-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathProfile.hpp
10502 lines (9487 loc) · 384 KB
/
Profile.hpp
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
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/**
* \file Profile.hpp
* \author D'Oleris Paul Thatcher Edlefsen [email protected]
* \par Library:
* \brief
* Class definition for the Galosh Profile HMM class.
*
* A Profile is a data
* structure for the model parameters. Conceptually, for every position
* of the profile there are a bunch of parameters for each kind of Plan 7
* profile transition/emission. We make this a vector of maps from
* ProfileKeys (eg. Transition) to maps from ProfileKey-specific params
* (eg. Transition_M_to_D) to the values of those params.
*
* Also defines dirichlet priors for each set of profile parameters.
*
* More about Plan7 can be found at
* http://www.csb.yale.edu/userguides/seq/hmmer/docs/node11.html
* (or any other HMMER docs mirror, node 11)
* \par Overview:
* This file is part of prolific, a library of useful C++ classes for
* working with genomic sequence data and Profile HMMs. Please see the
* document CITING, which should have been included with this file. You may
* use at will, subject to the license (Apache v2.0), but *please cite the
* relevant papers* in your documentation and publications associated with
* uses of this library. Thank you!
*
* \copyright © 2008, 2011 by Paul T. Edlefsen, Fred Hutchinson Cancer
* Research Center.
* \par License:
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*****************************************************************************/
#if _MSC_VER > 1000
#pragma once
#endif
#ifndef __GALOSH_PROFILE_HPP__
#define __GALOSH_PROFILE_HPP__
#include "Prolific.hpp"
#include "ProfileHMM.hpp"
#include "Parameters.hpp"
#include "MultinomialDistribution.hpp"
#include "Sequence.hpp"
#include <string>
using std::string;
#include <iostream>
using std::cerr;
using std::cout;
using std::endl;
#include <sstream>
#include <fstream>
#include <map>
using std::map;
#include <vector>
using std::vector;
#include <boost/serialization/nvp.hpp>
#include <boost/serialization/utility.hpp>
#include <boost/serialization/vector.hpp>
#include <boost/serialization/version.hpp>
#include <boost/lexical_cast.hpp>
// TODO: REMOVE
//#include <cassert>
#include <seqan/basic.h>
/// Note that in the ProfileTreeRoot code we differentiate between size(), which returns the
/// actual underlying size of the vector that holds the ProfilePositions, and length(), which
/// might be overridden to return something other than size() (as it is in the case of the
/// PositionEntente in DynamicProgramming.hpp). Also for this reason we differentiate between
/// operator[] (which might be overridden) and vector<ProfilePosition<ResidueType, ProbabilityType> >\::operator[]
/// (which always returns the corresponding index into the underlying array).
namespace galosh {
// TODO: I want to support global parameter sets as well as missing values.
struct profile_distribution_tag
{
// Identifying tag for profile distributions.
};
struct profile_transition_distribution_tag : public profile_distribution_tag
{
// Identifying tag for transition distributions.
};
struct profile_Match_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the Match state.
};
struct profile_Insertion_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the Insertion state.
};
struct profile_Deletion_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the Deletion state.
};
struct profile_PreAlign_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the PreAlign (N) state.
};
struct profile_Begin_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the Begin (B) state.
};
#ifdef USE_END_DISTRIBUTION
struct profile_End_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the End (E) state.
};
#endif // USE_END_DISTRIBUTION
struct profile_PostAlign_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the PostAlign (C) state.
};
struct profile_Loop_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the Loop (J) state.
};
#ifdef USE_DEL_IN_DEL_OUT
struct profile_DeletionIn_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the DeletionIn (Z) state.
};
struct profile_DeletionOut_distribution_tag :
public profile_transition_distribution_tag
{
// Identifying tag for the transition distribution from the DeletionOut (W) state.
};
#endif // USE_DEL_IN_DEL_OUT
struct profile_emission_distribution_tag : public profile_distribution_tag
{
// Identifying tag for emission distributions.
};
struct profile_Match_emission_distribution_tag : public profile_emission_distribution_tag
{
// Identifying tag for match emission distributions.
};
struct profile_Insertion_emission_distribution_tag : public profile_emission_distribution_tag
{
// Identifying tag for Insertion emission distributions.
};
struct profile_PreAlign_emission_distribution_tag :
public profile_emission_distribution_tag
{
// Identifying tag for PreAlign Insertion emission distributions.
