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
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
|
// ==========================================================================
// 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: Stefan Budach <budach@molgen.mpg.de>
// ==========================================================================
// DPScout_ specialization for the SIMD alignment implementation.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SIMD_DP_SCOUT_SIMD_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_SIMD_DP_SCOUT_SIMD_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
struct SimdAlignEqualLength_;
typedef Tag<SimdAlignEqualLength_> SimdAlignEqualLength;
template <typename TTraits>
struct SimdAlignVariableLength
{};
template <typename TSpec = SimdAlignEqualLength>
struct SimdAlignmentScout {};
// ----------------------------------------------------------------------------
// Class DPScoutState_
// ----------------------------------------------------------------------------
template <>
class DPScoutState_<SimdAlignEqualLength>
{};
template <typename TTraits>
class DPScoutState_<SimdAlignVariableLength<TTraits> >
{
public:
using TSizeH = typename Size<typename TTraits::TSeqH>::Type;
using TSizeV = typename Size<typename TTraits::TSeqV>::Type;
using TIterator = typename Iterator<String<size_t>, Rooted>::Type;
typename TTraits::TSimdVector endPosVecH;
typename TTraits::TSimdVector endPosVecV;
size_t posH;
size_t posV;
TIterator nextEndsH;
TIterator nextEndsV;
};
// ----------------------------------------------------------------------------
// Class DPScout_
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TSpec>
class DPScout_<TDPCell, SimdAlignmentScout<TSpec> > :
public DPScout_<TDPCell, Default>
{
public:
using TSimdVec = typename Value<TDPCell>::Type;
using TBase = DPScout_<TDPCell, Default>;
using TScoutState = DPScoutState_<TSpec>;
TSimdVec mCurrentColumnPosition{};
TSimdVec mCurrentRowPosition{};
TSimdVec mHorizontalPos{};
TSimdVec mVerticalPos{};
TScoutState * state{nullptr};
unsigned _simdLane{0};
DPScout_(TScoutState & pState) : TBase(), state(&pState)
{}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction ScoutSpecForSimdAlignment_
// ----------------------------------------------------------------------------
template<typename TAlignmentAlgorithm>
struct ScoutSpecForAlignmentAlgorithm_<TAlignmentAlgorithm, DPScoutState_<SimdAlignEqualLength> >
{
typedef SimdAlignmentScout<SimdAlignEqualLength> Type;
};
template<typename TAlignmentAlgorithm, typename TTraits>
struct ScoutSpecForAlignmentAlgorithm_<TAlignmentAlgorithm, DPScoutState_<SimdAlignVariableLength<TTraits> > >
{
typedef SimdAlignmentScout<SimdAlignVariableLength<TTraits> > Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _copySimdCell()
// ----------------------------------------------------------------------------
template <typename TValue, typename TGapSpec, typename TSpec,
typename TScoreValue,
typename TTraceConfig>
inline void
_copySimdCell(DPScout_<DPCell_<TValue, TGapSpec>, SimdAlignmentScout<TSpec> > & dpScout,
DPCell_<TValue, TGapSpec> const & activeCell,
TScoreValue const & cmp,
DPTraceMatrix<TTraceConfig> const & /**/)
{
dpScout._maxScore._score = blend(dpScout._maxScore._score, activeCell._score, cmp);
}
template <typename TValue, typename TSpec,
typename TScoreValue,
typename TTraceConfig>
inline void
_copySimdCell(DPScout_<DPCell_<TValue, AffineGaps>, SimdAlignmentScout<TSpec> > & dpScout,
DPCell_<TValue, AffineGaps> const & activeCell,
TScoreValue const & cmp,
DPTraceMatrix<TracebackOn<TTraceConfig>> const & /**/)
{
dpScout._maxScore._score = blend(dpScout._maxScore._score, activeCell._score, cmp);
dpScout._maxScore._horizontalScore = blend(dpScout._maxScore._horizontalScore, activeCell._horizontalScore, cmp);
dpScout._maxScore._verticalScore = blend(dpScout._maxScore._verticalScore, activeCell._verticalScore, cmp);
}
template <typename TValue, typename TSpec,
typename TScoreValue,
typename TTraceConfig, typename TGapsPlacement>
inline void
_copySimdCell(DPScout_<DPCell_<TValue, DynamicGaps>, SimdAlignmentScout<TSpec> > & dpScout,
DPCell_<TValue, DynamicGaps> const & activeCell,
TScoreValue const & cmp,
DPTraceMatrix<TracebackOn<TTraceConfig>> const & /**/)
{
dpScout._maxScore._score = blend(dpScout._maxScore._score, activeCell._score, cmp);
dpScout._maxScore._flagMask = blend(dpScout._maxScore._flagMask, activeCell._flagMask, cmp);
}
// ----------------------------------------------------------------------------
// Function _updateHostPositions()
// ----------------------------------------------------------------------------
// No trace needed, hence we do not track the max positions.
