-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmscore.cpp
1944 lines (1883 loc) · 57.7 KB
/
mscore.cpp
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
/*
Copyright (C) 2003-2004 Ronald C Beavis, all rights reserved
X! tandem
This software is a component of the X! proteomics software
development project
Use of this software governed by the Artistic license, as reproduced here:
The Artistic License for all X! software, binaries and documentation
Preamble
The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some
semblance of artistic control over the development of the package,
while giving the users of the package the right to use and distribute
the Package in a more-or-less customary fashion, plus the right to
make reasonable modifications.
Definitions
"Package" refers to the collection of files distributed by the Copyright
Holder, and derivatives of that collection of files created through
textual modification.
"Standard Version" refers to such a Package if it has not been modified,
or has been modified in accordance with the wishes of the Copyright
Holder as specified below.
"Copyright Holder" is whoever is named in the copyright or copyrights
for the package.
"You" is you, if you're thinking about copying or distributing this Package.
"Reasonable copying fee" is whatever you can justify on the basis of
media cost, duplication charges, time of people involved, and so on.
(You will not be required to justify it to the Copyright Holder, but
only to the computing community at large as a market that must bear
the fee.)
"Freely Available" means that no fee is charged for the item itself,
though there may be fees involved in handling the item. It also means
that recipients of the item may redistribute it under the same
conditions they received it.
1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that
you duplicate all of the original copyright notices and associated
disclaimers.
2. You may apply bug fixes, portability fixes and other modifications
derived from the Public Domain or from the Copyright Holder. A
Package modified in such a way shall still be considered the Standard
Version.
3. You may otherwise modify your copy of this Package in any way, provided
that you insert a prominent notice in each changed file stating how and
when you changed that file, and provided that you do at least ONE of the
following:
a. place your modifications in the Public Domain or otherwise make them
Freely Available, such as by posting said modifications to Usenet
or an equivalent medium, or placing the modifications on a major
archive site such as uunet.uu.net, or by allowing the Copyright Holder
to include your modifications in the Standard Version of the Package.
b. use the modified Package only within your corporation or organization.
c. rename any non-standard executables so the names do not conflict
with standard executables, which must also be provided, and provide
a separate manual page for each non-standard executable that clearly
documents how it differs from the Standard Version.
d. make other distribution arrangements with the Copyright Holder.
4. You may distribute the programs of this Package in object code or
executable form, provided that you do at least ONE of the following:
a. distribute a Standard Version of the executables and library files,
together with instructions (in the manual page or equivalent) on
where to get the Standard Version.
b. accompany the distribution with the machine-readable source of the
Package with your modifications.
c. give non-standard executables non-standard names, and clearly
document the differences in manual pages (or equivalent), together
with instructions on where to get the Standard Version.
d. make other distribution arrangements with the Copyright Holder.
5. You may charge a reasonable copying fee for any distribution of
this Package. You may charge any fee you choose for support of
this Package. You may not charge a fee for this Package itself.
However, you may distribute this Package in aggregate with other
(possibly commercial) programs as part of a larger (possibly
commercial) software distribution provided that you do not a
dvertise this Package as a product of your own. You may embed this
Package's interpreter within an executable of yours (by linking);
this shall be construed as a mere form of aggregation, provided that
the complete Standard Version of the interpreter is so embedded.
6. The scripts and library files supplied as input to or produced as
output from the programs of this Package do not automatically fall
under the copyright of this Package, but belong to whomever generated
them, and may be sold commercially, and may be aggregated with this
Package. If such scripts or library files are aggregated with this
Package via the so-called "undump" or "unexec" methods of producing
a binary executable image, then distribution of such an image shall
neither be construed as a distribution of this Package nor shall it
fall under the restrictions of Paragraphs 3 and 4, provided that you
do not represent such an executable image as a Standard Version of
this Package.
7. C subroutines (or comparably compiled subroutines in other languages)
supplied by you and linked into this Package in order to emulate
subroutines and variables of the language defined by this Package
shall not be considered part of this Package, but are the equivalent
of input as in Paragraph 6, provided these subroutines do not change
the language in any way that would cause it to fail the regression
tests for the language.
