
2021 fprintf( stderr, "----\n\n" );
2027 free( parttree[v1] ); parttree[v1] = NULL;
2028 // fprintf( stderr, "*tree = %s\n", *tree );
2029 // FreeCharMtx( parttree );
2030 free( parttree ); parttree = NULL;
2035 fprintf( stderr, "after alignment\n" );
2036 for( i=0; i<npick; i++ )
2038 for( j=0; j<numin[i]; j++ )
2039 fprintf( stderr, "%s\n", seq[outs[i][j].numinseq] );
2046 mptr = mem1; while( *mptr != -1 )
2049 fprintf( stdout, "==g1-%d \n", *mptr+1 );
2050 fprintf( stdout, "%s \n", seq[*mptr] );
2052 whichgroup[*mptr] = groupid;
2053 weight[*mptr++] *= 0.5;
2056 mptr = mem2; while( *mptr != -1 )
2059 fprintf( stdout, "=g2-%d ", *mptr+1 );
2060 fprintf( stdout, "%s \n", seq[*mptr] );
2062 whichgroup[*mptr] = groupid;
2063 weight[*mptr++] *= 0.5;
2068 mptr = mem1; while( *mptr != -1 )
2070 whichgroup[*mptr] = groupid;
2071 weight[*mptr++] *= (double)2.0/numin[0];
2076 if( *depthpt > maxdepth ) maxdepth = *depthpt;
2085 sprintf( *tree, "%s", children[0] );
2086 free( children[0] );
2091 for( i=0; i<npick; i++ ) free( (void *)outs[i] );
2092 FreeFloatHalfMtx( pickmtx, npick );
2093 FreeFloatMtx( len );
2094 FreeIntCub( topol );
2095 FreeIntVec( treeorder );
2102 free( minscoreinpick );
2106 if( doalign && doalign != 'b' )
2108 FreeCharMtx( mseq1 );
2109 FreeCharMtx( mseq2 );
2115 static void alignparaphiles( int nseq, int *nlen, double *weight, char **seq, int nmem, int *members, int *alloclen )
2118 int *mem1 = AllocateIntVec( nmem );
2119 int *mem2 = AllocateIntVec( 2 );
2123 for( i=0; i<ilim; i++ )
2125 mem1[i] = members[i];
2127 mem2[0] = members[i+1];
2128 pairalign( nseq, nlen, seq, mem1, mem2, weight, alloclen );
2144 int main( int argc, char *argv[] )
2146 static char **name, **seq;
2148 static char *tmpseq;
2149 static int **pointt;
2159 static int *whichgroup;
2160 static double *weight;
2161 static char tmpname[B+100];
2172 double *blastresults;
2173 static char com[1000];
2176 static Scores *scores;
2177 static short *table1;
2182 arguments( argc, argv );
2186 infp = fopen( inputfile, "r" );
2189 fprintf( stderr, "Cannot open %s\n", inputfile );
2201 fprintf( stderr, "At least 2 sequences should be input!\n"
2202 "Only %d sequence found.\n", njob );
2206 if( picksize == NOTSPECIFIED )
2207 picksize = PICKSIZE;
2209 if( classsize == NOTSPECIFIED || classsize == 0 )
2211 classsize = njob + 1;
2215 // picksize = MIN( picksize, (int)sqrt( classsize ) + 1);
2218 alloclen = nlenmax * 2;
2219 name = AllocateCharMtx( njob, B+1 );
2220 seq = AllocateCharMtx( njob, alloclen+1 );
2221 nlen = AllocateIntVec( njob );
2222 tmpseq = calloc( nlenmax+1, sizeof( char ) );
2223 pointt = AllocateIntMtx( njob, nlenmax+1 );
2224 grpseq = AllocateIntVec( nlenmax + 1 );
2225 order = (int *)calloc( njob + 1, sizeof( int ) );
2226 whichgroup = (int *)calloc( njob, sizeof( int ) );
2227 weight = (double *)calloc( njob, sizeof( double ) );
2229 fprintf( stderr, "alloclen = %d in main\n", alloclen );
2231 for( i=0; i<njob; i++ ) whichgroup[i] = 0;
2232 for( i=0; i<njob; i++ ) weight[i] = 1.0;
2233 for( i=0; i<njob; i++ ) order[i] = -1;
2235 // readData( infp, name, nlen, seq );
2236 readData_pointer( infp, name, nlen, seq );
2240 constants( njob, seq );
2242 if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
2243 else tsize = (int)pow( 6, 6 );
2261 for( i=0; i<njob; i++ )
2263 gappick0( tmpseq, seq[i] );
2264 nlen[i] = strlen( tmpseq );
2265 strcpy( seq[i], tmpseq );
2269 fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
2270 fprintf( stderr, "name = %s\n", name[i] );
2271 fprintf( stderr, "seq = %s\n", seq[i] );