template<typename TDPCell, typename TScoutSpec,
typename TMask,
typename TNavigator>
inline void
_updateHostPositions(DPScout_<TDPCell, TScoutSpec> & /*dpScout*/,
TMask const & /*cmp*/,
TNavigator const & /*navi*/,
DPTraceMatrix<TracebackOff> const & /**/)
{}
template<typename TDPCell, typename TScoutSpec,
typename TMask,
typename TNavigator,
typename TTraceConfig>
inline void
_updateHostPositions(DPScout_<TDPCell, TScoutSpec> & dpScout,
TMask const & cmp,
TNavigator const & /*navi*/,
DPTraceMatrix<TTraceConfig> const & /**/)
{
dpScout.mHorizontalPos = blend(dpScout.mHorizontalPos, dpScout.mCurrentColumnPosition, cmp);
dpScout.mVerticalPos = blend(dpScout.mVerticalPos, dpScout.mCurrentRowPosition, cmp);
}
// ----------------------------------------------------------------------------
// Function _scoutBestScore() [SimdAlignEqualLength]
// ----------------------------------------------------------------------------
template <typename TDPCell,
typename TTraceMatrixNavigator,
typename TIsLastColumn,
typename TIsLastRow>
inline void
_scoutBestScore(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> > & dpScout,
TDPCell const & activeCell,
TTraceMatrixNavigator const & navigator,
TIsLastColumn const & /**/,
TIsLastRow const & /**/)
{
using TMatrixType = typename MatrixType<TTraceMatrixNavigator>::Type;
auto cmp = cmpGt(_scoreOfCell(activeCell), _scoreOfCell(dpScout._maxScore));
_copySimdCell(dpScout, activeCell, cmp, TMatrixType());
_updateHostPositions(dpScout, cmp, navigator, TMatrixType());
}
// ----------------------------------------------------------------------------
// Function _getCompareMask()
// ----------------------------------------------------------------------------
// Helper functions to resolve the correct tracking of cells for different
// alignment modes.
// Standard global alignment.
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
True const & /*lastCol*/,
True const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, False>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return ((dpScout.state->endPosVecH) == createVector<TSimdVec>(dpScout.state->posH)) &
((dpScout.state->endPosVecV) == createVector<TSimdVec>(dpScout.state->posV));
}
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, False>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdMaskVec = typename SimdMaskVector<typename TTraits::TSimdVector>::Type;
return createVector<TSimdMaskVec>(0);
}
// Tracking the last row is enabled
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, False>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) == (dpScout.state->endPosVecV));
}
// ----------------------------------------------------------------------------
// Function _getCompareMask()
// ----------------------------------------------------------------------------
// Helper functions to resolve the correct tracking of cells for different
// alignment modes.
// Standard global alignment.
