| OpenMS 2.5.0

TargetedExperimentHelper.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
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10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
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15 // without specific prior written permission.
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20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38
39 #include <OpenMS/KERNEL/StandardDeclarations.h>
40 #include <OpenMS/CONCEPT/Types.h>
41 #include <OpenMS/CONCEPT/Exception.h>
42 #include <OpenMS/CONCEPT/Macros.h>
43
44 #include <OpenMS/CHEMISTRY/AASequence.h>
45 #include <OpenMS/METADATA/CVTerm.h>
46 #include <OpenMS/METADATA/CVTermList.h>
47 #include <OpenMS/METADATA/CVTermListInterface.h>
48 #include <OpenMS/CHEMISTRY/Residue.h>
49
50 #include <boost/numeric/conversion/cast.hpp>
51
52 namespace OpenMS
53 {
54
61 namespace TargetedExperimentHelper
62 {
63
64 struct Configuration :
65 public CVTermList
66 {
67 String contact_ref;
68 String instrument_ref;
69 std::vector<CVTermList> validations;
70 };
71
72 struct CV
73 {
74 CV(const String & new_id, const String & new_fullname, const String & new_version, const String & new_URI) :
75 id(new_id),
76 fullname(new_fullname),
77 version(new_version),
78 URI(new_URI)
79 {
80
81 }
82
83 String id;
84 String fullname;
85 String version;
86 String URI;
87
88 bool operator==(const CV & cv) const
89 {
90 return id == cv.id &&
91 fullname == cv.fullname &&
92 version == cv.version &&
93 URI == cv.URI;
94 }
95
96 };
97
98 struct Protein :
99 public CVTermList
100 {
101 Protein() :
102 CVTermList()
103 {
104 }
105
106 String id;
107 String sequence;
108
109 bool operator==(const Protein & rhs) const
110 {
111 return CVTermList::operator==(rhs) &&
112 id == rhs.id &&
113 sequence == rhs.sequence;
114 }
115 };
116
127 class OPENMS_DLLAPI RetentionTime :
128 public CVTermListInterface
129 {
130 public:
131
132 enum class RTUnit : std::int8_t
133 {
134 SECOND = 0,
135 MINUTE,
136 UNKNOWN,
137 SIZE_OF_RTUNIT
138 };
139
140 enum class RTType : std::int8_t
141 {
142 LOCAL = 0,
143 NORMALIZED,
144 PREDICTED,
145 HPINS,
146 IRT,
147 UNKNOWN,
148 SIZE_OF_RTTYPE
149 };
150
151 RetentionTime() :
152 CVTermListInterface(),
153 software_ref(""),
154 retention_time_unit(RTUnit::SIZE_OF_RTUNIT),
155 retention_time_type(RTType::SIZE_OF_RTTYPE),
156 retention_time_set_(false),
157 retention_time_(0.0)
158 // retention_time_width(0.0),
159 // retention_time_lower(0.0),
160 // retention_time_upper(0.0)
161 {
162 }
163
164 RetentionTime(const RetentionTime &) = default;
165 RetentionTime(RetentionTime &&) noexcept = default;
166 virtual ~RetentionTime() = default;
167 RetentionTime & operator=(const RetentionTime &) & = default;
168 RetentionTime & operator=(RetentionTime &&) & = default;
169
170 bool operator==(const RetentionTime & rhs) const
171 {
172 return CVTermListInterface::operator==(rhs) &&
173 software_ref == rhs.software_ref &&
174 retention_time_unit == rhs.retention_time_unit &&
175 retention_time_type == rhs.retention_time_type &&
176 retention_time_set_ == rhs.retention_time_set_ &&
177 retention_time_ == rhs.retention_time_;
178 }
179
180 bool isRTset() const
181 {
182 return retention_time_set_;
183 }
184 void setRT(double rt)
185 {
186 retention_time_ = rt;
187 retention_time_set_ = true;
188 }
189 double getRT() const
190 {
191 OPENMS_PRECONDITION(isRTset(), "RT needs to be set")
192 return retention_time_;
193 }
194
195 String software_ref;
196 RTUnit retention_time_unit;
197 RTType retention_time_type;
198
199 private:
200
201 bool retention_time_set_;
202 double retention_time_;
203 // double retention_time_width;
204 // double retention_time_lower;
205 // double retention_time_upper;
206 };
207
213 class OPENMS_DLLAPI PeptideCompound :
214 public CVTermList
215 {
216 public:
217
218 PeptideCompound() :
219 CVTermList(),
220 charge_(0),
221 charge_set_(false),
222 drift_time_(-1)
223 {
224 }
225
226 PeptideCompound(const PeptideCompound &) = default;
227 PeptideCompound(PeptideCompound &&) noexcept = default;
228 PeptideCompound & operator=(const PeptideCompound &) & = default;
229 PeptideCompound & operator=(PeptideCompound &&) & = default;
230
231 bool operator==(const PeptideCompound & rhs) const
232 {
233 return CVTermList::operator==(rhs) &&
234 rts == rhs.rts &&
235 id == rhs.id &&
236 charge_ == rhs.charge_ &&
237 charge_set_ == rhs.charge_set_;
238 }
239
241 void setChargeState(int charge)
242 {
243 charge_ = charge;
244 charge_set_ = true;
245 }
246
248 bool hasCharge() const
249 {
250 return charge_set_;
251 }
252
254 int getChargeState() const
255 {
256 OPENMS_PRECONDITION(charge_set_, "Cannot return charge which was never set")
257 return charge_;
258 }
259
261 void setDriftTime(double dt)
262 {
263 drift_time_ = dt;
264 }
265
267 double getDriftTime() const
268 {
269 return drift_time_;
270 }
271
273
275 bool hasRetentionTime() const
276 {
277 return (!rts.empty() && rts[0].isRTset());
