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void | clearAlignment () |
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void | clear () |
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| SmithWaterman (Atype *A, QualityType *qualities, Btype *B, int m, int n, int allowedInsertDelete=INT_MAX, int direction=1, readIndexType MOffset=0, referenceIndexType NOffset=0) |
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void | setRead (Atype *A) |
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void | setReadQuality (QualityType *qualities) |
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void | setReference (Btype *B) |
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void | setReadLength (int m) |
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void | setReadOffset (readIndexType MOffset) |
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void | setReferenceLength (int n) |
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void | setReferenceOffset (referenceIndexType NOffset) |
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void | setAllowedInsertDelete (int allowedInsertDelete=INT_MAX) |
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void | setDirection (int direction) |
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void | clearH () |
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void | populateH () |
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void | printH (bool prettyPrint=true) |
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void | debugPrint (bool doPrintH=true) |
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void | populateAlignment () |
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int | getSumQ () |
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int | getSumQForward () |
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int | getSumQBackward () |
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void | rollCigarForward (CigarRoller &cigar) |
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void | rollCigarBackward (CigarRoller &cigar) |
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int | getSoftClipCount () |
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void | rollCigar (CigarRoller &cigar) |
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bool | localAlignment (uint32_t bandSize, Atype &read, readIndexType readLength, QualityType &quality, Btype &reference, referenceIndexType referenceLength, referenceIndexType referenceOffset, CigarRoller &cigarRoller, uint32_t &softClipCount, referenceIndexType &cigarStartingPoint, int &sumQ) |
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template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>
class SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
Definition at line 127 of file SmithWaterman.h.
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::SmithWaterman |
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| ) |
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inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::SmithWaterman |
( |
Atype * |
A, |
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QualityType * |
qualities, |
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Btype * |
B, |
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int |
m, |
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int |
n, |
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int |
allowedInsertDelete = INT_MAX , |
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int |
direction = 1 , |
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readIndexType |
MOffset = 0 , |
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referenceIndexType |
NOffset = 0 |
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) |
| |
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inline |
Definition at line 211 of file SmithWaterman.h.
220 :
221 A(A),
222 qualities(qualities),
223 B(B),
224 m(m),
225 n(n),
226 allowedInsertDelete(allowedInsertDelete),
227 direction(direction),
228 MOffset(MOffset),
229 NOffset(NOffset),
230 maxCostValue((HCellType) 0)
231 {
232 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::clear |
( |
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inline |
Definition at line 185 of file SmithWaterman.h.
186 {
187 maxCostPosition.first = 0;
188 maxCostPosition.second = 0;
189 A = NULL;
190 B = NULL;
191 qualities = NULL;
192 m = 0;
193 n = 0;
194 MOffset = 0;
195 NOffset = 0;
196 allowedInsertDelete = 0;
197 direction = 0;
198 gapOpenCount = 0;
199 gapCloseCount = 0;
200 gapExtendCount = 0;
201 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::clearAlignment |
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inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::clearH |
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inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::debugPrint |
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bool |
doPrintH = true | ) |
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inline |
Definition at line 369 of file SmithWaterman.h.
370 {
371 if (doPrintH) printH();
372 cout << "maxCostPosition = " << maxCostPosition << std::endl;
373 if (alignment.empty()) cout << "alignment vector is empty.\n";
374 else
375 {
376 cout << "alignment vector:\n";
377 for (vector<pair<int,int> >::iterator i=alignment.begin(); i < alignment.end(); i++)
378 {
379 cout << (i - alignment.begin()) << ": " << *i << "\n";
380 }
381 }
382 cout << std::endl;
383 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSoftClipCount |
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inline |
Definition at line 680 of file SmithWaterman.h.
681 {
682 if (direction>0)
683 {
684
685 return m - maxCostPosition.first;
686 }
687 else
688 {
689
690
691
692 return m - maxCostPosition.first;
693 }
694 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSumQ |
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inline |
Definition at line 448 of file SmithWaterman.h.
449 {
450 if (direction>0) return getSumQForward();
451 else return getSumQBackward();
452 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSumQBackward |
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| ) |
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inline |
Definition at line 497 of file SmithWaterman.h.
498 {
499 int sumQ = 0;
500 vector<pair<int,int> >::iterator i;
501
502 for (i=alignment.begin(); i < alignment.end() - 1; i++)
503 {
504#if defined(DEBUG_GETSUMQ)
505 cout << *i << ": ";
506#endif
507 if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second - 1))
508 {
509
510#if defined(DEBUG_GETSUMQ)
511 cout << "Match/Mismatch";
512#endif
513 if ((*A)[MOffset + m - (*i).first] != (*B)[NOffset + n - (*i).second])
514 sumQ += (*qualities)[MOffset + m - (*i).first] - '!';
515 }
516 else if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second))
517 {
518
519#if defined(DEBUG_GETSUMQ)
520 cout << "Insert?";
521#endif
522 sumQ += 50;
523 }
524 else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second - 1))
525 {
526
527#if defined(DEBUG_GETSUMQ)
528 cout << "Delete?";
529#endif
530 sumQ += 50;
531 }
532 }
533#if defined(DEBUG_GETSUMQ)
534 cout << endl;
535#endif
536 return sumQ;
537 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSumQForward |
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| ) |
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inline |
Definition at line 454 of file SmithWaterman.h.