};
struct profile_PostAlign_emission_distribution_tag :
public profile_emission_distribution_tag
{
// Identifying tag for PostAlign Insertion emission distributions.
};
class Emission : public profile_emission_distribution_tag
{
public:
static profile_Match_emission_distribution_tag const Match;
static profile_Insertion_emission_distribution_tag const Insertion;
static profile_PreAlign_emission_distribution_tag const PreAlignInsertion;
static profile_PostAlign_emission_distribution_tag const PostAlignInsertion;
Emission ()
{
// Do nothing.
} // <init>()
}; // End class galosh::Emission
const profile_Match_emission_distribution_tag Emission::Match =
profile_Match_emission_distribution_tag();
const profile_Insertion_emission_distribution_tag Emission::Insertion =
profile_Insertion_emission_distribution_tag();
const profile_PreAlign_emission_distribution_tag Emission::PreAlignInsertion =
profile_PreAlign_emission_distribution_tag();
const profile_PostAlign_emission_distribution_tag Emission::PostAlignInsertion =
profile_PostAlign_emission_distribution_tag();
//////////////
// These are holdovers to keep the old DynamicProgramming.hpp stuff happy.
class TransitionFromMatch
{
public:
static const galosh::StateLabelTransitionTargets<galosh::MatchStateLabel, galosh::Plan7>::Type toMatch, toInsertion, toDeletion;
#ifdef USE_DEL_IN_DEL_OUT
static const galosh::StateLabelTransitionTargets<galosh::MatchStateLabel, galosh::Plan7>::Type toDeletionOut;
#endif // USE_DEL_IN_DEL_OUT
}; // End class galosh::TransitionFromMatch
galosh::StateLabelTransitionTargets<galosh::MatchStateLabel, galosh::Plan7>::Type const
TransitionFromMatch::toMatch( 'M' ),
TransitionFromMatch::toInsertion( 'I' ),
TransitionFromMatch::toDeletion( 'D' );
#ifdef USE_DEL_IN_DEL_OUT
galosh::StateLabelTransitionTargets<galosh::MatchStateLabel, galosh::Plan7>::Type const
TransitionFromMatch::toDeletionOut( 'W' );
#endif // USE_DEL_IN_DEL_OUT
class TransitionFromInsertion
{
public:
static const galosh::StateLabelTransitionTargets<galosh::InsertionStateLabel, galosh::Plan7>::Type toMatch, toInsertion;
}; // End class galosh::TransitionFromInsertion
galosh::StateLabelTransitionTargets<galosh::InsertionStateLabel, galosh::Plan7>::Type const
TransitionFromInsertion::toMatch( 'M' ),
TransitionFromInsertion::toInsertion( 'I' );
class TransitionFromDeletion
{
public:
static const galosh::StateLabelTransitionTargets<galosh::DeletionStateLabel, galosh::Plan7>::Type toMatch, toDeletion;
}; // End class galosh::TransitionFromDeletion
galosh::StateLabelTransitionTargets<galosh::DeletionStateLabel, galosh::Plan7>::Type const
TransitionFromDeletion::toMatch( 'M' ),
TransitionFromDeletion::toDeletion( 'D' );
class TransitionFromPreAlign
{
public:
static const galosh::StateLabelTransitionTargets<galosh::PreAlignStateLabel, galosh::Plan7>::Type toPreAlign, toBegin;
}; // End class galosh::TransitionFromPreAlign
galosh::StateLabelTransitionTargets<galosh::PreAlignStateLabel, galosh::Plan7>::Type const
TransitionFromPreAlign::toPreAlign( 'N' ),
TransitionFromPreAlign::toBegin( 'B' );
class TransitionFromBegin
{
public:
static const galosh::StateLabelTransitionTargets<galosh::BeginStateLabel, galosh::Plan7>::Type toMatch, toDeletion;
#ifdef USE_DEL_IN_DEL_OUT
static const galosh::StateLabelTransitionTargets<galosh::BeginStateLabel, galosh::Plan7>::Type toDeletionIn;