8. Aggregation of this Package with a commercial distribution is always
permitted provided that the use of this Package is embedded; that is,
when no overt attempt is made to make this Package's interfaces visible
to the end user of the commercial distribution. Such use shall not be
construed as a distribution of this Package.
9. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.
10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
The End
*/
// File version: 2003-08-01
// File version: 2004-02-01
// File version: 2004-03-01
// File version: 2004-09-01
// File version: 2004-09-30
// File version: 2005-01-01
/*
modified December 2010 by Insilicos LLC to support object serialization for
Hadoop and MPI use
*/
/*
* mscore is the class that contains most of the logic for comparing one sequence with
* many tandem mass spectra. mprocess contains a comprehensive example of how to use an mscore
* class. mscore has been optimized for speed, without any specific modifications to take
* advantage of processor architectures.
*/
#include "stdafx.h"
#include <cmath>
#include <float.h>
#include <algorithm>
#include "msequence.h"
#include "msequencecollection.h"
#include "msequenceserver.h"
#include "msequtilities.h"
#include "mspectrum.h"
#include "xmlparameter.h"
#include "mscore.h"
#include <assert.h>
/*
* global less than operator for mspectrumdetails classes: to be used in sort operations
*/
bool lessThanDetails(const mspectrumdetails &_l,const mspectrumdetails &_r)
{
return _l.m_fL < _r.m_fL;
}
/*
* global less than operator for mi classes: to be used in sort operations to achieve
* list ordered from most intense to least intense
*/
bool lessThanMI(const mi &_l,const mi &_r)
{
return _l.m_fI > _r.m_fI;
}
mscore::mscore(void) :
m_seqUtil(masscalc::monoisotopic),
m_seqUtilAvg(masscalc::average)
{
m_pSeqUtilFrag = &m_seqUtil; // default to monoisotopic masses for fragment ions
m_bIsC = false;
m_bIsN = false;
m_pSeq = NULL;
m_lType = T_Y|T_B;
m_lErrorType = T_PARENT_DALTONS|T_FRAGMENT_DALTONS;
m_fParentErrPlus = 2.0;
m_fParentErrMinus = 2.0;
m_fErr = (float)0.45;
m_fWidth = 1.0;
m_lMaxCharge = 100;
m_dSeqMH = -1.0;
m_lSize = 256;
m_lSeqLength = 0; // bpratt 9-20-2010
m_pfSeq = new float[m_lSize];
m_plSeq = new unsigned long[m_lSize];
m_pSeq = new char[m_lSize];
m_bIsotopeError = false;
long a = 0;
while(a < 20) {
m_plCount[a] = 0;
m_pfScore[a] = 0;
a++;
}
m_fMinMass = 0.0;
m_fMaxMass = 1.0;
m_bUsePam = false;
m_bUseSaps = false; // bpratt 9/30/2010
m_fHomoError = 4.5;
m_dScale = 1.0;
m_bMini = false;
m_iCharge = 1;
}
mscore::~mscore(void)
{
if(m_pfSeq != NULL)
delete m_pfSeq;
if(m_plSeq != NULL)
delete m_plSeq;
if(m_pSeq != NULL)
delete m_pSeq;
}
bool mscore::set_mini(const bool _b)
{
m_bMini = _b;
return m_bMini;
}
/*
* allows score object to issue warnings, or set variable based on xml.
* default implementation does nothing.
*/
bool mscore::load_param(XmlParameter &_x)
{
string strKey = "spectrum, fragment mass type";
string strValue;
_x.get(strKey,strValue);
if (strValue == "average") {
set_fragment_masstype(masscalc::average);
}
return true;
}
/*
* called before spectrum conditioning to allow the score object to
* modify the spectrum in ways specific to the scoring algorithm.
* default implementation does nothing.
*/
bool mscore::precondition(mspectrum &_s)
{
return true;
}
/*
* called before scoring inside the score() function to allow any
* necessary resetting of member variables.
