1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668
|
// PatMaN DNA pattern matcher
// (C) 2007 Kay Pruefer, Udo Stenzel
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or (at
// your option) any later version. See the LICENSE file for details.
#include "prefix_tree.h"
#include <cassert>
#include <iostream>
#include <queue>
#include <cstdlib>
using namespace std ;
// Why a deque? Because allocation of many small objects of
// equal size is faster in it and deallocation of the whole
// deque is much faster than deallocation of the small objects,
// especially with our extremely simple allocation pattern.
// This is probably the most sensible way to plug this memory
// leak.
prefix_tree::prefix_tree( ) : nodes()
{
nodes.push_back( node() ) ;
}
#ifndef NDEBUG
void prefix_tree::debug( std::ostream& s, const node& n ) const
{
if( debug_flags & debug_trie )
{
for( int i = 0 ; i != 5 ; ++i )
s << n.label << " -" << "ACGTN"[i] << "> " << n.childs[i]->label << '/' << (int)n.drop[i] << std::endl ;
if( n.suffix ) s << n.label << " ==> " << n.suffix->label << '/' << n.drop_suffix << std::endl ;
for( int i = 0 ; i != 5 ; ++i )
if( !n.drop[i] ) debug( s, *n.childs[i] ) ;
}
}
#endif
static mismatch_ptr *junk_yard = 0 ;
static mismatch_ptr *new_node()
{
if( junk_yard )
{
mismatch_ptr *p = junk_yard ;
junk_yard = p->next ;
return p ;
}
else
{
return new mismatch_ptr ;
}
}
mismatch_ptr *prefix_tree::seed() const
{
// add ptr to the root node
mismatch_ptr *p = new_node() ;
p->ptr = &nodes[0] ;
p->mismatch = 0 ;
p->gaps = 0 ;
p->first = 0 ;
p->isgap = 0 ;
p->matched = 0 ;
p->next = 0 ;
return p ;
}
mismatch_ptr *prefix_tree::init( mismatch_ptr *p ) const
{
if( p ) {
mismatch_ptr *q = p ;
while( p->next ) p = p->next ;
p->next = junk_yard ;
junk_yard = q ;
}
return seed() ;
}
// creates child node # pos if necessary and returns ptr to this child node
node* prefix_tree::create_go_node( node* n, int pos ) {
if ( n->childs[pos] == 0 ) {
node o ;
o.depth = n->depth + 1 ;
nodes.push_back( o ) ;
node *next = &nodes.back() ;
n->childs[pos] = next ;
#ifndef NDEBUG
if( debug_flags & debug_trie )
n->childs[pos]->label = n->label + "ACGTN"[pos] ;
#endif
return next ;
} else {
return n->childs[pos] ;
}
}
void prefix_tree::add_recursion( const string& seq, const string& name, node* ptr, size_t i, char strand )
{
// is this a leaf?
if ( i == seq.size() ) {
probe_s *probe = new probe_s() ;
probe->name = name ;
probe->strand = strand ;
probe->length = seq.size() ;
probe->next = ptr->probes ;
ptr->probes = probe ;
// no leaf -> add
} else {
switch ( toupper(seq[i]) ) {
case 'A':
add_recursion( seq, name, create_go_node( ptr, 0 ), ++i, strand ) ;
break ;
case 'C':
add_recursion( seq, name, create_go_node( ptr, 1 ), ++i, strand ) ;
break ;
case 'G':
add_recursion( seq, name, create_go_node( ptr, 2 ), ++i, strand ) ;
break ;
case 'T':
case 'U':
add_recursion( seq, name, create_go_node( ptr, 3 ), ++i, strand ) ;
break ;
case 'N':
case 'X':
add_recursion( seq, name, create_go_node( ptr, 4 ), ++i, strand ) ;
break ;
case '-':
break ;
default:
add_recursion( seq, name, create_go_node( ptr, 4 ), ++i, strand ) ;
if( debug_flags & debug_notquiet )
clog << "Warning: Sequence with name " << name
<< " has character '" << seq[i]
<< "' other than ACGTUXN." << endl ;
debug_flags &= ~debug_notquiet ;
break ;
}
}
}
/***
* Adding the sequence taking into account the ambiguity codes.