#endif // USE_DEL_IN_DEL_OUT
}; // End class galosh::TransitionFromBegin
galosh::StateLabelTransitionTargets<galosh::BeginStateLabel, galosh::Plan7>::Type const
TransitionFromBegin::toMatch( 'M' ),
TransitionFromBegin::toDeletion( 'D' );
#ifdef USE_DEL_IN_DEL_OUT
galosh::StateLabelTransitionTargets<galosh::BeginStateLabel, galosh::Plan7>::Type const
TransitionFromBegin::toDeletionIn( 'Z' );
#endif // USE_DEL_IN_DEL_OUT
#ifdef USE_END_DISTRIBUTION
class TransitionFromEnd
{
public:
static const galosh::StateLabelTransitionTargets<galosh::EndStateLabel, galosh::Plan7>::Type toPostAlign, toLoop;
}; // End class galosh::TransitionFromEnd
galosh::StateLabelTransitionTargets<galosh::EndStateLabel, galosh::Plan7>::Type const
TransitionFromEnd::toPostAlign( 'C' ),
TransitionFromEnd::toLoop( 'J' );
#endif // USE_END_DISTRIBUTION
class TransitionFromPostAlign
{
public:
static const galosh::StateLabelTransitionTargets<galosh::PostAlignStateLabel, galosh::Plan7>::Type toPostAlign, toTerminal;
}; // End class galosh::TransitionFromPostAlign
galosh::StateLabelTransitionTargets<galosh::PostAlignStateLabel, galosh::Plan7>::Type const
TransitionFromPostAlign::toPostAlign( 'C' ),
TransitionFromPostAlign::toTerminal( 'T' );
#ifdef USE_DEL_IN_DEL_OUT
class TransitionFromDeletionIn
{
public:
static const galosh::StateLabelTransitionTargets<galosh::DeletionInStateLabel, galosh::Plan7>::Type toDeletionIn, toMatch;
}; // End class galosh::TransitionFromDeletionIn
galosh::StateLabelTransitionTargets<galosh::DeletionInStateLabel, galosh::Plan7>::Type const
TransitionFromDeletionIn::toDeletionIn( 'Z' ),
TransitionFromDeletionIn::toMatch( 'M' );
class TransitionFromDeletionOut
{
public:
static const galosh::StateLabelTransitionTargets<galosh::DeletionOutStateLabel, galosh::Plan7>::Type toDeletionOut, toEnd;
}; // End class galosh::TransitionFromDeletionOut
galosh::StateLabelTransitionTargets<galosh::DeletionOutStateLabel, galosh::Plan7>::Type const
TransitionFromDeletionOut::toDeletionOut( 'W' ),
TransitionFromDeletionOut::toEnd( 'E' );
#endif // USE_DEL_IN_DEL_OUT
// End TransitionFrom ...
//////////////
class Transition : public profile_transition_distribution_tag
{
#define TRANSITION_CONSTS( state ) \
class From ## state : public profile_ ## state ## _distribution_tag \
{ \
public: \
From ## state () \
{ \
} /* <init>() */ \
}; /* End inner class Transition::From ## state */ \
static From ## state const from ## state;
public:
TRANSITION_CONSTS( Match )
TRANSITION_CONSTS( Insertion )
TRANSITION_CONSTS( Deletion )
TRANSITION_CONSTS( PreAlign )
TRANSITION_CONSTS( Begin )
#ifdef USE_END_DISTRIBUTION
TRANSITION_CONSTS( End )
#endif // USE_END_DISTRIBUTION
TRANSITION_CONSTS( PostAlign )
TRANSITION_CONSTS( Loop )
#ifdef USE_DEL_IN_DEL_OUT
TRANSITION_CONSTS( DeletionIn )
TRANSITION_CONSTS( DeletionOut )
#endif // USE_DEL_IN_DEL_OUT
Transition ()
{
// Do nothing.
} // <init>()
}; // End class galosh::Transition
/**
* This static template fn applies to anything that supports the operator[](
* tag ) method. Calculate and return the probability that if
* you drew one emission from each object, the emission from the given first
* object would be identical to the emission from the given second object,
* using the emission values of the two objects as the relevant
* probabilities. Note that this is symmetric, so the order of the arguments
* does not matter.