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
True const & /*lastCol*/,
True const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, False>>,
TGapModel, TTraceConfig> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return ((dpScout.state->endPosVecH) == createVector<TSimdVec>(dpScout.state->posH)) &
((dpScout.state->endPosVecV) == createVector<TSimdVec>(dpScout.state->posV));
}
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, False>>,
TGapModel, TTraceConfig> const &)
{
using TSimdMaskVec = typename SimdMaskVector<typename TTraits::TSimdVector>::Type;
return createVector<TSimdMaskVec>(0);
}
// Tracking the last row is enabled
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, False>>,
TGapModel, TTraceConfig> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) == (dpScout.state->endPosVecV));
}
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
TIsLastColumn const & /*lastCol*/,
False const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, False>>,
TGapModel, TTraceConfig> const &)
{
using TSimdMaskVec = typename SimdMaskVector<typename TTraits::TSimdVector>::Type;
return createVector<TSimdMaskVec>(0);
}
// Tracking if the last column is enabled
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, True>>,
TGapModel, TTraceConfig> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) == (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV));
}
template <typename TDPCell, typename TTraits,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
False const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, True>>,
TGapModel, TTraceConfig> const &)
{
using TSimdMaskVec = typename SimdMaskVector<typename TTraits::TSimdVector>::Type;
return createVector<TSimdMaskVec>(0);
}
// Tracking if the last column and last row is enabled
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
True const & /*lastCol*/,
True const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return ((createVector<TSimdVec>(dpScout.state->posH) == (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV))) |
((createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) == (dpScout.state->endPosVecV)));
}
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
False const & /*lastCol*/,
True const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) == (dpScout.state->endPosVecV));
}
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
True const & /*lastCol*/,
False const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) == (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV));
}
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
False const & /*lastCol*/,
False const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig> const &)
{
using TSimdMaskVec = typename SimdMaskVector<typename TTraits::TSimdVector>::Type;
return createVector<TSimdMaskVec>(0);
}
// If local alignment.
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TAlgoSpec, typename TGapModel, typename TTraceConfig>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<LocalAlignment_<TAlgoSpec>, TGapModel, TTraceConfig> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV));
}
// ----------------------------------------------------------------------------
// Function _scoutBestScore() [SimdAlignVariableLength]
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
TIsLastColumn const & /*lastCol*/,
False const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, False>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdMaskVec = typename SimdMaskVector<typename TTraits::TSimdVector>::Type;
return createVector<TSimdMaskVec>(0);
}
// Tracking if the last column is enabled
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, True>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) == (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV));
}
template <typename TDPCell, typename TTraits,
typename TIsLastRow,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
False const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, False, True>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return createVector<TSimdVec>(0);
}
// Tracking if the last column and last row is enabled
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
True const & /*lastCol*/,
True const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return ((createVector<TSimdVec>(dpScout.state->posH) == (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV))) |
((createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) == (dpScout.state->endPosVecV)));
}
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
False const & /*lastCol*/,
True const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) == (dpScout.state->endPosVecV));
}
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
True const & /*lastCol*/,
False const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) == (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV));
}
template <typename TDPCell, typename TTraits,
typename TTop, typename TLeft, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & /*dpScout*/,
False const & /*lastCol*/,
False const & /*lastRow*/,
DPProfile_<GlobalAlignment_<FreeEndGaps_<TTop, TLeft, True, True>>,
TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdMaskVec = typename SimdMaskVector<typename TTraits::TSimdVector>::Type;
return createVector<TSimdMaskVec>(0);
}
// If local alignment.