* i.e. Sequence with "N" will be added to A, C, G and T node
*/
void prefix_tree::add_recursion_ambiguity( const string& seq, const string& name, node* ptr, size_t i, char strand )
{
// is this a leaf?
if ( i == seq.size() ) {
probe_s *probe = new probe_s() ;
probe->name = name ;
probe->strand = strand ;
probe->length = seq.size() ;
probe->next = ptr->probes ;
ptr->probes = probe ;
// no leaf -> add
} else {
switch ( toupper(seq[i]) ) {
case 'A':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
break ;
case 'C':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
break ;
case 'G':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
break ;
case 'T':
case 'U':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'N':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'R':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
break ;
case 'Y':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'M':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
break ;
case 'K':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'S':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
break ;
case 'W':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'B':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'D':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'H':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 3 ), i+1, strand ) ;
break ;
case 'V':
add_recursion_ambiguity( seq, name, create_go_node( ptr, 0 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 1 ), i+1, strand ) ;
add_recursion_ambiguity( seq, name, create_go_node( ptr, 2 ), i+1, strand ) ;
break ;
case '-':
break ;
default:
add_recursion_ambiguity( seq, name, create_go_node( ptr, 4 ), i+1, strand ) ;
if( debug_flags & debug_notquiet )
clog << "Warning: Sequence with name " << name
<< " has character '" << seq[i]
<< "' other than ACGTU, BDH, SWKMRY, or XN." << endl ;
debug_flags &= ~debug_notquiet ;
break ;
}
}
}
/* Ambiguity codes:
* R = G or A (puRine)
* Y = C or T (pYrimidine)
* M = A or C (aMine)
* K = G or T (Ketone)
* S = G or C (Strong coupling)
* W = A or T (Weak coupling)
* B = not A (C or G or T)
* D = not C (A or G or T)
* H = not G (A or C or T)
* V = not U (A or C or G)
* N = A or C or G or T (Nucleotide)
*/
/*
* reverse complement of a dna sequence, including correct ambiguity mapping
*/
inline static string reverse_complement( const string& s ) {
string ret ;
for ( int i = s.size()-1 ; i >= 0 ; i-- ) {
switch ( toupper( s[i] ) ) {
case 'A':
ret += 'T' ; break ;
case 'C':
ret += 'G' ; break ;
case 'G':
ret += 'C' ; break ;
case 'T':
case 'U':
ret += 'A' ; break ;
case 'R':
ret += 'Y' ; break ;
case 'Y':
ret += 'R' ; break ;
case 'M':
ret += 'K' ; break ;
case 'K':
ret += 'M' ; break ;
case 'B':
ret += 'V' ; break ;
case 'V':
ret += 'B' ; break ;
case 'D':
ret += 'H' ; break ;
case 'H':
ret += 'D' ; break ;
case 'S':
case 'W':
case 'N':
case '-':
ret += s[i] ;
break ;
default:
clog << "Sequence has invalid character '"
<< s[i] << "'." << endl ;
exit( 1 ) ;
}
}
return ret ;
}
void prefix_tree::add_seq( const string& seq, const string& name, bool ambi_codes )
{
node *ptr = &nodes[0] ;
int i = 0 ;
if ( ! ambi_codes ) {
add_recursion( seq, name, ptr, i, '+' ) ;
if ( only_plus_strand != 1 ) {
string rev_seq = reverse_complement( seq ) ;
add_recursion( rev_seq, name, ptr, i, '-' ) ;
}
} else {
add_recursion_ambiguity( seq, name, ptr, i, '+' ) ;
if ( only_plus_strand != 1 ) {
string rev_seq = reverse_complement( seq ) ;
add_recursion_ambiguity( rev_seq, name, ptr, i, '-' ) ;
}
}
}
// Suffix links. These are only needed as an intermediate step. Each
// node gets a suffix link, which points to the node that is the longest
// existing true suffix. Given a node that already has a suffix, we
// find the suffix of child "A" by following the "A" link from our
// suffix and adding the 'drop' values for the "suffix" and the "A"
// link. We can then fill in the missing children for this node in the
// same fashion. To ensure that any node we visit already has a suffix,
// we do a breadth-first search.