*/
template <typename ProbabilityType,
typename EmissionContainerType1,
typename EmissionContainerType2,
typename EmissionType>
static inline
ProbabilityType
calculateEmissionCooccurrenceProbability (
EmissionContainerType1 const & obj1,
EmissionContainerType2 const & obj2,
EmissionType const & tag
)
{
return
obj1[ tag ].calculateExpectedValue(
obj2[ tag ]
);
} // static template ProbabilityType calculateEmissionCooccurrenceProbability ( EmissionContainerType1 const&, EmissionContainerType2 const&, EmissionType const & )
// Forward declarations
//template <typename InternalNodeOrRoot> class ProfileTreeNode;
template <typename ResidueType, typename ProbabilityType> class ProfileTreeRoot;
template <typename ResidueType, typename ProbabilityType> class ProfileTreeInternalNode;
template <typename ProfileType> struct profile_traits;
template <typename ScoreType, typename ParameterCollectionType> class ScalableParameterCollection;
// Declarations and accessors for the transition parameter collections
#define GALOSH_OPERATOR_DECLARE_TRANSITION( probability_type, state ) \
/*protected: */ \
public: \
galosh::MultinomialDistribution<galosh::StateLabelTransitionTargets< state ## StateLabel, galosh::Plan7>::Type, probability_type> m_ ## state ## _Distribution; \
public: \
galosh::MultinomialDistribution<galosh::StateLabelTransitionTargets< state ## StateLabel, galosh::Plan7>::Type, probability_type> & \
operator[] ( profile_ ## state ## _distribution_tag const ) \
{ \
return m_ ## state ## _Distribution; \
} /* operator[] ( profile_ ## state ## _distribution_tag const ) */ \
galosh::MultinomialDistribution<galosh::StateLabelTransitionTargets< state ## StateLabel, galosh::Plan7>::Type, probability_type> const& \
operator[] ( profile_ ## state ## _distribution_tag const ) const\
{ \
return m_ ## state ## _Distribution; \
} /* operator[] ( profile_ ## state ## _distribution_tag const ) */ \
// Accessors for derived classes of the transition parameter collections
#define GALOSH_OPERATOR_TRANSITION( collection_type, probability_type, state ) \
public: \
galosh::MultinomialDistribution<galosh::StateLabelTransitionTargets< state ## StateLabel, galosh::Plan7>::Type, probability_type> & \
operator[] ( profile_ ## state ## _distribution_tag const tag ) \
{ \
return this->collection_type<ResidueType, probability_type>::operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _distribution_tag const ) */ \
galosh::MultinomialDistribution<galosh::StateLabelTransitionTargets< state ## StateLabel, galosh::Plan7>::Type, probability_type> const& \
operator[] ( profile_ ## state ## _distribution_tag const tag ) const\
{ \
return this->collection_type<ResidueType, probability_type>::operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _distribution_tag const ) */ \
// Accessors for classes delegating to a transition parameter collection
#define GALOSH_OPERATOR_DELEGATING_TRANSITION( obj, probability_type, state ) \
public: \
galosh::MultinomialDistribution<galosh::StateLabelTransitionTargets< state ## StateLabel, galosh::Plan7>::Type, probability_type> & \
operator[] ( profile_ ## state ## _distribution_tag const tag ) \
{ \
return obj .operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _distribution_tag const ) */ \
galosh::MultinomialDistribution<galosh::StateLabelTransitionTargets< state ## StateLabel, galosh::Plan7>::Type, probability_type> const& \
operator[] ( profile_ ## state ## _distribution_tag const tag ) const\
{ \
return obj .operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _distribution_tag const ) */ \
// Declarations and accessors for the emission parameter collections
#define GALOSH_OPERATOR_DECLARE_EMISSION( state, probability_type ) \
/* protected: */ \
public: \
MultinomialDistribution<ResidueType, probability_type> m_ ## state ## _Emission_Distribution; \
GALOSH_OPERATOR_DECLARE_EMISSION_OPERATORS( state, state, probability_type )
#define GALOSH_OPERATOR_DECLARE_EMISSION_OPERATORS( tag_state, dist_state, probability_type ) \
public: \
galosh::MultinomialDistribution<ResidueType, probability_type> & \
operator[] ( profile_ ## tag_state ## _emission_distribution_tag const ) \
{ \
return m_ ## dist_state ## _Emission_Distribution; \
} /* operator[] ( profile_ ## tag_state ## _emission_distribution_tag const ) */ \
galosh::MultinomialDistribution<ResidueType, probability_type> const& \
operator[] ( profile_ ## tag_state ## _emission_distribution_tag const ) const\
{ \
return m_ ## dist_state ## _Emission_Distribution; \
} /* operator[] ( profile_ ## tag_state ## _emission_distribution_tag const ) */ \
// TODO: REMOVE? TESTING.