2274 if( nlen[i] > maxl ) maxl = nlen[i];
2275 if( dorp == 'd' ) /* nuc */
2277 seq_grp_nuc( grpseq, tmpseq );
2278 makepointtable_nuc( pointt[i], grpseq );
2282 seq_grp( grpseq, tmpseq );
2283 makepointtable( pointt[i], grpseq );
2288 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
2295 WriteOptions( trap_g );
2297 c = seqcheck( seq );
2300 fprintf( stderr, "Illeagal character %c\n", c );
2304 pid = (int)getpid();
2305 sprintf( datafile, "/tmp/data-%d\0", pid );
2306 sprintf( queryfile, "/tmp/query-%d\0", pid );
2307 sprintf( resultfile, "/tmp/fasta-%d\0", pid );
2309 scores = (Scores *)calloc( njob, sizeof( Scores ) );
2311 fprintf( stderr, "\nCalculating i-i scores ... \n" );
2312 for( i=0; i<njob; i++ )
2314 orilen = strlen( seq[i] );
2315 scores[i].numinseq = i; // irimasu
2316 scores[i].orilen = orilen;
2319 for( i=0; i<njob; i++ )
2321 scores[i].pointt = pointt[i];
2322 scores[i].shimon = (int)pointt[i][0] + (int)pointt[i][1] + (int)pointt[i][scores[i].orilen-6];
2323 scores[i].name = name[i];
2326 fprintf( stderr, "\r %05d/%05d ", i, njob );
2327 free( scores[i].pointt );
2328 if( doalign == 'f' )
2331 int ipos = (int)( i / KIZAMI ) * KIZAMI;
2332 int iposamari = i % KIZAMI;
2334 fprintf( stderr, "%d / %d\r", i, njob );
2335 // fprintf( stderr, "ipos = %d\n", ipos );
2336 // fprintf( stderr, "iposamari = %d\n", iposamari );
2338 // fprintf( stderr, " calling blast, i=%d\n", i );
2339 // blastresults = callfasta( seq, scores+i, 1, 0, 1 );
2340 blastresults = callfasta( seq, scores+ipos, MIN(KIZAMI,njob-ipos), iposamari, (iposamari==0) );
2341 // fprintf( stderr, "done., i=%d\n\n", i );
2342 scores[i].selfscore = (int)blastresults[iposamari];
2344 for( j=0; j<100; j++ )
2346 fprintf( stderr, "res[%d] = %f\n", j, blastresults[j] );
2349 // fprintf( stderr, "%d->selfscore = %d\n", i, scores[i].selfscore );
2350 free( blastresults );
2355 for( pt=seq[i]; *pt; pt++ )
2357 pscore += amino_dis[(int)*pt][(int)*pt];
2359 scores[i].selfscore = pscore;
2361 // fprintf( stderr, "selfscore[%d] = %d\n", i+1, scores[i].selfscore );
2365 table1 = (short *)calloc( tsize, sizeof( short ) );
2366 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
2367 makecompositiontable_p( table1, pointt[i] );
2368 scores[i].selfscore = commonsextet_p( table1, pointt[i] );
2377 tree = (char **)calloc( 1, sizeof( char *) );
2379 // splitseq_bin( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight );
2380 completed = splitseq_mq( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth );
2381 treefile = (char *)calloc( strlen( inputfile ) + 10, sizeof( char ) );
2383 sprintf( treefile, "%s.tree", inputfile );
2385 sprintf( treefile, "splittbfast.tree" );
2386 treefp = fopen( treefile, "w" );
2387 fprintf( treefp, "%s\n", *tree );
2391 completed = splitseq_mq( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth );
2393 completed = splitseq_mq( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth );
2396 fprintf( stderr, "\nDone.\n\n" );
2403 for( i=0; i<njob; i++ )
2406 if( whichgroup[pos] != groupid )
2409 groupid = whichgroup[pos];
2411 if( whichgroup[pos] )
2415 paramem[npara] = -1;
2416 if( npara > 1 && classsize > 2 )
2418 qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
2419 // selhead( paramem, npara );
2420 alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
2422 free( paramem ); paramem = NULL; npara = 0;
2424 sprintf( tmpname, "Group-%d %s", groupnum, name[pos]+1 );
2428 paramem = realloc( paramem, sizeof( int) * ( npara + 2 ) );
2429 paramem[npara++] = pos;
2430 sprintf( tmpname, "Group-para %s", name[pos]+1 );
2433 strcpy( name[pos]+1, tmpname );