//
// The root never has a suffix. To start the fill-in, each missing
// child of the root becomes the root itself with a "drop" of one and
// the existing ones get the root as suffix with a drop of one.
//
// Also, after we added the missing children, we no longer need the
// suffix link for anything but accessing query sequences that happen to
// be substrings of other queries. So we can optimize these.
void prefix_tree::add_suffix_links()
{
std::queue< node* > q ;
node& root = nodes[0] ;
for( int i = 0 ; i != 5 ; ++i )
{
if( root.childs[i] )
{
root.childs[i]->suffix = &root ;
root.childs[i]->drop_suffix = 1 ;
q.push( root.childs[i] ) ;
}
else
{
root.childs[i] = &root ;
root.drop[i] = 1 ;
}
}
while( !q.empty() )
{
node* n = q.front() ;
q.pop() ;
for( int i = 0 ; i != 5 ; ++i )
{
if( n->childs[i] )
{
n->childs[i]->suffix = n->suffix->childs[i] ;
n->childs[i]->drop_suffix = n->drop_suffix + n->suffix->drop[i] ;
q.push( n->childs[i] ) ;
}
else
{
n->childs[i] = n->suffix->childs[i] ;
n->drop[i] = n->drop_suffix + n->suffix->drop[i] ;
}
}
if( !n->suffix->probes )
{
if( n->suffix->suffix )
{
n->drop_suffix += n->suffix->drop_suffix ;
n->suffix = n->suffix->suffix ;
}
else
{
n->suffix = 0 ;
}
}
}
}
inline static void out( int mm, const node* n, int mlen )
{
for( const probe_s *probe = n->probes ; probe ; probe = probe->next )
{
( output ? *output : cout )
<< genome_name << '\t' << probe->name << '\t'
<< position_genome - mlen << '\t'
<< position_genome - 1 << '\t'
<< probe->strand << '\t' << mm << '\n' ;
}
}
// Why does this work? Because when we follow suffix links (to print
// matches that are completely inside other matches), we know that we
// only drop perfectly matching stuff from the beginning. This allows
// us to update "mlen".
inline static void out_rec( int mm, const node* n, int first, int mlen )
{
if( n->probes ) out( mm, n, mlen ) ;
const node* nn = n ;
while( nn->suffix && nn->drop_suffix <= first )
{
first -= nn->drop_suffix ;
mlen -= nn->drop_suffix ;
nn = nn->suffix ;
if( nn->probes ) out( mm, nn, mlen ) ;
}
}
/* Advancing the mismatch pointers.
* - We receive a (singly linked) list of mps. There has to be exactly
* one mp that didn't encounter any mismatches in its history (keeping
* this one ensures that the algorithm reduces to Aho-Corasick if
* mismatches aren't allowed). Too avoid to much special treatment,
* this special pointer will always be the first in the list. We
* process it first, initalize the result list with it or re-seed the
* result list, then go into the loop over the rest of the list. This
* implies an if-block in the middle of the loop and it also implies
* that some pointers are only initialized in the loop.
*
* - We will keep multiple pointers into the two involved lists: one to
* the end of the result list; this is where we splice in pointers to
* be queued for the next round. This list is at all time properly
* terminated and disconnected from the stuff we're processing this
* round.