#define GALOSH_OPERATOR_DECLARE_EMISSION_USEINSERTION( state, probability_type ) \
/* protected: */ \
public: \
MultinomialDistribution<ResidueType, probability_type> m_ ## state ## _Emission_Distribution;
// Accessors for derived classes of the emission parameter collections
#define GALOSH_OPERATOR_EMISSION( collection_type, state, probability_type ) \
public: \
galosh::MultinomialDistribution<ResidueType, probability_type> & \
operator[] ( profile_ ## state ## _emission_distribution_tag const tag ) \
{ \
return this->collection_type<ResidueType, probability_type>::operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _emission_distribution_tag const ) */ \
galosh::MultinomialDistribution<ResidueType, probability_type> const& \
operator[] ( profile_ ## state ## _emission_distribution_tag const tag ) const\
{ \
return this->collection_type<ResidueType, probability_type>::operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _emission_distribution_tag const ) */ \
// Accessors for classes delegating to an emission parameter collection
#define GALOSH_OPERATOR_DELEGATING_EMISSION( obj, state, probability_type ) \
public: \
galosh::MultinomialDistribution<ResidueType, probability_type> & \
operator[] ( profile_ ## state ## _emission_distribution_tag const tag ) \
{ \
return obj .operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _emission_distribution_tag const ) */ \
galosh::MultinomialDistribution<ResidueType, probability_type> const& \
operator[] ( profile_ ## state ## _emission_distribution_tag const tag ) const\
{ \
return obj .operator[]( tag ); \
} /* operator[] ( profile_ ## state ## _emission_distribution_tag const ) */ \
/**
* These are the emission parameters for the Match distribution.
*/
template <typename ResidueType, typename ProbabilityType>
class MatchEmissionParameters
{
// Boost serialization
private:
friend class boost::serialization::access;
template<class Archive>
void serialize ( Archive & ar, const unsigned int /* file_version */ )
{
ar & BOOST_SERIALIZATION_NVP( m_Match_Emission_Distribution );
} // serialize( Archive &, const unsigned int )
protected:
// Accessors and declarations for emissions
GALOSH_OPERATOR_DECLARE_EMISSION( Match, ProbabilityType )
// Accessors for derived classes
#define GALOSH_OPERATORS_MatchEmissionParameters( probability_type ) \
GALOSH_OPERATOR_EMISSION( MatchEmissionParameters, Match, probability_type ) \
// Accessors for delegating classes
#define GALOSH_OPERATORS_DELEGATING_MatchEmissionParameters( obj, probability_type ) \
GALOSH_OPERATOR_DELEGATING_EMISSION( obj, Match, probability_type ) \
public:
MatchEmissionParameters ();
template <typename AnyProbabilityType>
MatchEmissionParameters (
MatchEmissionParameters<ResidueType, AnyProbabilityType> const & copy_from
);
MatchEmissionParameters (
MatchEmissionParameters const & copy_from
);
void
reinitialize ();
template <typename AnyProbabilityType>
MatchEmissionParameters<ResidueType, ProbabilityType> &
operator= ( MatchEmissionParameters<ResidueType, AnyProbabilityType> const& other_pos );
MatchEmissionParameters<ResidueType, ProbabilityType> &
operator= ( MatchEmissionParameters<ResidueType, ProbabilityType> const& other_pos );
template <typename AnyProbabilityType>
void
copyFrom ( MatchEmissionParameters<ResidueType, AnyProbabilityType> const& other_pos );
/**
* Divide each contained distribution value by denominator. Note that
* this violates the rule that the probabilities sum to 1.
*/
template <typename AnyProbabilityType>
MatchEmissionParameters &
operator/= ( AnyProbabilityType const& denominator );
/**
* Multiply each contained distrubution value by scalar. Note that
* this violates the rule that the probabilities sum to 1.
*/
template <typename AnyProbabilityType>
MatchEmissionParameters<ResidueType, ProbabilityType> &
operator*= ( AnyProbabilityType const& scalar );
/**
* Add to each contained distribution the values in the given other
* MatchEmissionParameters. Note that this violates the rule
* that the probabilities sum to 1.
*/
template <typename AnyProbabilityType>
MatchEmissionParameters<ResidueType, ProbabilityType> &
operator+= ( MatchEmissionParameters<ResidueType, AnyProbabilityType> const& other_pos );
/**
* Subtract from each contained distribution the values in the given other
* MatchEmissionParameters. Note that this may violate the rule that the
* probabilities are greater than 0.
*/
template <typename AnyProbabilityType>
MatchEmissionParameters<ResidueType, ProbabilityType> &
operator-= ( MatchEmissionParameters<ResidueType, AnyProbabilityType> const& other_pos );
/**
* Calculate and return the cross entropy E(-log(other_pos)). Note that
* the cross entropy is non-symmetric (calling other_pos.crossEntropy(
* *this ) will return a different value).
