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
|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Implements the traceback algorithm.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
// TODO(holtgrew): GapsRight traceback is currently untested.
// TODO(rmaerker): Change Tracback to TraceConfig<TGapsPlacement, TPathSpec> | TraceBackOff
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class TracebackCoordinator_
// ----------------------------------------------------------------------------
template <typename TPosition>
class TracebackCoordinator_
{
public:
TPosition _currColumn;
TPosition _currRow;
TPosition _endColumn;
TPosition _endRow;
TPosition _breakpoint1; // First breakpoint where banded trace switches to unbanded trace.
TPosition _breakpoint2; // Second breakpoint where unbanded trace switches back to banded trace. Only if begin of upper diagonal is bigger than end of lower diagonal.
bool _isInBand;
template <typename TBandFlag, typename TSizeH, typename TSizeV>
TracebackCoordinator_(TPosition currColumn,
TPosition currRow,
DPBandConfig<TBandFlag> const & band,
TSizeH seqHSize,
TSizeV seqVSize)
: _currColumn(currColumn),
_currRow(currRow),
_endColumn(0u),
_endRow(0u),
_breakpoint1(0u),
_breakpoint2(0u),
_isInBand(false)
{
_initTracebackCoordinator(*this, band, seqHSize, seqVSize);
}
template <typename TBandFlag, typename TSizeH, typename TSizeV>
TracebackCoordinator_(TPosition currColumn,
TPosition currRow,
TPosition endColumn,
TPosition endRow,
DPBandConfig<TBandFlag> const & band,
TSizeH seqHSize,
TSizeV seqVSize)
: _currColumn(currColumn),
_currRow(currRow),
_endColumn(endColumn),
_endRow(endRow),
_breakpoint1(0u),
_breakpoint2(0u),
_isInBand(false)
{
_initTracebackCoordinator(*this, band, seqHSize, seqVSize);
}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction PreferGapsAtEnd_
// ----------------------------------------------------------------------------
// Checks whether the gaps at the end should be preferred over a matching area.
template <typename TDPProfile>
struct PreferGapsAtEnd_ : False{};
template <typename TAlgorithm, typename TTracebackSpec, typename TExecSpec>
struct PreferGapsAtEnd_<DPProfile_<TAlgorithm, AffineGaps, TTracebackSpec, TExecSpec> > : True{};
template <typename TAlgorithm, typename TTraceSpec, typename TExecSpec>
struct PreferGapsAtEnd_<DPProfile_<TAlgorithm, LinearGaps, TracebackOn<TracebackConfig_<TTraceSpec, GapsRight> >, TExecSpec> > : True{};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _hasReachedEnd()
// ----------------------------------------------------------------------------
template <typename TPosition>
inline bool
_hasReachedEnd(TracebackCoordinator_<TPosition> const & coordinator)
{
return coordinator._currColumn <= coordinator._endColumn || coordinator._currRow <= coordinator._endRow;
}
// ----------------------------------------------------------------------------
// Function _initTracebackCoordinator()
// ----------------------------------------------------------------------------
template <typename TPosition, typename TBandFlag, typename TSizeH, typename TSizeV>
inline void
_initTracebackCoordinator(SEQAN_UNUSED TracebackCoordinator_<TPosition> & coordinator,
SEQAN_UNUSED DPBandConfig<TBandFlag> const & band,
SEQAN_UNUSED TSizeH seqHSize,
SEQAN_UNUSED TSizeV seqVSize)
{
typedef typename Position<DPBandConfig<TBandFlag> >::Type TBandPosition;
SEQAN_IF_CONSTEXPR (IsSameType<TBandFlag, BandOn>::VALUE)
{
// Adapt the current column value when the lower diagonal is positive (shift right in horizontal direction).
if (lowerDiagonal(band) >= 0)
coordinator._currColumn += static_cast<TPosition>(lowerDiagonal(band));
// Adapt the current row value when the current column comes after the upper diagonal (shift down in vertical direction).
if (static_cast<TBandPosition>(coordinator._currColumn) > upperDiagonal(band))
coordinator._currRow += coordinator._currColumn - upperDiagonal(band);
// Adapt the end row value when the end column comes after the upper diagonal (shift down in vertical direction).
