8 #include <sys/resource.h>
13 getrusage(RUSAGE_SELF, &t);
15 return tv.tv_sec + (double)tv.tv_usec*1e-6;
20 int intcmp( int *str1, int *str2 )
22 while( *str1 != -1 && *str2 != -1 )
23 if( *str1++ != *str2++ ) return( 1 );
24 if( *str1 != *str2 ) return( 1 );
28 char **arguments( int argc, char *argv[] )
55 ppenalty = NOTSPECIFIED;
56 ppenalty_ex = NOTSPECIFIED;
57 poffset = 0; // chokusetsu yobareru kara
58 kimuraR = NOTSPECIFIED;
60 fftWinSize = NOTSPECIFIED;
61 fftThreshold = NOTSPECIFIED;
66 while( --argc > 0 && (*++argv)[0] == '-' )
68 while ( ( c = *++argv[0] ) )
112 fftThreshold = atoi( *++argv );
116 fftWinSize = atoi( *++argv );
123 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
124 fprintf( stderr, "ppenalty = %d\n", ppenalty );
128 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
129 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
133 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
134 fprintf( stderr, "poffset = %d\n", poffset );
138 kimuraR = atoi( *++argv );
139 fprintf( stderr, "kappa = %d\n", kimuraR );
143 nblosum = atoi( *++argv );
145 fprintf( stderr, "blosum %d\n", nblosum );
149 pamN = atoi( *++argv );
152 fprintf( stderr, "jtt %d\n", pamN );
156 pamN = atoi( *++argv );
159 fprintf( stderr, "tm %d\n", pamN );
163 fprintf( stderr, "illegal option %c\n", c );
173 fprintf( stderr, "options: Check source file ! %c ?\n", c );
176 fprintf( stderr, "tbitr = %d, tbrweight = %d, tbweight = %d\n", tbitr, tbrweight, tbweight );
177 // readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
182 void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double **len, double *eff, int alloclen )
188 static char **name1, **name2;
189 double *effarr = eff;
190 double *effarr1 = NULL;
191 double *effarr2 = NULL;
192 static char *indication1, *indication2;
200 // fprintf( stderr, "in GroupAlign fftWinSize = %d\n", fftWinSize );
201 // fprintf( stderr, "in GroupAlign fftThreshold = %d\n", fftThreshold );
203 if( effarr1 == NULL )
205 name1 = AllocateCharMtx( nseq1, B );
206 name2 = AllocateCharMtx( nseq2, B );
207 indication1 = AllocateCharVec( 150 );
208 indication2 = AllocateCharVec( 150 );
209 effarr1 = AllocateDoubleVec( njob );
210 effarr2 = AllocateDoubleVec( njob );
216 for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
222 // fprintf( stdout, "nseq1 = %d\n", nseq1 );
226 clus1 = conjuctionforgaln( 0, nseq1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
227 clus2 = conjuctionforgaln( nseq1, njob, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
229 fprintf( stderr, "before align all\n" );
230 display( aseq, njob );
231 fprintf( stderr, "\n" );
232 fprintf( stderr, "before align 1 %s \n", indication1 );
233 display( mseq1, clus1 );
234 fprintf( stderr, "\n" );
235 fprintf( stderr, "before align 2 %s \n", indication2 );
236 display( mseq2, clus2 );
237 fprintf( stderr, "\n" );
241 fprintf( stderr, "before realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
242 else if( alg == 'H' )
243 fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
245 commongappick( nseq1, mseq1 );
246 commongappick( nseq2, mseq2 );
250 time1 = getrusage_sec();
251 fprintf( stderr, "entering Falign\n" );
256 pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
258 pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
263 pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
264 else if( alg == 'H' )
265 pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
266 else if( alg == 'Q' )
267 pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
269 pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
272 time2 = getrusage_sec();
273 fprintf( stdout, "### %d - %d, %f\n", clus1, clus2, time2-time1 );
278 fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
279 else if( alg == 'Q' )
280 fprintf( stderr, "after realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
284 fprintf( stderr, "after align 1 %s \n", indication1 );
285 display( mseq1, clus1 );
286 fprintf( stderr, "\n" );
287 fprintf( stderr, "after align 2 %s \n", indication2 );
288 display( mseq2, clus2 );
289 fprintf( stderr, "\n" );
292 fprintf( stderr, "group-to-group %s /%s %f\n", indication1, indication2, pscore );
293 if( disp ) display( aseq, njob );
294 fprintf( stderr, "\n" );