*
* This can be used to calculate the (self-)entropy by calling
* this->crossEntropy( *this ). It can also be used to calculate the KL
* divergence by taking the difference of the cross-entropy and the
* self-entropy, or the symmeterized KL divergence by summing the KL
* divergences computed both ways.
*
* See also the other crossEntropy method, which accepts a weights argument.
*/
template <typename AnyProbabilityType>
double
crossEntropy (
MatchEmissionParameters<ResidueType, AnyProbabilityType> const& other_pos
) const;
/**
* Calculate and return the (possibly weighted) cross entropy
* E(-log(other_pos)). The weights (if non-null) may be of any type
* convertible to a double, and the cross entropy will be computed as
* E(-log(weights*other_pos)). Note that the cross entropy is
* non-symmetric (calling other_pos.crossEntropy( *this, weights ) will
* return a different value).
*
* This can be used to calculate the (possibly weighted) (self-)entropy by
* calling this->crossEntropy( *this, weights ). It can also be used to
* calculate the KL divergence by taking the difference of the
* cross-entropy and the self-entropy, or the symmeterized KL divergence by
* summing the KL divergences computed both ways. Note, though, that
* weights should all be the same within any Multinomial distribution if
* this is to be used to calculate weighted entropies or KL divergences.
* Otherwise the usual properties of these metrics will be violated.
*/
template <typename AnyProbabilityType,
typename AnyMatchEmissionParametersType>
double
crossEntropy (
MatchEmissionParameters<ResidueType, AnyProbabilityType> const& other_pos,
AnyMatchEmissionParametersType const * const weights
) const;
/**
* Calculate and return the Euclidean distance between this set of emission
* parameters and another set (treating every probability as an orthogonal
* dimension).
*/
double
euclideanDistance (
MatchEmissionParameters const& other_pos
) const;
/**
* Calculate and return the square of the Euclidean distance between this
* set of emission parameters and another set (treating every probability
* as an orthogonal dimension).
*/
double
euclideanDistanceSquared (
MatchEmissionParameters const& other_pos
) const;
/**
* How many free parameters are there? This is the sum of the free
* parameters in the contained distributions.
*/
uint32_t
freeParameterCount () const;
/**
* Set all values to 0. Note that this violates the rule that the values
* sum to 1.
*/
void
zero ();
/**
* Set all values such that each distrubution is evenly distributed.
*/
void
even ();
/**
* Calculate the total of all contained values.
*/
ProbabilityType
total () const;
/**
* Adjust each distribution's values such that they sum to one, ensuring
* that no value is less than the specified minimum.
*/
template <typename other_type>
void
normalize ( other_type const & min );
/**
* Adjust each distribution's values such that they sum to one, ensuring
* that no value is less than the specified minimum.
*/
void
normalize ( ProbabilityType const & min );
/**
* Set all values such that each distrubution is randomly distributed.
*/
void
uniform ( Random & random );
/**
* Change the probabilities of the contained Multinomials to values drawn
* from dirichlet distributions with the given counts. AnyCountType can be
* a Real type (anything coercible to a double using toDouble( count )).
*/
template <typename AnyMatchEmissionParametersType>
void
dirichlet (
AnyMatchEmissionParametersType const & counts,
Random & random
);
/**
* Set all values such that each distrubution is distributed according to
* the given DirichletMixture distribution (which should be a
* DynamicProgramming::DirichletMixtureMatchEmissionPrior class).
*/
template <typename DirichletMixtureType>
void
dirichletMixture (
DirichletMixtureType const & me_prior,
Random & random
);
/**
* Return the largest value in the contained distributions.
*/
ProbabilityType
maximumValue () const;
/**
* Stream reader.
*/
friend std::istream&
operator>> (
std::istream & is,
MatchEmissionParameters & pos
)
{
//is >> "[ ";
is.ignore( 2 );
pos.readMatchEmissionParameters( is );
//is >> " ]";
is.ignore( 2 );
return is;
} // operator>> ( istream &, MatchEmissionParameters & )
/**
* Read a comma-separated list of the parameters from the stream.
*/
void
readMatchEmissionParameters (
std::istream& is
);
/**
* Read a comma-separated list of the parameters from the stream.
*/
void
readParameterCollection (
std::istream & is
)
{
readMatchEmissionParameters( is );
} // readParameterCollection( istream & )
/**
* Stream writer.