2437 paramem[npara] = -1;
2438 if( npara > 1 && classsize > 2 )
2440 qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
2441 // selhead( paramem, npara );
2442 alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
2444 free( paramem ); paramem = NULL; npara = 0;
2447 for( i=0; i<njob; i++ )
2449 sprintf( tmpname, "Group-%d %s", whichgroup[i], name[i]+1 );
2450 strcpy( name[i]+1, tmpname );
2455 // maketanni( name, seq, njob, nlenmax, nlen );
2460 fprintf( stderr, "writing alignment to stdout\n" );
2463 writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
2465 writeData_pointer( stdout, njob, name, nlen, seq );
2467 fprintf( stderr, "OSHIMAI\n" );
2469 if( classsize == 1 )
2471 fprintf( stderr, "\n\n", njob );
2472 fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
2473 fprintf( stderr, "\n", njob );
2474 fprintf( stderr, "nseq = %d\n", njob );
2475 fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
2476 fprintf( stderr, "The input sequences have been sorted so that similar sequences are close.\n" );
2480 fprintf( stderr, "\n" );
2481 fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
2485 // fprintf( stderr, "To output guide tree,\n" );
2486 // fprintf( stderr, "%% %s -t -i %s\n", progName( argv[0] ), "inputfile" );
2489 fprintf( stderr, "\n", njob );
2490 fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
2492 else if( groupnum > 1 )
2494 fprintf( stderr, "\n\n" );
2495 fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
2496 fprintf( stderr, "\n" );
2497 fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
2498 fprintf( stderr, "The input sequences have been classified into %d groups + some paraphyletic groups\n", groupnum );
2499 fprintf( stderr, "Note that the alignment is not completed.\n" );
2503 fprintf( stderr, "\n" );
2504 fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
2508 // fprintf( stderr, "To output guide tree,\n" );
2509 // fprintf( stderr, "%% %s -t -i %s\n", progName( argv[0] ), "inputfile" );
2512 fprintf( stderr, "\n" );
2513 fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
2517 fprintf( stderr, "\n\n" );
2518 fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
2519 fprintf( stderr, "\n", njob );
2520 fprintf( stderr, "nseq = %d\n", njob );
2521 fprintf( stderr, "groupsize = %d, partsize=%d\n", classsize, picksize );
2522 // fprintf( stderr, "A single alignment containing all the input sequences has been computed.\n" );
2523 // fprintf( stderr, "If the sequences are highly diverged and you feel there are too many gaps,\n" );
2524 // fprintf( stderr, "please try \n" );
2525 // fprintf( stderr, "%% mafft --parttree --groupsize 100 inputfile\n" );
2526 // fprintf( stderr, "which classifies the sequences into several groups with <~ 100 sequences\n" );
2527 // fprintf( stderr, "and performs only intra-group alignments.\n" );
2531 fprintf( stderr, "\n" );
2532 fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
2536 // fprintf( stderr, "To output guide tree,\n" );
2537 // fprintf( stderr, "%% %s -t -i %s\n", progName( argv[0] ), "inputfile" );
2540 fprintf( stderr, "\n", njob );
2541 fprintf( stderr, "----------------------------------------------------------------------------\n", njob );
2544 if( treeout ) free( treefile );
2548 fprintf( stdout, "weight =\n" );
2549 for( i=0; i<njob; i++ )
2550 fprintf( stdout, "%d: %f\n", i+1, weight[i] );
2553 if( doalign == 'b' )
2555 strcpy( com, "rm -f" );
2557 strcat( com, datafile );
2558 strcat( com, "* " );
2559 strcat( com, queryfile );
2561 strcat( com, resultfile );
2562 fprintf( stderr, "%s\n", com );