if (static_cast<TBandPosition>(coordinator._endColumn) > upperDiagonal(band))
coordinator._endRow += coordinator._endColumn - upperDiagonal(band);
coordinator._breakpoint1 = _min(seqHSize, static_cast<TSizeH>(_max(0, upperDiagonal(band))));
coordinator._breakpoint2 = _min(seqHSize, static_cast<TSizeH>(_max(0, static_cast<TBandPosition>(seqVSize) +
lowerDiagonal(band))));
// Update the current row if the current column is before the upper diagoal or the first column where the maximal band size is reached.
if (coordinator._currColumn < _min(coordinator._breakpoint1, coordinator._breakpoint2))
coordinator._currRow -= _min(coordinator._breakpoint1, coordinator._breakpoint2) - coordinator._currColumn;
coordinator._isInBand = true;
}
}
// ----------------------------------------------------------------------------
// Function _isInBand()
// ----------------------------------------------------------------------------
template <typename TPosition>
inline bool
_isInBand(TracebackCoordinator_<TPosition> const & coordinator)
{
if (!coordinator._isInBand)
return coordinator._isInBand;
return (coordinator._currColumn > coordinator._breakpoint1 || coordinator._currColumn <= coordinator._breakpoint2);
}
// ----------------------------------------------------------------------------
// Function _doTracebackGoDiagonal()
// ----------------------------------------------------------------------------
template <typename TTarget, typename TDPTraceMatrixNavigator, typename TTraceValue, typename TSize, typename TPosition,
typename TGapCosts>
inline void
_doTracebackGoDiagonal(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
TTraceValue & traceValue,
TTraceValue & lastTraceValue,
TSize & fragmentLength,
TracebackCoordinator_<TPosition> & tracebackCoordinator,
TGapCosts const &)
{
if (!(lastTraceValue & TraceBitMap_<>::DIAGONAL)) // the old trace value was not diagonal
{
_recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength,
lastTraceValue);
lastTraceValue = TraceBitMap_<>::DIAGONAL;
fragmentLength = 0;
}
_traceDiagonal(matrixNavigator, _isInBand(tracebackCoordinator));
traceValue = scalarValue(matrixNavigator);
--tracebackCoordinator._currColumn;
--tracebackCoordinator._currRow;
++fragmentLength;
}
// ----------------------------------------------------------------------------
// Function _doTracebackGoVertical()
// ----------------------------------------------------------------------------
template <typename TTarget, typename TDPTraceMatrixNavigator, typename TTraceValue, typename TSize, typename TPosition,
typename TGapCosts>
inline void
_doTracebackGoVertical(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
TTraceValue & traceValue,
TTraceValue & lastTraceValue,
TSize & fragmentLength,
TracebackCoordinator_<TPosition> & tracebackCoordinator,
TGapCosts const &)
{
if (!(lastTraceValue & TraceBitMap_<>::VERTICAL)) // the old trace value was not diagonal
{
_recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength,
lastTraceValue);
lastTraceValue = TraceBitMap_<>::VERTICAL;
fragmentLength = 0;
}
// We are in a vertical gap. So continue after we reach the end of the vertical gap.
SEQAN_IF_CONSTEXPR (IsSameType<TGapCosts, AffineGaps>::VALUE)
{
while ((!(traceValue & TraceBitMap_<>::VERTICAL_OPEN) || (traceValue & TraceBitMap_<>::VERTICAL)) &&
tracebackCoordinator._currRow != 1)
{
_traceVertical(matrixNavigator, _isInBand(tracebackCoordinator));
traceValue = scalarValue(matrixNavigator);
--tracebackCoordinator._currRow;
++fragmentLength;
}
// We have to ensure, that we do not continue in vertical direction if we reached a vertical_open sign.
_traceVertical(matrixNavigator, _isInBand(tracebackCoordinator));
// Forbid continuing in vertical direction.
traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_VERTICAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX);
--tracebackCoordinator._currRow;
++fragmentLength;
}
else
{
_traceVertical(matrixNavigator, _isInBand(tracebackCoordinator));
traceValue = scalarValue(matrixNavigator);
--tracebackCoordinator._currRow;
++fragmentLength;
}
}
// ----------------------------------------------------------------------------
// Function _doTracebackMaxFromVertical()
// ----------------------------------------------------------------------------
template <typename TTarget, typename TDPTraceMatrixNavigator, typename TTraceValue, typename TSize, typename TPosition,
typename TGapCosts>
inline void
_doTracebackMaxFromVertical(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
TTraceValue & traceValue,
TTraceValue & lastTraceValue,
TSize & fragmentLength,
TracebackCoordinator_<TPosition> & tracebackCoordinator,
TGapCosts const &)
{
if (!(lastTraceValue & TraceBitMap_<>::VERTICAL)) // the old trace value was not diagonal
{
_recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength,
lastTraceValue);
lastTraceValue = TraceBitMap_<>::VERTICAL;
fragmentLength = 0;
}
_traceVertical(matrixNavigator, _isInBand(tracebackCoordinator));
// Forbid continuing in vertical direction.
traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_VERTICAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX);
--tracebackCoordinator._currRow;
++fragmentLength;
}
// ----------------------------------------------------------------------------
// Function _doTracebackGoHorizontal()
// ----------------------------------------------------------------------------
template <typename TTarget, typename TDPTraceMatrixNavigator, typename TTraceValue, typename TSize, typename TPosition,
typename TGapCosts>
inline void
_doTracebackGoHorizontal(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
TTraceValue & traceValue,
TTraceValue & lastTraceValue,
TSize & fragmentLength,
TracebackCoordinator_<TPosition> & tracebackCoordinator,
TGapCosts const &)
{
if (!(lastTraceValue & TraceBitMap_<>::HORIZONTAL)) // the old trace value was not diagonal
{
_recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength,
lastTraceValue);
lastTraceValue = TraceBitMap_<>::HORIZONTAL;
fragmentLength = 0;
}
SEQAN_IF_CONSTEXPR (IsSameType<TGapCosts, AffineGaps>::VALUE)
{
while ((!(traceValue & TraceBitMap_<>::HORIZONTAL_OPEN) || (traceValue & TraceBitMap_<>::HORIZONTAL)) &&
tracebackCoordinator._currColumn != 1)
{
_traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator));
traceValue = scalarValue(matrixNavigator);
--tracebackCoordinator._currColumn;
++fragmentLength;
}
_traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator));
// Forbid continuing in horizontal direction.
traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_HORIZONTAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX);
--tracebackCoordinator._currColumn;
++fragmentLength;
}
else
{
_traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator));
traceValue = scalarValue(matrixNavigator);
--tracebackCoordinator._currColumn;
++fragmentLength;
}
}
// ----------------------------------------------------------------------------
// Function _doTracebackMaxFromHorizontal()
// ----------------------------------------------------------------------------
template <typename TTarget, typename TDPTraceMatrixNavigator, typename TTraceValue, typename TSize, typename TPosition,
typename TGapCosts>
inline void
_doTracebackMaxFromHorizontal(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
TTraceValue & traceValue,
TTraceValue & lastTraceValue,
TSize & fragmentLength,
TracebackCoordinator_<TPosition> & tracebackCoordinator,
TGapCosts const &)
{
if (!(lastTraceValue & TraceBitMap_<>::HORIZONTAL)) // the old trace value was not diagonal
{
_recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength,
lastTraceValue);
lastTraceValue = TraceBitMap_<>::HORIZONTAL;
fragmentLength = 0;
}
_traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator));
// Forbid continuing in horizontal direction.
traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_HORIZONTAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX);
--tracebackCoordinator._currColumn;
++fragmentLength;
}
// ----------------------------------------------------------------------------
// Function _doTraceback()
// ----------------------------------------------------------------------------
template <typename TTarget, typename TDPTraceMatrixNavigator, typename TTraceValue, typename TSize, typename TPosition,
typename TGapCosts, typename TIsGapsLeft>
inline void
_doTraceback(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
TTraceValue & traceValue,
TTraceValue & lastTraceValue,
TSize & fragmentLength,
TracebackCoordinator_<TPosition> & tracebackCoordinator,
TGapCosts const & gapsCost,
TIsGapsLeft const & /*isGapsLeft*/)
{
if (TIsGapsLeft::VALUE) // Gaps should be placed on the left.
{
if (traceValue & TraceBitMap_<>::DIAGONAL)
{
_doTracebackGoDiagonal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
} // In case of Gotoh we prefer the longest possible way in this direction.
else if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL)
{
_doTracebackGoVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
}
else if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL_OPEN)
{
_doTracebackMaxFromVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
}
else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL)
{
_doTracebackGoHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
}
else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL_OPEN)
{
_doTracebackMaxFromHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
} // In case of Gotoh we prefer the longest possible way in this direction.
else // the trace back is either NONE or something else
{
if (traceValue == TraceBitMap_<>::NONE)
{
return;
}
SEQAN_ASSERT_FAIL("Reached undefined traceback value!");
}
}
else // Gaps should be placed on the right.