*
* - One to the next node to be processed. This one is easy, it is
* advanced once per loop, it's the head of the incoming list and
* we're done if it becomes null.
*
* - One several places ahead of the current one. We prefetch the node
* pointed to by this one and its next link. Keeping another yet more
* advanced pointer to prefetch mismatch pointers is useless because
* of the need to follow the chain of next pointers. This one has to
* be valid at all times (see next point), so if it would become null,
* we don't advance it.
*
* - When gapping, we need to splice new mps into the queue being
* processed. We do this after the node we prefetched last. That
* makes sense, because we already have that mp in cache, so we can
* splice without penalty. It works fine, as long as there is such a
* pointer, and to ensure that, we first handle gaps (in this
* direction) while the current node is still in the queue, then
* cache the contents of the current node, handle the node itself,
* thereby removing and or splicing it, then handle mismatches and/or
* gaps.
*/
inline static mismatch_ptr *splice_fresh_after( mismatch_ptr *mp )
{
if( junk_yard )
{
mismatch_ptr *p0 = junk_yard ;
junk_yard = junk_yard->next ;
p0->next = mp->next ;
mp->next = p0 ;
return p0 ;
}
else
{
mismatch_ptr *p0 = new mismatch_ptr ;
p0->next = mp->next ;
mp->next = p0 ;
return p0 ;
}
}
mismatch_ptr *prefix_tree::compare( char c, mismatch_ptr *ptrs ) const
{
int pos ;
switch( c )
{
case '-': return ptrs ;
case 'A': case 'a': pos = 0 ; break ;
case 'C': case 'c': pos = 1 ; break ;
case 'G': case 'g': pos = 2 ; break ;
case 'T': case 't': pos = 3 ; break ;
case 'U': case 'u': pos = 3 ; break ;
default: pos = -1 ; break ;
}
bool is_first = true ;
mismatch_ptr *new_head = 0, *last_done = 0 ;
mismatch_ptr *next_in_queue = ptrs ;
mismatch_ptr *next_to_prefetch = ptrs ;
for( int i = 0 ; i != do_prefetch && next_to_prefetch->next ; ++i )
next_to_prefetch = next_to_prefetch->next ;
while( next_in_queue )
{
++total_nodes ;
if( next_to_prefetch && next_to_prefetch->ptr ) __builtin_prefetch( next_to_prefetch->ptr ) ;
if( next_to_prefetch && next_to_prefetch->next ) __builtin_prefetch( next_to_prefetch->next ) ;
const node* n = next_in_queue->ptr ;
size_t mm = next_in_queue->mismatch ;
size_t gg = next_in_queue->gaps ;
int ff = next_in_queue->first ;
int nn = next_in_queue->matched ;
if( !next_in_queue->isgap ) out_rec( mm, n, is_first ? 255 : ff, nn ) ;
// If gaps are allowed, also add gapped nodes for
// processing _in_this_iteration_. If
// discount_adenine is set, don't gap an A (makes
// bookkeeping difficult).
if( gg < allow_gaps && mm < cutoff && n->depth > 0 ) {
for ( int i = discount_adenine ? 1 : 0 ; i != 5 ; i++ ) {
int ff_ = is_first ? n->depth-1 : ff ;
if( ff_ >= n->drop[i] ) {
assert( next_to_prefetch ) ;
mismatch_ptr *mp2 = splice_fresh_after( next_to_prefetch ) ;
mp2->ptr = n->childs[i] ;
mp2->mismatch = mm + 1 ;
mp2->gaps = gg + 1 ;
mp2->first = ff_ - n->drop[i] ;
mp2->isgap = 1 ;
mp2->matched = nn ;
}
}
}
// Are we gapping As? then queue that up, no matter how many
// mismatches we've already accumulated. (Note how this isn't
// even considered a gap, note that gapping the root actually
// makes a certain kind of sense.)