*/
__inline__ void mscore::prescore(const size_t _i)
{
m_lId = _i;
m_fHyper = (float)0.0;
}
bool mscore::clear()
{
m_vSpec.clear(); // vector of all spectra being considered
// for all spectra being considered
m_vDetails.clear(); // vector of mspectrumdetails objects, for looking up parent ion M+H
// values of mass spectra
m_lDetails = 0; // bpratt
return true;
}
/*
* create list of non-zero predicted intensity values for a-ions and their
* integer converted m/z values
*/
bool mscore::add_A(const unsigned long _t,const long _c)
{
unsigned long a = 0;
/*
* get the conversion factor between a straight sequence mass and an a-ion
*/
double dValue = m_pSeqUtilFrag->m_dA;
/*
* deal with protein N-terminus
*/
if(m_bIsN) {
dValue += m_pSeqUtilFrag->m_fNT;
}
/*
* deal with non-hydrolytic cleavage
*/
dValue += (m_pSeqUtilFrag->m_dCleaveN - m_pSeqUtilFrag->m_dCleaveNdefault);
if(m_Term.m_lN) {
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
}
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
unsigned long lValue = 0;
/*
* calculate the conversion factor between an m/z value and its integer value
* as referenced in m_vsmapMI
*/
char cValue = '\0';
float *pfScore = m_pSeqUtilFrag->m_pfAScore;
unsigned long lCount = 0;
/*
* from N- to C-terminus, calcuate fragment ion m/z values and store the results
* look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
*/
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a < m_lSeqLength) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
m_pfSeq[lCount] = pfScore[cValue];
lCount++;
a++;
}
/*
* set the next integer mass value to 0: this marks the end of the array
*/
m_plSeq[lCount] = 0;
return true;
}
/*
* create list of non-zero predicted intensity values for b-ions and their
* integer converted m/z values
*/
bool mscore::add_B(const unsigned long _t,const long _c)
{
unsigned long a = 0;
/*
* get the conversion factor between a straight sequence mass and a b-ion
*/
double dValue = m_pSeqUtilFrag->m_dB;
/*
* deal with protein N-terminus
*/
if(m_bIsN) {
dValue += m_pSeqUtilFrag->m_fNT;
}
/*
* deal with non-hydrolytic cleavage
*/
dValue += (m_pSeqUtilFrag->m_dCleaveN - m_pSeqUtilFrag->m_dCleaveNdefault);
if(m_Term.m_lN) {
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
}
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
unsigned long lValue = 0;
/*
* calculate the conversion factor between an m/z value and its integer value
* as referenced in m_vsmapMI
*/
char cValue = '\0';
long lCount = 0;
float *pfScore = m_pSeqUtilFrag->m_pfBScore;
float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
/*
* from N- to C-terminus, calcuate fragment ion m/z values and store the results
* look up appropriate scores from m_pSeqUtilFrag->m_pfBScore
*/
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a < m_lSeqLength-1) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
m_pfSeq[lCount] = pfScore[cValue]*pfScorePlus[m_pSeq[a+1]];
if(a == 1) {
if(m_pSeq[1] == 'P') {
m_pfSeq[lCount] *= 10;
}
else {
m_pfSeq[lCount] *= 3;
}
}
lCount++;
a++;
}
m_plSeq[lCount] = 0;
return true;
}
/*
* create list of non-zero predicted intensity values for c-ions and their
* integer converted m/z values
*/
bool mscore::add_C(const unsigned long _t,const long _c)
{
unsigned long a = 0;
/*
* get the conversion factor between a straight sequence mass and a b-ion
*/
double dValue = m_pSeqUtilFrag->m_dC;
/*
* deal with protein N-terminus
*/
if(m_bIsN) {
dValue += m_pSeqUtilFrag->m_fNT;
}
/*
* deal with non-hydrolytic cleavage
*/
dValue += (m_pSeqUtilFrag->m_dCleaveN - m_pSeqUtilFrag->m_dCleaveNdefault);
if(m_Term.m_lN) {
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
}
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
unsigned long lValue = 0;
/*
* calculate the conversion factor between an m/z value and its integer value
* as referenced in m_vsmapMI
*/