template <typename TDPCell, typename TTraits,
typename TIsLastColumn,
typename TIsLastRow,
typename TAlgoSpec, typename TGapModel, typename TTraceConfig, typename TExecPolicy>
inline auto _getCompareMask(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & dpScout,
TIsLastColumn const & /*lastCol*/,
TIsLastRow const & /*lastRow*/,
DPProfile_<LocalAlignment_<TAlgoSpec>, TGapModel, TTraceConfig, TExecPolicy> const &)
{
using TSimdVec = typename TTraits::TSimdVector;
return (createVector<TSimdVec>(dpScout.state->posH) <= (dpScout.state->endPosVecH)) &
(createVector<TSimdVec>(dpScout.state->posV) <= (dpScout.state->endPosVecV));
}
// ----------------------------------------------------------------------------
// Function _scoutBestScore() [SimdAlignVariableLength]
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TTraits,
typename TTraceMatrixNavigator,
typename TIsLastColumn,
typename TIsLastRow>
inline void
_scoutBestScore(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & dpScout,
TDPCell const & activeCell,
TTraceMatrixNavigator const & navigator,
TIsLastColumn const & /**/,
TIsLastRow const & /**/)
{
using TMatrixType = typename MatrixType<TTraceMatrixNavigator>::Type;
auto mask = cmpGt(_scoreOfCell(activeCell), _scoreOfCell(dpScout._maxScore)) &
_getCompareMask(dpScout, TIsLastColumn{}, TIsLastRow{}, typename TTraits::TDPProfile{});
_copySimdCell(dpScout, activeCell, mask, TMatrixType());
_updateHostPositions(dpScout, mask, navigator, TMatrixType());
}
// ----------------------------------------------------------------------------
// Function maxHostCoordinate()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TScoutSpec,
typename TDimension>
inline auto
maxHostCoordinate(DPScout_<TDPCell, SimdAlignmentScout<TScoutSpec> > const & dpScout,
TDimension const dimension)
{
return (dimension == DPMatrixDimension_::HORIZONTAL) ? dpScout.mHorizontalPos[dpScout._simdLane] :
dpScout.mVerticalPos[dpScout._simdLane];
}
template <typename TDPCell, typename TScoutSpec>
inline auto
maxHostCoordinates(DPScout_<TDPCell, SimdAlignmentScout<TScoutSpec> > const & dpScout)
{
return std::make_pair(maxHostCoordinate(dpScout, DPMatrixDimension_::HORIZONTAL),
maxHostCoordinate(dpScout, DPMatrixDimension_::VERTICAL));
}
// ----------------------------------------------------------------------------
// Function maxScoreAt()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TScoutSpec>
inline auto
maxScoreAt(DPScout_<TDPCell, SimdAlignmentScout<TScoutSpec> > const & dpScout)
{
return maxScore(dpScout)[dpScout._simdLane];
}
// ----------------------------------------------------------------------------
// Function maxHostPosition()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TScoutSpec>
[[deprecated("Use maxHostCoordinate instead!")]] auto
maxHostPosition(DPScout_<TDPCell, SimdAlignmentScout<TScoutSpec> > const & /*unused*/)
{}
// ----------------------------------------------------------------------------
// Function _setSimdLane()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TScoutSpec, typename TPosition>
inline void
_setSimdLane(DPScout_<TDPCell, TScoutSpec> & dpScout, TPosition const pos)
{
dpScout._simdLane = pos;
}
// ----------------------------------------------------------------------------
// Function _preInitScoutHorizontal()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TPosition>
inline void
_preInitScoutHorizontal(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> > & scout,
TPosition const offset = 0)
{
using TSimdVec = decltype(scout.mCurrentColumnPosition);
scout.mCurrentColumnPosition = createVector<TSimdVec>(offset);
}
template <typename TDPCell, typename TTraits, typename TPosition>
inline void
_preInitScoutHorizontal(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout,
TPosition const offset = 0)
{
using TSimdVec = decltype(scout.mCurrentColumnPosition);
scout.mCurrentColumnPosition = createVector<TSimdVec>(offset);
goBegin(scout.state->nextEndsH);
scout.state->posH = 0;
}
// ----------------------------------------------------------------------------
// Function _preInitScoutVertical()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TPosition>
inline void
_preInitScoutVertical(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> > & scout,
TPosition const offset)
{
using TSimdVec = decltype(scout.mCurrentRowPosition);
scout.mCurrentRowPosition = createVector<TSimdVec>(offset);
}
template <typename TDPCell, typename TTraits, typename TPosition>
inline void
_preInitScoutVertical(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout,