if( discount_adenine ) {
int ff_ = is_first ? n->depth-1 : ff ;
if( ff_ >= n->drop[0] && n->drop[0] ) {
assert( next_to_prefetch ) ;
mismatch_ptr *mp2 = splice_fresh_after( next_to_prefetch ) ;
mp2->ptr = n->childs[0] ;
mp2->mismatch = mm ;
mp2->gaps = gg ;
mp2->first = ff_ - n->drop[0] ;
mp2->isgap = 0 ;
mp2->matched = nn ;
}
}
// No longer is anything enqueued into the old queue, so we no
// longer need the next_to_prefetch pointer and can move it
// ahead.
if( next_to_prefetch->next ) next_to_prefetch = next_to_prefetch->next ;
// At this point, we no longer run into difficulties if the
// incoming queue gets emptied. So now we move the pointer to its
// matching child and throw it out if dropping the prefix kills
// a mismatch. Also, we can move the next_to_prefetch pointer,
// since it's not needed anymore in this iteration and might
// point to nowhere now. Moreover, if we're at the first node
// (the one without any mismatches), this is the place to
// initialize the new list.
int pos_ = pos == -1 ? 4 : pos ;
if( is_first ) {
next_in_queue = ptrs->next ;
if( pos == -1 ) {
new_head = seed() ;
ptrs->next = junk_yard ;
junk_yard = ptrs ;
} else {
new_head = ptrs ;
new_head->matched += 1 - ptrs->ptr->drop[pos] ;
new_head->ptr = ptrs->ptr->childs[pos] ;
new_head->next = 0 ;
}
last_done = new_head ;
} else if( ff >= n->drop[pos_] ) {
next_in_queue->ptr = n->childs[pos_] ;
next_in_queue->first -= n->drop[pos_] ;
next_in_queue->matched ++ ;
next_in_queue->matched -= n->drop[pos_] ;
next_in_queue->isgap = 0 ;
assert( !last_done->next ) ;
last_done->next = next_in_queue ;
last_done = next_in_queue ;
next_in_queue = next_in_queue->next ;
last_done->next = 0 ;
} else {
mismatch_ptr *p = next_in_queue ;
next_in_queue = next_in_queue->next ;
p->next = junk_yard ;
junk_yard = p ;
}
// The following always produces new mismatches, so skip it
// completely if we're already at the limit.
if ( mm < cutoff ) {
// if gaps are allowed, always keep the node (but don't
// uselessly gap the root node)
if( gg < allow_gaps && n->depth > 0 )
{
assert( last_done ) ;
mismatch_ptr *p = splice_fresh_after( last_done ) ;
p->ptr = n ;
p->mismatch = mm + 1 ;
p->gaps = gg + 1 ;
p->isgap = 1 ;
p->first = is_first ? n->depth-1 : ff ;
p->matched = nn + 1 ;
last_done = p ;
}
// Take care of the children, but not the one that matches.
// (That one has already been handled.)
for ( int i = 0 ; i != 5 ; i++ ) {
if( i != pos ) {
// The child always exists, but we follow it only
// iff the first mismatch would not be forgotten by
// following a suffix link.
assert( n->childs[i] ) ;
int ff_ = is_first ? n->depth : ff ;
if( ff_ >= n->drop[i] )
{
mismatch_ptr *p = splice_fresh_after( last_done ) ;
p->ptr = n->childs[i] ;
p->first = ff_ - n->drop[i] ;
p->mismatch = mm + 1 ;
p->gaps = gg ;
p->isgap = 0 ;
p->matched = nn + 1 - n->drop[i] ;
assert( !p->next ) ;
assert( last_done->next == p ) ;
last_done = p ;
}
}
}
}
is_first = false ;
assert( !last_done->next ) ;
}
if( debug_flags & debug_numnodes )
{
int n = 0 ;
for( mismatch_ptr *p = new_head ; p ; p=p->next ) ++n ;
std::clog << '\r' << n << std::endl;
}
return new_head ;
}
|