char cValue = '\0';
long lCount = 0;
float *pfScore = m_pSeqUtilFrag->m_pfBScore;
float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
/*
* from N- to C-terminus, calcuate fragment ion m/z values and store the results
* look up appropriate scores from m_pSeqUtilFrag->m_pfBScore
*/
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a < m_lSeqLength-2) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
m_pfSeq[lCount] = pfScore[cValue]*pfScorePlus[m_pSeq[a+1]];
lCount++;
a++;
}
m_plSeq[lCount] = 0;
return true;
}
/*
* create list of non-zero predicted intensity values for x-ions and their
* integer converted m/z values
*/
bool mscore::add_X(const unsigned long _t,const long _c)
{
long a = m_lSeqLength - 1;
/*
* get the conversion factor between a straight sequence mass and an x-ion
*/
double dValue = m_pSeqUtilFrag->m_dX;
/*
* deal with non-hydrolytic cleavage
*/
dValue += (m_pSeqUtilFrag->m_dCleaveC - m_pSeqUtilFrag->m_dCleaveCdefault);
if(m_Term.m_lC) {
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
}
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
/*
* deal with protein C-teminus
*/
if(m_bIsC) {
dValue += m_pSeqUtilFrag->m_fCT;
}
unsigned long lValue = 0;
/*
* calculate the conversion factor between an m/z value and its integer value
* as referenced in m_vsmapMI
*/
char cValue = '\0';
unsigned long lCount = 0;
float fSub = 0.0;
float *pfScore = m_pSeqUtilFrag->m_pfXScore;
/*
* from C- to N-terminus, calcuate fragment ion m/z values and store the results
* look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
*/
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a > 0) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
m_pfSeq[lCount] = pfScore[cValue];
lCount++;
a--;
}
/*
* set the next integer mass value to 0: this marks the end of the array
*/
m_plSeq[lCount] = 0;
return true;
}
/*
* create list of non-zero predicted intensity values for y-ions and their
* integer converted m/z values
*/
bool mscore::add_Y(const unsigned long _t,const long _c)
{
long a = m_lSeqLength - 1;
/*
* get the conversion factor between a straight sequence mass and a y-ion
*/
double dValue = m_pSeqUtilFrag->m_dY;
unsigned long lValue = 0;
/*
* deal with non-hydrolytic cleavage
*/
dValue += (m_pSeqUtilFrag->m_dCleaveC - m_pSeqUtilFrag->m_dCleaveCdefault);
if(m_Term.m_lC) {
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
}
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
/*
/*
* deal with protein C-teminus
*/
if(m_bIsC) {
dValue += m_pSeqUtilFrag->m_fCT;
}
char cValue = '\0';
unsigned long lCount = 0;
float fSub = 0.0;
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
/*
* from C- to N-terminus, calcuate fragment ion m/z values and store the results
* look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
*/
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a > 0) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
if(_t == 0) {
if(a < 5) {
m_plSeq[lCount] = lValue;
m_pfSeq[lCount] = pfScore[cValue]*pfScoreMinus[m_pSeq[a-1]];
lCount++;
}
}
else {
m_plSeq[lCount] = lValue;
m_pfSeq[lCount] = pfScore[cValue]*pfScoreMinus[m_pSeq[a-1]];
if(a == 2) {
if(m_pSeq[1] == 'P') {
m_pfSeq[lCount] *= 10;
}
else {
m_pfSeq[lCount] *= 3;
}
}
lCount++;
}
a--;
}
/*
* set the next integer mass value to 0: this marks the end of the array
*/
m_plSeq[lCount] = 0;
return true;
}
/*
* create list of non-zero predicted intensity values for y-ions and their
* integer converted m/z values
*/
bool mscore::add_Z(const unsigned long _t,const long _c)
{
long a = m_lSeqLength - 1;
/*
* get the conversion factor between a straight sequence mass and a y-ion
*/
double dValue = m_pSeqUtilFrag->m_dZ;
unsigned long lValue = 0;
/*
* deal with non-hydrolytic cleavage
*/
dValue += (m_pSeqUtilFrag->m_dCleaveC - m_pSeqUtilFrag->m_dCleaveCdefault);
if(m_Term.m_lC) {
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