TPosition const offset)
{
using TSimdVec = decltype(scout.mCurrentRowPosition);
scout.mCurrentRowPosition = createVector<TSimdVec>(offset);
// scout.state->updateMasks();
goBegin(scout.state->nextEndsV);
scout.state->posV = 0;
}
// ----------------------------------------------------------------------------
// Function _reachedHorizontalEndPoint()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TTraits, typename TIter>
inline bool
_reachedHorizontalEndPoint(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout,
TIter const & hIt)
{
return *(scout.state->nextEndsH) == position(hIt) + 1;
}
// ----------------------------------------------------------------------------
// Function _reachedVerticalEndPoint()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TTraits, typename TIter>
inline bool
_reachedVerticalEndPoint(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout,
TIter const & vIt)
{
return *(scout.state->nextEndsV) == position(vIt) + 1;
}
// ----------------------------------------------------------------------------
// Function _nextHorizontalEndPos()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TTraits>
inline void
_nextHorizontalEndPos(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout)
{
++scout.state->nextEndsH;
}
// ----------------------------------------------------------------------------
// Function _nextVerticalEndPos()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TTraits>
inline void
_nextVerticalEndPos(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout)
{
++scout.state->nextEndsV;
}
// ----------------------------------------------------------------------------
// Function _incHorizontalPos()
// ----------------------------------------------------------------------------
template <typename TDPCell>
inline void
_incHorizontalPos(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> > & scout)
{
using TDPScout = DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> >;
scout.mCurrentColumnPosition += createVector<typename TDPScout::TSimdVec>(1);
}
template <typename TDPCell, typename TTraits>
inline void
_incHorizontalPos(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout)
{
using TDPScout = DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > >;
scout.mCurrentColumnPosition += createVector<typename TDPScout::TSimdVec>(1);
++scout.state->posH;
}
// ----------------------------------------------------------------------------
// Function _incVerticalPos()
// ----------------------------------------------------------------------------
template <typename TDPCell>
inline void
_incVerticalPos(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> > & scout)
{
using TDPScout = DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> >;
scout.mCurrentRowPosition += createVector<typename TDPScout::TSimdVec>(1);
}
template <typename TDPCell, typename TTraits>
inline void
_incVerticalPos(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > & scout)
{
using TDPScout = DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > >;
scout.mCurrentRowPosition += createVector<typename TDPScout::TSimdVec>(1);
++scout.state->posV;
}
// ----------------------------------------------------------------------------
// Function _hostLengthH()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TSeqH>
inline auto
_hostLengthH(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> > const & /*scout*/,
TSeqH const & seqH)
{
return length(seqH);
}
template <typename TDPCell, typename TTraits, typename TSeqH>
inline auto
_hostLengthH(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & scout,
TSeqH const & /*seqH*/)
{
using TInnerValue = typename Value<typename TTraits::TSimdVector>::Type;
return static_cast<TInnerValue>(scout.state->endPosVecH[scout._simdLane]);
}
// ----------------------------------------------------------------------------
// Function _hostLengthV()
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TSeqV>
inline auto
_hostLengthV(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignEqualLength> > const & /*scout*/,
TSeqV const & seqV)
{
return length(seqV);
}
template <typename TDPCell, typename TTraits, typename TSeqV>
inline auto
_hostLengthV(DPScout_<TDPCell, SimdAlignmentScout<SimdAlignVariableLength<TTraits> > > const & scout,
TSeqV const & /*seqV*/)
{
using TInnerValue = typename Value<typename TTraits::TSimdVector>::Type;
return static_cast<TInnerValue>(scout.state->endPosVecV[scout._simdLane]);
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SIMD_DP_SCOUT_SIMD_H_
|