*/
template<class CharT, class Traits>
friend std::basic_ostream<CharT,Traits>&
operator<< (
std::basic_ostream<CharT,Traits>& os,
MatchEmissionParameters const& pos
)
{
os << "[ ";
pos.writeMatchEmissionParameters( os );
os << " ]";
return os;
} // friend operator<< ( basic_ostream &, MatchEmissionParameters const& )
/**
* Write a comma-separated list of the parameters to the stream.
*/
template<class CharT, class Traits>
void writeMatchEmissionParameters (
std::basic_ostream<CharT,Traits>& os
) const;
/**
* Write a comma-separated list of the parameters to the stream.
*/
template<class CharT, class Traits>
void
writeParameterCollection (
std::basic_ostream<CharT,Traits>& os
) const
{
writeMatchEmissionParameters( os );
} // writeParameterCollection( basic_ostream & ) const
}; // End class MatchEmissionParameters
/**
* These are the emission parameters for the Insertion distribution.
*/
template <typename ResidueType, typename ProbabilityType, typename IsActualInsertionEmissionParametersType = seqan::True>
class InsertionEmissionParameters
{
// Boost serialization
private:
friend class boost::serialization::access;
template<class Archive>
void serialize ( Archive & ar, const unsigned int /* file_version */ )
{
ar & BOOST_SERIALIZATION_NVP( m_Insertion_Emission_Distribution );
} // serialize( Archive &, const unsigned int )
protected:
// Accessors and declarations for emissions
GALOSH_OPERATOR_DECLARE_EMISSION( Insertion, ProbabilityType )
#ifdef USE_FLANKING_EMISSION_DISTRIBUTIONS
// Accessors for derived classes
#define GALOSH_OPERATORS_InsertionEmissionParameters( probability_type ) \
GALOSH_OPERATOR_EMISSION( InsertionEmissionParameters, Insertion, probability_type ) \
// Accessors for delegating classes
#define GALOSH_OPERATORS_DELEGATING_InsertionEmissionParameters( obj, probability_type ) \
GALOSH_OPERATOR_DELEGATING_EMISSION( obj, Insertion, probability_type ) \
#else // !USE_FLANKING_EMISSION_DISTRIBUTIONS
GALOSH_OPERATOR_DECLARE_EMISSION_OPERATORS( PreAlign, Insertion, ProbabilityType )
GALOSH_OPERATOR_DECLARE_EMISSION_OPERATORS( PostAlign, Insertion, ProbabilityType )
// Accessors for derived classes
#define GALOSH_OPERATORS_InsertionEmissionParameters( probability_type ) \
GALOSH_OPERATOR_EMISSION( InsertionEmissionParameters, Insertion, probability_type ) \
GALOSH_OPERATOR_EMISSION( InsertionEmissionParameters, PreAlign, probability_type ) \
GALOSH_OPERATOR_EMISSION( InsertionEmissionParameters, PostAlign, probability_type ) \
// Accessors for delegating classes
#define GALOSH_OPERATORS_DELEGATING_InsertionEmissionParameters( obj, probability_type ) \
GALOSH_OPERATOR_DELEGATING_EMISSION( obj, Insertion, probability_type ) \
GALOSH_OPERATOR_DELEGATING_EMISSION( obj, PreAlign, probability_type ) \
GALOSH_OPERATOR_DELEGATING_EMISSION( obj, PostAlign, probability_type ) \
#endif // USE_FLANKING_EMISSION_DISTRIBUTIONS .. else ..
public:
InsertionEmissionParameters ();
InsertionEmissionParameters (
InsertionEmissionParameters const & copy_from
);
void
reinitialize ();
template <typename AnyProbabilityType>
InsertionEmissionParameters<ResidueType, ProbabilityType, IsActualInsertionEmissionParametersType> &
operator= ( InsertionEmissionParameters<ResidueType, AnyProbabilityType, IsActualInsertionEmissionParametersType> const& other_pos );
InsertionEmissionParameters<ResidueType, ProbabilityType, IsActualInsertionEmissionParametersType> &
operator= ( InsertionEmissionParameters<ResidueType, ProbabilityType, IsActualInsertionEmissionParametersType> const& other_pos );
template <typename AnyProbabilityType>
void
copyFrom ( InsertionEmissionParameters<ResidueType, AnyProbabilityType, IsActualInsertionEmissionParametersType> const& other_pos );
/**
* Divide each contained distrubution value by denominator. Note that
* this violates the rule that the probabilities sum to 1.