}
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
/*
/*
* deal with protein C-teminus
*/
if(m_bIsC) {
dValue += m_pSeqUtilFrag->m_fCT;
}
char cValue = '\0';
unsigned long lCount = 0;
float fSub = 0.0;
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
/*
* from C- to N-terminus, calcuate fragment ion m/z values and store the results
* look up appropriate scores from m_pSeqUtilFrag->m_pfAScore
*/
const unsigned long tPos = (unsigned long) m_tSeqPos;
while(a > 0) {
cValue = m_pSeq[a];
dValue += m_pSeqUtilFrag->getAaMass(cValue, tPos+a);
lValue = mconvert(dValue, _c);
m_plSeq[lCount] = lValue;
m_pfSeq[lCount] = pfScore[cValue]*pfScoreMinus[m_pSeq[a-1]];
lCount++;
a--;
}
/*
* set the next integer mass value to 0: this marks the end of the array
*/
m_plSeq[lCount] = 0;
return true;
}
bool mscore::sort_details()
{
/*
* update the mstate object
*/
m_State.create_equals((long)m_vSpec.size());
/*
* sort the m_vDetails vector to improve efficiency at modeling the vector
*/
sort(m_vDetails.begin(),m_vDetails.end(),lessThanDetails);
/*
* store the mspectrumdetails object for the mspectrum
*/
m_lDetails = (long)m_vDetails.size();
size_t tLimit = m_vDetails.size();
size_t a = 0;
m_sIndex.clear();
mspectrumindex indTemp;
float fLast = 0.0;
while(a < tLimit) {
indTemp.m_fM = m_vDetails[a].m_fU;
indTemp.m_tA = (unsigned long)a;
if(indTemp.m_fM != fLast) {
m_sIndex.insert(indTemp);
}
fLast = indTemp.m_fM;
a += 5;
}
return true;
}
/*
* add_mi does the work necessary to set up an mspectrum object for modeling.
* default implementation simply checks for errors, and sets spectrum count.
* override in an mscore derived class implementation to do algorithm specific
* processing.
*/
bool mscore::add_mi(mspectrum &_s)
{
/*
* the fragment ion error cannot be zero
*/
if(m_fErr == 0.0)
return false;
m_lSpectra = (long)m_vSpec.size();
return true;
}
/*
* add_mi does the work necessary to set up an mspectrum object for modeling.
* - a copy of the mspectrum object is added to m_vSpec
* - an entry in the m_State object is made for the parent ion M+H
* once an mspectrum has been added, the original mspectrum is no longer
* needed for modeling, as all of the work associated with a spectrum
* is only done once, prior to modeling sequences.
*/
bool mscore::add_details(mspectrum &_s)
{
/*
* if there is a limit on the number of peaks, sort the temporary mspectrum.m_vMI member
* using lessThanMI (see top of this file). the sort results in m_vMI having the most
* intense peaks first in the vector. then, simply erase all but the top m_lMaxPeaks values
* from that vector and continue.
/*
* the fragment ion error cannot be zero
*/
if(m_fErr == 0.0)
return false;
/*
* create a temporary mspec object
*/
mspec spCurrent;
spCurrent = _s;
/*
* store the mspec object
*/
m_vSpec.push_back(spCurrent);
mspectrumdetails detTemp;
if(m_lErrorType & T_PARENT_PPM) {
detTemp.m_fL = (float)(_s.m_dMH - (_s.m_dMH*m_fParentErrPlus/1e6));
detTemp.m_fU = (float)(_s.m_dMH + (_s.m_dMH*m_fParentErrMinus/1e6));
}
else {
detTemp.m_fL = (float)(_s.m_dMH - m_fParentErrPlus);
detTemp.m_fU = (float)(_s.m_dMH + m_fParentErrMinus);
}
if(detTemp.m_fU > m_fMaxMass) {
m_fMaxMass = detTemp.m_fU;
}
detTemp.m_lA = (unsigned long)m_vSpec.size() - 1;
m_vDetails.push_back(detTemp);
if(m_bIsotopeError) {
if(spCurrent.m_fMH > 1000.0) {
detTemp.m_fL -= (float)(1.00335);
detTemp.m_fU -= (float)(1.00335);
m_vDetails.push_back(detTemp);
}
if(spCurrent.m_fMH > 1500.0) {
detTemp.m_fL -= (float)1.00335;
detTemp.m_fU -= (float)1.00335;
m_vDetails.push_back(detTemp);
}
}
return true;
}
/*
* add_seq stores a sequence, if the current value of m_pSeq contains the N-terminal portion
* of the new sequence. this method is part of optimizing the scoring process: all references
* to it could be replaced by set_seq. set_seq must be called before add_seq is called.