{
if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL)
{
_doTracebackGoVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
}
else if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL_OPEN)
{
_doTracebackMaxFromVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
}
else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL)
{
_doTracebackGoHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
}
else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL_OPEN)
{
_doTracebackMaxFromHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
} // In case of Gotoh we prefer the longest possible way in this direction.
else if (traceValue & TraceBitMap_<>::DIAGONAL)
{
_doTracebackGoDiagonal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost);
} // In case of Gotoh we prefer the longest possible way in this direction.
else // the trace back is either NONE or something else
{
if (traceValue == TraceBitMap_<>::NONE)
{
return;
}
SEQAN_ASSERT_FAIL("Reached undefined traceback value!");
}
}
}
// ----------------------------------------------------------------------------
// Function _retrieveInitialTraceDirection()
// ----------------------------------------------------------------------------
template <typename TTraceValue, typename TDPProfile>
inline TTraceValue
_retrieveInitialTraceDirection(TTraceValue & traceValue, TDPProfile const & /*dpProfile*/)
{
if (PreferGapsAtEnd_<TDPProfile>::VALUE)
{
if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX)
{
traceValue &= (TraceBitMap_<>::VERTICAL | TraceBitMap_<>::VERTICAL_OPEN | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX);
return TraceBitMap_<>::VERTICAL;
}
else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX)
{
traceValue &= (TraceBitMap_<>::HORIZONTAL | TraceBitMap_<>::HORIZONTAL_OPEN | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX);
return TraceBitMap_<>::HORIZONTAL;
}
return TraceBitMap_<>::DIAGONAL; // We set the last value to the
}
if (traceValue & TraceBitMap_<>::DIAGONAL)
return TraceBitMap_<>::DIAGONAL;
if (traceValue & (TraceBitMap_<>::VERTICAL | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX))
return TraceBitMap_<>::VERTICAL;
if (traceValue & (TraceBitMap_<>::HORIZONTAL | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX))
return TraceBitMap_<>::HORIZONTAL;
return TraceBitMap_<>::NONE;
}
// ----------------------------------------------------------------------------
// Function _computeTraceback()
// ----------------------------------------------------------------------------
template <typename TTarget,
typename TTraceValue,
typename TDPTraceMatrixNavigator,
typename TSizeH,
typename TSizeV,
typename TBandFlag,
typename TAlgorithm, typename TGapCosts, typename TTracebackSpec, typename TExecPolicy,
typename TTraceHead,
typename TTraceTail>
void _computeTraceback(TTarget & target,
TTraceValue & traceValue,
TTraceValue & lastTraceValue,
TDPTraceMatrixNavigator & matrixNavigator,
TSizeH const & seqHSize,
TSizeV const & seqVSize,
DPBandConfig<TBandFlag> const & band,
DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec, TExecPolicy> const & /*dpProfile*/,
TTraceHead const &,
TTraceTail const &)
{
typedef typename Size<TTarget>::Type TSize;
typedef typename Position<TDPTraceMatrixNavigator>::Type TPosition;
SEQAN_IF_CONSTEXPR (IsSameType<TTracebackSpec, TracebackOff>::VALUE)
return;
// Determine whether or not we place gaps to the left.
typedef typename IsGapsLeft_<TTracebackSpec>::Type TIsGapsLeft;
TracebackCoordinator_<TPosition> tracebackCoordinator(coordinate(matrixNavigator, +DPMatrixDimension_::HORIZONTAL),
coordinate(matrixNavigator, +DPMatrixDimension_::VERTICAL),
band, seqHSize, seqVSize);
if (TTraceTail::VALUE)
{
if (tracebackCoordinator._currRow != static_cast<TSize>(seqVSize))
_recordSegment(target, seqHSize, tracebackCoordinator._currRow, seqVSize - tracebackCoordinator._currRow,
TraceBitMap_<>::VERTICAL);
if (tracebackCoordinator._currColumn != static_cast<TSize>(seqHSize))
_recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, seqHSize -
tracebackCoordinator._currColumn, TraceBitMap_<>::HORIZONTAL);
}
TSize fragmentLength = 0;
while (!_hasReachedEnd(tracebackCoordinator) && traceValue != TraceBitMap_<>::NONE)
_doTraceback(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, TGapCosts(), TIsGapsLeft());
// Record last detected fragment.
_recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength, lastTraceValue);
if (TTraceHead::VALUE)
{
// Record leading gaps if any.
if (tracebackCoordinator._currRow != 0u)
_recordSegment(target, 0, 0, tracebackCoordinator._currRow, TraceBitMap_<>::VERTICAL);
if (tracebackCoordinator._currColumn != 0u)
_recordSegment(target, 0, 0, tracebackCoordinator._currColumn, TraceBitMap_<>::HORIZONTAL);
}
}
// Needed as a delegation method to allow invocation of both methods with host position and dpScout.
// With sizes and maxHostPosition.
template <typename TTarget,
typename TDPTraceMatrixNavigator,
typename TSeqHSize,
typename TSeqVSize,
typename TBandFlag,
typename TAlgorithm, typename TGapCosts, typename TTracebackSpec, typename TExecPolicy>
inline SEQAN_FUNC_DISABLE_IF(Is<ContainerConcept<TSeqHSize> >, void)
_computeTraceback(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
unsigned maxHostPosition,
TSeqHSize const & seqHSize,
TSeqVSize const & seqVSize,
DPBandConfig<TBandFlag> const & band,
DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec, TExecPolicy> const & dpProfile)
{
using TSize SEQAN_TYPEDEF_FOR_DEBUG = typename Size<TTarget>::Type;
// Set the navigator to the position where the maximum was found.
_setToPosition(matrixNavigator, maxHostPosition);
SEQAN_ASSERT_LEQ(coordinate(matrixNavigator, +DPMatrixDimension_::HORIZONTAL), static_cast<TSize>(seqHSize));
SEQAN_ASSERT_LEQ(coordinate(matrixNavigator, +DPMatrixDimension_::VERTICAL), static_cast<TSize>(seqVSize));
typename TraceBitMap_<>::Type traceValue = scalarValue(matrixNavigator);
typename TraceBitMap_<>::Type lastTraceValue = _retrieveInitialTraceDirection(traceValue, dpProfile);
_computeTraceback(target, traceValue, lastTraceValue, matrixNavigator, seqHSize, seqVSize, band, dpProfile,
TraceHead_<TAlgorithm>(), TraceTail_<TAlgorithm>());
}
// With sizes and dpScout.
template <typename TTarget,
typename TDPTraceMatrixNavigator,
typename TDPCell, typename TScoutSpec,
typename TSeqHSize,
typename TSeqVSize,
typename TBandFlag,
typename TAlgorithm, typename TGapCosts, typename TTracebackSpec, typename TExecPolicy>
inline SEQAN_FUNC_DISABLE_IF(Is<ContainerConcept<TSeqHSize> >, void)
_computeTraceback(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
DPScout_<TDPCell, TScoutSpec> const & dpScout,
TSeqHSize const & seqHSize,
TSeqVSize const & seqVSize,
DPBandConfig<TBandFlag> const & band,
DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec, TExecPolicy> const & dpProfile)
{
_computeTraceback(target, matrixNavigator, maxHostPosition(dpScout), seqHSize, seqVSize, band, dpProfile);
}
// With sequences and maxHostPosition.
template <typename TTarget,
typename TDPTraceMatrixNavigator,
typename TSequenceH,
typename TSequenceV,
typename TBandFlag,
typename TAlgorithm, typename TGapCosts, typename TTracebackSpec, typename TExecPolicy>
inline SEQAN_FUNC_ENABLE_IF(Is<ContainerConcept<TSequenceH> >, void)
_computeTraceback(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
unsigned maxHostPosition,
TSequenceH const & seqH,
TSequenceV const & seqV,
DPBandConfig<TBandFlag> const & band,
DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec, TExecPolicy> const & dpProfile)
{
_computeTraceback(target, matrixNavigator, maxHostPosition, length(seqH), length(seqV), band, dpProfile);
}
// With sequences and dpScout.
template <typename TTarget,
typename TDPTraceMatrixNavigator,
typename TDPCell, typename TScoutSpec,
typename TSequenceH,
typename TSequenceV,
typename TBandFlag,
typename TAlgorithm, typename TGapCosts, typename TTracebackSpec, typename TExecPolicy>
inline SEQAN_FUNC_ENABLE_IF(Is<ContainerConcept<TSequenceH> >, void)
_computeTraceback(TTarget & target,
TDPTraceMatrixNavigator & matrixNavigator,
DPScout_<TDPCell, TScoutSpec> const & dpScout,
TSequenceH const & seqH,
TSequenceV const & seqV,
DPBandConfig<TBandFlag> const & band,
DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec, TExecPolicy> const & dpProfile)
{
_computeTraceback(target, matrixNavigator, maxHostPosition(dpScout), seqH, seqV, band, dpProfile);
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
|