*/
template <typename AnyProbabilityType>
InsertionEmissionParameters &
operator/= ( AnyProbabilityType const& denominator );
/**
* Multiply each contained distrubution value by scalar. Note that
* this violates the rule that the probabilities sum to 1.
*/
template <typename AnyProbabilityType>
InsertionEmissionParameters<ResidueType, ProbabilityType, IsActualInsertionEmissionParametersType> &
operator*= ( AnyProbabilityType const& scalar );
/**
* Add to each contained distribution the values in the given other
* InsertionEmissionParameters. Note that this violates the rule
* that the probabilities sum to 1.
*/
template <typename AnyProbabilityType>
InsertionEmissionParameters<ResidueType, ProbabilityType, IsActualInsertionEmissionParametersType> &
operator+= ( InsertionEmissionParameters<ResidueType, AnyProbabilityType, IsActualInsertionEmissionParametersType> const& other_pos );
/**
* Subtract from each contained distribution the values in the given other
* InsertionEmissionParameters. Note that this may violate the rule that the
* probabilities are greater than 0.
*/
template <typename AnyProbabilityType>
InsertionEmissionParameters<ResidueType, ProbabilityType, IsActualInsertionEmissionParametersType> &
operator-= ( InsertionEmissionParameters<ResidueType, AnyProbabilityType, IsActualInsertionEmissionParametersType> const& other_pos );
/**
* Calculate and return the cross entropy E(-log(other_pos)). Note that
* the cross entropy is non-symmetric (calling other_pos.crossEntropy(
* *this ) will return a different value).
*
* This can be used to calculate the (self-)entropy by calling
* this->crossEntropy( *this ). It can also be used to calculate the KL
* divergence by taking the difference of the cross-entropy and the
* self-entropy, or the symmeterized KL divergence by summing the KL
* divergences computed both ways.
*
* See also the other crossEntropy method, which accepts a weights argument.
*/
template <typename AnyProbabilityType>
double
crossEntropy (
InsertionEmissionParameters<ResidueType, AnyProbabilityType, IsActualInsertionEmissionParametersType> const& other_pos
) const;
/**
* Calculate and return the (possibly weighted) cross entropy
* E(-log(other_pos)). The weights (if non-null) may be of any type
* convertible to a double, and the cross entropy will be computed as
* E(-log(weights*other_pos)). Note that the cross entropy is
* non-symmetric (calling other_pos.crossEntropy( *this, weights ) will
* return a different value).
*
* This can be used to calculate the (possibly weighted) (self-)entropy by
* calling this->crossEntropy( *this, weights ). It can also be used to
* calculate the KL divergence by taking the difference of the
* cross-entropy and the self-entropy, or the symmeterized KL divergence by
* summing the KL divergences computed both ways. Note, though, that
* weights should all be the same within any Multinomial distribution if
* this is to be used to calculate weighted entropies or KL divergences.
* Otherwise the usual properties of these metrics will be violated.
*/
template <typename AnyProbabilityType,
typename AnyInsertionEmissionParametersType>
double
crossEntropy (
InsertionEmissionParameters<ResidueType, AnyProbabilityType, IsActualInsertionEmissionParametersType> const& other_pos,
AnyInsertionEmissionParametersType const * const weights
) const;
/**
* Calculate and return the Euclidean distance between this set of emission
* parameters and another set (treating every probability as an orthogonal
* dimension).
*/
double
euclideanDistance (
InsertionEmissionParameters const& other_pos
) const;
/**
* Calculate and return the square of the Euclidean distance between this
* set of emission parameters and another set (treating every probability
* as an orthogonal dimension).
*/
double
euclideanDistanceSquared (
InsertionEmissionParameters const& other_pos
) const;
/**
* How many free parameters are there? This is the sum of the free
* paramters in the contained distributions.
*/
uint32_t
freeParameterCount () const;
/**
* Set all values to 0. Note that this violates the rule that the values
* sum to 1.
*/
void
zero ();
/**
* Set all values such that each distrubution is evenly distributed.
*/
void
even ();
/**
* Calculate the total of all contained values.
*/
ProbabilityType
total () const;
/**
* Adjust each distribution's values such that they sum to one, ensuring
* that no value is less than the specified minimum.
*/
template <typename other_type>
void
normalize ( other_type const & min );
/**
* Adjust each distribution's values such that they sum to one, ensuring
* that no value is less than the specified minimum.
*/
void normalize ( ProbabilityType const & min );
/**
* Set all values such that each distrubution is randomly distributed.
*/
void
uniform ( Random & random );