455 {
456 int sumQ = 0;
457 vector<pair<int,int> >::reverse_iterator i;
458
459 for (i=alignment.rbegin(); i < alignment.rend() - 1; i++)
460 {
461
462#if defined(DEBUG_GETSUMQ)
463 cout << *i << ": ";
464#endif
465 if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second + 1))
466 {
467
468#if defined(DEBUG_GETSUMQ)
469 cout << "Match/Mismatch";
470#endif
471 if ((*A)[MOffset + (*i).first] != (*B)[NOffset + (*i).second])
472 sumQ += (*qualities)[MOffset + (*i).first] - '!';
473 }
474 else if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second))
475 {
476
477#if defined(DEBUG_GETSUMQ)
478 cout << "Insert";
479#endif
480 sumQ += 50;
481 }
482 else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second + 1))
483 {
484
485#if defined(DEBUG_GETSUMQ)
486 cout << "Delete";
487#endif
488 sumQ += 50;
489 }
490 }
491#if defined(DEBUG_GETSUMQ)
492 cout << endl;
493#endif
494 return sumQ;
495 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
bool SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::localAlignment |
( |
uint32_t |
bandSize, |
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Atype & |
read, |
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readIndexType |
readLength, |
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QualityType & |
quality, |
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Btype & |
reference, |
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referenceIndexType |
referenceLength, |
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referenceIndexType |
referenceOffset, |
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CigarRoller & |
cigarRoller, |
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uint32_t & |
softClipCount, |
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referenceIndexType & |
cigarStartingPoint, |
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int & |
sumQ |
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) |
| |
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inline |
Definition at line 713 of file SmithWaterman.h.
726 {
727
728 clear();
729
731
732 setDirection(+1);
733 setAllowedInsertDelete(bandSize);
734
735 setRead(&read);
736 setReadOffset(0);
737 setReadLength(readLength);
738
739 setReadQuality(&quality);
740
741 setReference(&reference);
742 setReferenceOffset(referenceOffset);
743 setReferenceLength(referenceLength);
744
745 populateH();
746
747 softClipCount = getSoftClipCount();
748
749 populateAlignment();
750
751 rollCigar(cigarRoller);
752
753 sumQ = getSumQ();
754
755 return false;
756
757 };
void clear()
Clear this object so that it has no Cigar Operations.
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::populateAlignment |
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| ) |
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inline |
Definition at line 389 of file SmithWaterman.h.
390 {
391 alignment.clear();
392 int i = m, j = n;
393
394 i = maxCostPosition.first;
395 j = maxCostPosition.second;
396
397
398
399
400
401
402
403 while (H[i][j] > 0 || (i>0 && j>0))
404 {
405
406#if defined(DEBUG_ALIGNMENT_VECTOR)
407 cout << "alignment.push_back(" << i << ", " << j << ")" << endl;
408#endif
409 alignment.push_back(pair<int,int>(i,j));
410 if (H[i-1][j-1]>=H[i-1][j] && H[i-1][j-1]>=H[i][j-1])
411 {
412
413 i--;
414 j--;
415 }
416 else if (H[i-1][j] < H[i][j-1])
417 {
418
419 j--;
420 }
421 else
422 {
423
424 i--;
425 }
426 }
427 alignment.push_back(pair<int,int>(i,j));
428#if defined(DEBUG_ALIGNMENT_VECTOR)
429 cout << "alignment.push_back(" << i << ", " << j << ")" << endl;
430 cout << "alignment.size(): " << alignment.size() << endl;
431#endif
432 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::populateH |
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| ) |
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inline |
Definition at line 300 of file SmithWaterman.h.
301 {
302
303 maxCostValue = 0;
304
305 for (int i=1; i<=m ; i++)
306 {
307
308
309 int low = MAX(1, i - allowedInsertDelete);
310 int high = MIN(n, i + allowedInsertDelete);
311
312 for (int j=low; j<=high ; j++)
313 {
314 HCellType c;
315 c = 0;
316 if (direction>0) c = MAX(c, H[i-1][j-1] + (((*A)[MOffset + i-1]==(*B)[NOffset + j-1]) ? w.match : w.misMatch));
317 else c = MAX(c, H[i-1][j-1] + (((*A)[MOffset + m-i+0]==(*B)[NOffset + n-j+0]) ? w.match : w.misMatch));
318 c = MAX(c, H[i-1][j] + w.del);
319 c = MAX(c, H[i][j-1] + w.insert);
320 H[i][j] = c;
321 if (c>maxCostValue)
322 {
323 maxCostValue = c;
324 maxCostPosition.first = i;
325 maxCostPosition.second = j;
326 }
327 }
328 }
329 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::printH |
( |
bool |
prettyPrint = true | ) |
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inline |
Definition at line 334 of file SmithWaterman.h.