297 trap = fopen( "pre", "r+" );
298 if( !trap ) ErrorExit( 1 );
299 WriteGapFill( trap, njob, name, nlen, aseq );
301 fprintf( stdout, "nseq1 = %d\n", nseq1 );
305 static void WriteOptions( FILE *fp )
307 fprintf( fp, "tree-base method\n" );
308 if( tbweight == 0 ) fprintf( fp, "unweighted\n" );
309 else if( tbweight == 3 ) fprintf( fp, "reversely weighted\n" );
310 if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
311 else if( scoremtx == 1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
312 else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
313 else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
316 fprintf( fp, "Gap Penalty = %d, %d\n", penalty, offset );
318 fprintf( fp, "Gap Penalty = %d\n", penalty );
322 int main( int argc, char *argv[] )
326 static char **name, **seq;
327 static char **seq1, **seq2;
328 static char **mseq1, **mseq2;
331 static double **pscore;
333 int i, j, len1, len2;
338 int nlenmax1, nlenmax2, nseq1, nseq2;
341 argv2 = arguments( argc, argv );
343 fprintf( stderr, "####### in galn\n" );
347 fprintf( stderr, "file1 = %s\n", argv2[0] );
348 fprintf( stderr, "file2 = %s\n", argv2[1] );
350 gp1 = fopen( argv2[0], "r" ); if( !gp1 ) ErrorExit( "cannot open file1" );
351 gp2 = fopen( argv2[1], "r" ); if( !gp2 ) ErrorExit( "cannot open file2" );
354 PreRead( gp1, &nseq1, &nlenmax1 );
355 PreRead( gp2, &nseq2, &nlenmax2 );
358 nseq1 = njob; nlenmax1 = nlenmax;
360 nseq2 = njob; nlenmax2 = nlenmax;
363 njob = nseq1 + nseq2;
364 nlenmax = MAX( nlenmax1, nlenmax2 );
370 name = AllocateCharMtx( njob, B );
371 nlen = AllocateIntVec( njob );
372 seq1 = AllocateCharMtx( nseq1, nlenmax*3 );
373 seq2 = AllocateCharMtx( nseq2, nlenmax*3 );
374 seq = AllocateCharMtx( njob, 1 );
375 aseq = AllocateCharMtx( njob, nlenmax*3 );
376 bseq = AllocateCharMtx( njob, nlenmax*3 );
377 mseq1 = AllocateCharMtx( njob, 1 );
378 mseq2 = AllocateCharMtx( njob, 1 );
379 alloclen = nlenmax * 3;
381 topol = AllocateIntCub( njob, 2, njob );
382 len = AllocateDoubleMtx( njob, 2 );
383 pscore = AllocateDoubleMtx( njob, njob );
384 eff = AllocateDoubleVec( njob );
387 njob=nseq2; FRead( gp2, name+nseq1, nlen+nseq1, seq2 );
388 njob=nseq1; FRead( gp1, name, nlen, seq1 );
390 njob=nseq2; readDataforgaln( gp2, name+nseq1, nlen+nseq1, seq2 );
391 njob=nseq1; readDataforgaln( gp1, name, nlen, seq1 );
393 njob = nseq1 + nseq2;
397 commongappick( nseq1, seq1 );
398 commongappick( nseq2, seq2 );
401 for( i=0; i<nseq1; i++ ) seq[i] = seq1[i];
402 for( i=nseq1; i<njob; i++ ) seq[i] = seq2[i-nseq1];
404 Write( stdout, njob, name, nlen, seq );
407 constants( njob, seq );
409 WriteOptions( trap_g );
414 fprintf( stderr, "Illeagal character %c\n", c );
417 for( i=1; i<nseq1; i++ )
419 if( nlen[i] != nlen[0] )
420 ErrorExit( "group1 is not aligned." );
422 for( i=nseq1+1; i<njob; i++ )
424 if( nlen[i] != nlen[nseq1] )
425 ErrorExit( "group2 is not aligned." );
429 for( i=0; i<nseq1; i++ )
431 for( j=i+1; j<nseq1; j++ )
433 pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
434 // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
436 for( j=nseq1; j<njob; j++ )
439 // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
442 for( i=nseq1; i<njob-1; i++ )
444 for( j=i+1; j<njob; j++ )
446 pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
447 // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
450 // fprintf( stderr, "\n" );
456 fprintf( stderr, "Not supported\n" );
459 prep = fopen( "hat2", "r" );
460 if( prep == NULL ) ErrorExit( "Make hat2." );
461 readhat2( prep, njob, name, pscore );
465 fprintf( stderr, "Constructing dendrogram ... " );
466 if( treemethod == 'x' )
467 veryfastsupg( njob, pscore, topol, len );
469 ErrorExit( "Incorrect tree\n" );
470 fprintf( stderr, "done.\n" );
475 counteff_simple( njob, topol, len, eff );
476 // for( i=0; i<njob; i++ ) fprintf( stderr, "eff[%d] = %f\n", i, eff[i] );
480 for( i=0; i<njob; i++ ) eff[i] = 1.0;
483 len1 = strlen( seq[0] );
484 len2 = strlen( seq[nseq1] );
485 if( len1 > 30000 || len2 > 30000 )
487 fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
494 GroupAlign( nseq1, nseq2, name, nlen, seq, aseq, mseq1, mseq2, topol, len, eff, alloclen );
497 writePre( njob, name, nlen, aseq, 1 );
499 writeDataforgaln( stdout, njob, name, nlen, aseq );