*/
unsigned long mscore::add_seq(const char *_s,const bool _n,const bool _c,const unsigned long _l,const int _f)
{
if(_s == NULL)
return 0;
unsigned long lOldLength = m_lSeqLength;
m_lSeqLength = _l;
/*
* if the sequence is too long, use set_seq to adjust the arrays and store the sequence
*/
if(m_lSeqLength >= m_lSize-1) {
return set_seq(_s,_n,_c,_l,_f);
}
/*
* copy the new part of the sequence into m_pSeq
*/
strcpy(m_pSeq + lOldLength,_s + lOldLength);
unsigned long a = lOldLength;
m_bIsC = _c;
m_State.initialize(m_pSeq,m_lSize);
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
/*
* update the parent ion M+H value
*/
map<size_t,size_t>::iterator itValue;
map<size_t,size_t>::iterator itEnd = m_seqUtil.m_mapMotifs.end();
SMap::iterator itSeq;
SMap::iterator itSeqEnd = m_seqUtil.m_mapMods.end();
if(m_seqUtil.m_bPotentialMotif) {
m_seqUtil.clear_motifs(false);
}
while(a < m_lSeqLength) {
m_dSeqMH += m_seqUtil.m_pdAaMass[m_pSeq[a]] + m_seqUtil.m_pdAaMod[m_pSeq[a]] + m_seqUtil.m_pdAaFullMod[m_pSeq[a]];
if(m_seqUtil.m_bSequenceMods) {
itSeq = m_seqUtil.m_mapMods.find((unsigned long)(m_tSeqPos+a));
if(itSeq != itSeqEnd) {
m_dSeqMH += itSeq->second;
}
}
if(m_seqUtil.m_pdAaMod[m_pSeq[a]+32] != 0.0) {
m_State.add_mod(m_pSeq+a);
}
if(m_seqUtil.m_bPotentialMotif) {
itValue = m_seqUtil.m_mapMotifs.find(m_tSeqPos+a);
if(itValue != itEnd){
m_State.add_mod(m_pSeq+a);
m_seqUtil.add_mod(m_pSeq[a],itValue->second);
}
}
a++;
}
if(m_seqUtil.m_bPotentialMotif) {
m_seqUtil.set_motifs();
}
/*
* deal with protein terminii
*/
if(m_bIsC)
m_dSeqMH += m_seqUtil.m_fCT;
/*
* update the mstate object
*/
m_State.m_dSeqMHS = m_dSeqMH;
m_fMinMass = (float)m_dSeqMH;
if(m_bUsePam) {
m_Pam.initialize(m_pSeq,(size_t)m_lSize,(float)m_dSeqMH);
}
if(m_bUseSaps) {
m_Sap.initialize(m_pSeq,(size_t)m_lSize,(float)m_dSeqMH);
}
return m_lSeqLength;
}
/*
* check_parents is used by the state machine for dealing with potentially
* modified sequences. it determines how many parent ions are eligible
* to be generated by the current modified sequence and stores the
* vector indices of those eligible spectra in the m_State object.