335 {
336
337 for (int i=-1; i<=m ; i++)
338 {
339 for (int j=-1; j<=n ; j++)
340 {
341 if (prettyPrint) cout << setw(3);
342 if (i==-1 && j==-1)
343 {
344 if (prettyPrint) cout << " ";
345 else cout << "\t";
346 }
347 else if (j==-1)
348 {
349 if (!prettyPrint) cout << "\t";
350 if (i==0) cout << "-";
351 else cout << (*A)[MOffset + direction>0 ? i-1 : m - i];
352 }
353 else if (i==-1)
354 {
355 if (!prettyPrint) cout << "\t";
356 if (j==0) cout << "-";
357 else cout << (*B)[NOffset + direction>0 ? j-1 : n - j];
358 }
359 else
360 {
361 if (!prettyPrint) cout << "\t";
362 cout << H[i][j];
363 }
364 }
365 cout << endl;
366 }
367 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::rollCigar |
( |
CigarRoller & |
cigar | ) |
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inline |
Definition at line 696 of file SmithWaterman.h.
697 {
698 if (direction>0) rollCigarForward(cigar);
699 else rollCigarBackward(cigar);
700 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::rollCigarBackward |
( |
CigarRoller & |
cigar | ) |
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|
inline |
Definition at line 625 of file SmithWaterman.h.
626 {
627 vector<pair<int,int> >::iterator i;
628
629
630
632
633 i = alignment.begin();
634
635 for (i=alignment.begin();
636 i < alignment.end() - 1;
637 i++)
638 {
639#if defined(DEBUG_CIGAR)
640 cout << *i << ": ";
641#endif
642 if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second - 1))
643 {
644
645#if defined(DEBUG_CIGAR)
646 cout << "Match/Mismatch";
647#endif
649 }
650 else if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second))
651 {
652
653#if defined(DEBUG_CIGAR)
654 cout << "Insert?";
655#endif
657 }
658 else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second - 1))
659 {
660
661#if defined(DEBUG_CIGAR)
662 cout << "Delete?";
663#endif
665 }
666 }
667#if defined(DEBUG_CIGAR)
668 cout << endl;
669#endif
670 }
void Add(Operation operation, int count)
Append the specified operation with the specified count to this object.
@ del
deletion from the reference (the reference contains bases that have no corresponding base in the quer...
@ match
match/mismatch operation. Associated with CIGAR Operation "M"
@ insert
insertion to the reference (the query sequence contains bases that have no corresponding base in the ...
@ softClip
Soft clip on the read (clipped sequence present in the query sequence, but not in reference)....
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::rollCigarForward |
( |
CigarRoller & |
cigar | ) |
|
|
inline |
Definition at line 574 of file SmithWaterman.h.
575 {
576 vector<pair<int,int> >::reverse_iterator i;
577
578 for (i=alignment.rbegin(); i < alignment.rend() - 1; i++)
579 {
580
581#if defined(DEBUG_CIGAR)
582 cout << *i << ": ";
583#endif
584 if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second + 1))
585 {
586
587#if defined(DEBUG_CIGAR)
588 cout << "Match/Mismatch";
589#endif
591 }
592 else if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second))
593 {
594
595#if defined(DEBUG_CIGAR)
596 cout << "Insert";
597#endif
599 }
600 else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second + 1))
601 {
602
603#if defined(DEBUG_CIGAR)
604 cout << "Delete";
605#endif
607 }
608 }
609
610
612#if defined(DEBUG_CIGAR)
613 cout << endl;
614#endif
615 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setAllowedInsertDelete |
( |
int |
allowedInsertDelete = INT_MAX | ) |
|
|
inline |
Definition at line 281 of file SmithWaterman.h.
282 {
283 this->allowedInsertDelete = allowedInsertDelete;
284 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setDirection |
( |
int |
direction | ) |
|
|
inline |
Definition at line 290 of file SmithWaterman.h.
291 {
292 this->direction = direction;
293 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setRead |
( |
Atype * |
A | ) |
|
|
inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReadLength |
( |
int |
m | ) |
|
|
inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReadOffset |
( |
readIndexType |
MOffset | ) |
|
|
inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReadQuality |
( |
QualityType * |
qualities | ) |
|
|
inline |
Definition at line 238 of file SmithWaterman.h.
239 {
240 this->qualities = qualities;
241 }
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReference |
( |
Btype * |
B | ) |
|
|
inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReferenceLength |
( |
int |
n | ) |
|
|
inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReferenceOffset |
( |
referenceIndexType |
NOffset | ) |
|
|
inline |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
Atype* SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::A |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
vector<pair<int,int> > SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::alignment |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::allowedInsertDelete |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
Btype* SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::B |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::direction |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::gapCloseCount |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::gapExtendCount |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::gapOpenCount |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
HCellType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::H[maxReadLengthH][maxReferenceLengthH] |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::m |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
pair<int,int> SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::maxCostPosition |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
HCellType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::maxCostValue |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
readIndexType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::MOffset |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::n |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
referenceIndexType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::NOffset |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
QualityType* SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::qualities |
template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType , typename Atype , typename Btype , typename QualityType , typename readIndexType , typename referenceIndexType >
weight SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::w |