* this test is done to improve performance. inlining is not necessary,
* but this method is called very often in a normal protein modeling session, so removing
* the method calling overhead can improve overall performance
*/
__inline__ bool mscore::check_parents(void) {
/*
* this check improves performance because of the way the state machine assigns modifications
* if the state machine sequence order is modified, this mechanism should be reviewed
*/
if(m_State.m_dSeqMHFailedS == m_dSeqMH) {
m_State.m_lEqualsS = 0;
return false;
}
if(m_dSeqMH < m_vDetails[0].m_fL) {
return false;
}
if(m_dSeqMH > m_vDetails[m_lDetails-1].m_fU) {
return false;
}
vector<mspectrumdetails>::iterator itDetails = m_vDetails.begin();
vector<mspectrumdetails>::iterator itEnd = m_vDetails.end();
float fSeqMH = (float)m_dSeqMH;
set<mspectrumindex>::iterator itIndex;
mspectrumindex indTemp;
indTemp.m_fM = fSeqMH;
if(!m_sIndex.empty()) {
itIndex = m_sIndex.lower_bound(indTemp);
if(itIndex != m_sIndex.begin()) {
itIndex--;
}
itDetails = itDetails + (*itIndex).m_tA;
}
while(itDetails != itEnd) {
if(*itDetails == fSeqMH) {
m_State.m_lEqualsS = 0;
m_State.m_plEqualsS[m_State.m_lEqualsS] = itDetails->m_lA;
m_State.m_lEqualsS++;
itDetails++;
while(itDetails != itEnd && *itDetails == fSeqMH) {
m_State.m_plEqualsS[m_State.m_lEqualsS] = itDetails->m_lA;
m_State.m_lEqualsS++;
itDetails++;
}
return true;
}
if(fSeqMH < itDetails->m_fL) {
break;
}
itDetails++;
}
/*
* this check improves performance because of the way the state machine assigns modifications
* if the state machine sequence order is modified, this mechanism should be reviewed
*/
m_State.m_dSeqMHFailedS = m_dSeqMH;
m_State.m_lEqualsS = 0;
return false;
}
/*
* get_aa is used to check the current sequence and determine how many of
* the residues correspond to modification sites. this method is not used
* by mscore: check mprocess to see an example of how it is used to create
* a list of modified residues in a domain
*/
bool mscore::get_aa(vector<maa> &_m,const size_t _a,double &_d)
{
_d = 1000000.0;
if(!m_seqUtil.m_bComplete && !m_seqUtil.m_bPotential)
return false;
_m.clear();
long a = 0;
char cRes = '\0';
char *pValue = NULL;
maa aaValue;
double dDelta = 0.0;
while(a < 128) {
if(a == '[' && m_seqUtil.m_pdAaFullMod['['] != 0.0) {
cRes = m_pSeq[0];
aaValue.m_cRes = cRes;
aaValue.m_dMod = m_seqUtil.m_pdAaFullMod['['];
aaValue.m_lPos = (long)_a;
_m.push_back(aaValue);
}
if(a == ']' && m_seqUtil.m_pdAaFullMod[']'] != 0.0) {
cRes = m_pSeq[strlen(m_pSeq) - 1];
aaValue.m_cRes = cRes;
aaValue.m_dMod = m_seqUtil.m_pdAaFullMod[']'];
aaValue.m_lPos = (long)_a + (long)strlen(m_pSeq) - 1;
_m.push_back(aaValue);
}
if(m_seqUtil.m_pdAaMod[a] != 0.0) {
cRes = (char)a;
pValue = strchr(m_pSeq,cRes);
while(pValue != NULL) {
aaValue.m_cRes = cRes;
if(aaValue.m_cRes >= 'a' && aaValue.m_cRes <= 'z') {
aaValue.m_cRes -= 32;
}
aaValue.m_dMod = m_seqUtil.m_pdAaMod[a];
aaValue.m_dPrompt = m_seqUtil.m_pdAaPrompt[a];
aaValue.m_lPos = (long)_a + (long)(pValue - m_pSeq);
dDelta += aaValue.m_dMod;
_m.push_back(aaValue);
pValue++;
pValue = strchr(pValue,cRes);
}
}
if(m_seqUtil.m_pdAaFullMod[a] != 0.0) {
cRes = (char)a;
pValue = strchr(m_pSeq,cRes);
while(pValue != NULL) {
aaValue.m_cRes = cRes;
if(aaValue.m_cRes >= 'a' && aaValue.m_cRes <= 'z') {
aaValue.m_cRes -= 32;
}
aaValue.m_dMod = m_seqUtil.m_pdAaFullMod[a];
aaValue.m_lPos = (long)_a + (long)(pValue - m_pSeq);
aaValue.m_dPrompt = 0.0;
_m.push_back(aaValue);
pValue++;
pValue = strchr(pValue,cRes);
}
}
a++;
}
if(m_seqUtil.m_bSequenceMods) {
SMap::iterator itValue = m_seqUtil.m_mapMods.begin();
SMap::const_iterator itEnd = m_seqUtil.m_mapMods.end();
size_t tValue = 0;
size_t tEnd = m_tSeqPos + m_lSeqLength;
while(itValue != itEnd) {
tValue = itValue->first;
if(tValue >= m_tSeqPos || tValue < tEnd) {
tValue = tValue - m_tSeqPos;
cRes = m_pSeq[tValue];
aaValue.m_cRes = cRes;
if(aaValue.m_cRes >= 'a' && aaValue.m_cRes <= 'z') {
aaValue.m_cRes -= 32;
}
aaValue.m_dMod = itValue->second;
aaValue.m_lPos = (long)(_a+tValue);
if(cRes <= 'Z') {
cRes += 32;
}
dDelta += aaValue.m_dMod;
aaValue.m_dPrompt = m_seqUtil.m_pdAaPrompt[cRes];
_m.push_back(aaValue);
}
itValue++;
}
}
if(m_Term.m_lN) {
aaValue.m_dMod = m_seqUtil.m_pdAaMod['['];
aaValue.m_dPrompt = 0.0;
aaValue.m_lPos = (long)_a;
aaValue.m_cRes = m_pSeq[0];
if(aaValue.m_cRes >= 'a' && aaValue.m_cRes <= 'z') {
aaValue.m_cRes -= 32;
}
dDelta += aaValue.m_dMod;
_m.push_back(aaValue);
}
if(m_Term.m_lC) {
aaValue.m_dMod = m_seqUtil.m_pdAaMod[']'];
aaValue.m_dPrompt = 0.0;
aaValue.m_lPos = (long)_a+ m_lSeqLength - 1;
aaValue.m_cRes = m_pSeq[m_lSeqLength - 1];
if(aaValue.m_cRes >= 'a' && aaValue.m_cRes <= 'z') {
aaValue.m_cRes -= 32;
}
dDelta += aaValue.m_dMod;
_m.push_back(aaValue);
}
if(m_Pam.m_tCount > 0) {
aaValue.m_dMod = m_seqUtil.m_pdAaMass[m_pSeq[m_Pam.m_tPos]] - m_seqUtil.m_pdAaMass[m_Pam.m_pSeqTrue[m_Pam.m_tPos]];
aaValue.m_dPrompt = m_seqUtil.m_pdAaPrompt[m_pSeq[m_Pam.m_tPos]] - m_seqUtil.m_pdAaPrompt[m_Pam.m_pSeqTrue[m_Pam.m_tPos]];
aaValue.m_lPos = (long)(_a+ m_Pam.m_tPos);
aaValue.m_cRes = m_Pam.m_pSeqTrue[m_Pam.m_tPos];
if(aaValue.m_cRes >= 'a' && aaValue.m_cRes <= 'z') {
aaValue.m_cRes -= 32;
}
aaValue.m_cMut = m_pSeq[m_Pam.m_tPos];
aaValue.m_strId.clear();
dDelta += aaValue.m_dMod;
_d = dDelta;
_m.push_back(aaValue);
}
if(m_Sap.m_tCount > 0) {
aaValue.m_dMod = m_seqUtil.m_pdAaMass[m_pSeq[m_Sap.m_tPos]] - m_seqUtil.m_pdAaMass[m_Sap.m_pSeqTrue[m_Sap.m_tPos]];
aaValue.m_dPrompt = m_seqUtil.m_pdAaPrompt[m_pSeq[m_Sap.m_tPos]] - m_seqUtil.m_pdAaPrompt[m_Sap.m_pSeqTrue[m_Sap.m_tPos]];
aaValue.m_lPos = (long)(_a+ m_Sap.m_tPos);
aaValue.m_cRes = m_Sap.m_pSeqTrue[m_Sap.m_tPos];
if(aaValue.m_cRes >= 'a' && aaValue.m_cRes <= 'z') {
aaValue.m_cRes -= 32;
}