278 }
279
284 double getRetentionTime() const
285 {
286 if (!hasRetentionTime())
287 {
288 throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
289 "No retention time information available");
290 }
291 return rts[0].getRT();
292 }
293
295 RetentionTime::RTType getRetentionTimeType() const
296 {
297 if (!hasRetentionTime())
298 {
299 throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
300 "No retention time information available");
301 }
302 return rts[0].retention_time_type;
303 }
304
306 RetentionTime::RTUnit getRetentionTimeUnit() const
307 {
308 if (!hasRetentionTime())
309 {
310 throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
311 "No retention time information available");
312 }
313 return rts[0].retention_time_unit;
314 }
316
317 String id;
318 std::vector<RetentionTime> rts;
319
320 protected:
321 int charge_;
322 bool charge_set_;
323 double drift_time_;
324
325 };
326
333 class OPENMS_DLLAPI Compound :
334 public PeptideCompound
335 {
336 public:
337
338 Compound() :
339 theoretical_mass(0.0)
340 {
341 }
342
343 Compound(const Compound &) = default;
344 Compound(Compound &&) noexcept = default;
345 Compound & operator=(const Compound &) & = default;
346 Compound & operator=(Compound &&) & = default;
347
348 bool operator==(const Compound & rhs) const
349 {
350 return PeptideCompound::operator==(rhs) &&
351 molecular_formula == rhs.molecular_formula &&
352 smiles_string == rhs.smiles_string &&
353 theoretical_mass == rhs.theoretical_mass;
354 }
355
356 String molecular_formula;
357 String smiles_string;
358 double theoretical_mass;
359
360 protected:
361
362 };
363
370 class OPENMS_DLLAPI Peptide :
371 public PeptideCompound
372 {
373 public:
374
375 struct Modification :
376 public CVTermListInterface
377 {
378 double avg_mass_delta;
379 double mono_mass_delta;
380 Int32 location;
381 Int32 unimod_id;
382
383 Modification() :
384 CVTermListInterface(),
385 location(-1),
386 unimod_id(-1)
387 {
388 }
389
390 };
391
392 Peptide() :
393 PeptideCompound()
394 {
395 }
396
397 Peptide(const Peptide &) = default;
398 Peptide(Peptide &&) noexcept = default;
399 Peptide & operator=(const Peptide &) & = default;
400 Peptide & operator=(Peptide &&) & = default;
401
402 bool operator==(const Peptide & rhs) const
403 {
404 return PeptideCompound::operator==(rhs) &&
405 protein_refs == rhs.protein_refs &&
406 evidence == rhs.evidence &&
407 sequence == rhs.sequence &&
408 mods == rhs.mods &&
409 peptide_group_label_ == rhs.peptide_group_label_;
410 }
411
422 void setPeptideGroupLabel(const String & label)
424 {
425 peptide_group_label_ = label;
426 }
427
429 String getPeptideGroupLabel() const
430 {
431 return peptide_group_label_;
432 }
434
435 std::vector<String> protein_refs;
436 CVTermList evidence;
437 String sequence;
438 std::vector<Modification> mods;
439
440 protected:
441 String peptide_group_label_;
442 };
443
444 struct OPENMS_DLLAPI Contact :
445 public CVTermList
446 {
447 Contact() :
448 CVTermList()
449 {
450 }
451
452 bool operator==(const Contact & rhs) const
453 {
454 return CVTermList::operator==(rhs) &&
455 id == rhs.id;
456 }
457
458 String id;
459 };
460
461 struct OPENMS_DLLAPI Publication :
462 public CVTermList
463 {
464 Publication() :
465 CVTermList()
466 {
467 }
468
469 bool operator==(const Publication & rhs) const
470 {
471 return CVTermList::operator==(rhs) &&
472 id == rhs.id;
473 }
474
475 String id;
476 };
477
478 struct OPENMS_DLLAPI Instrument :
479 public CVTermList
480 {
481 Instrument() :
482 CVTermList()
483 {
484 }
485
486 bool operator==(const Instrument & rhs) const
487 {
488 return CVTermList::operator==(rhs) &&
489 id == rhs.id;
490 }
491
492 String id;
493 };
494
495 struct OPENMS_DLLAPI Prediction :
496 public CVTermList
497 {
498 Prediction() :
499 CVTermList()
500 {
501 }
502
503 bool operator==(const Prediction & rhs) const
504 {
505 return CVTermList::operator==(rhs) &&
506 contact_ref == rhs.contact_ref &&
507 software_ref == rhs.software_ref;
508 }
509
510 String software_ref;
511 String contact_ref;
512 };
513
520 struct OPENMS_DLLAPI Interpretation :
521 public CVTermListInterface
522 {
523
524 /*
525 enum ResidueType
526 {
527 Full = 0, // with N-terminus and C-terminus
528 Internal, // internal, without any termini
529 NTerminal, // only N-terminus
530 CTerminal, // only C-terminus
531 AIon, // MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond
532 BIon, // MS:1001224 N-terminus up to the peptide bond
533 CIon, // MS:1001231 N-terminus up to the amide/C-alpha bond
534 XIon, // MS:1001228 amide/C-alpha bond up to the C-terminus
535 YIon, // MS:1001220 peptide bond up to the C-terminus
536 ZIon, // MS:1001230 C-alpha/carbonyl carbon bond
537 Precursor, // MS:1001523 Precursor ion
538 BIonMinusH20, // MS:1001222 b ion without water
539 YIonMinusH20, // MS:1001223 y ion without water
540 BIonMinusNH3, // MS:1001232 b ion without ammonia
541 YIonMinusNH3, // MS:1001233 y ion without ammonia
542 NonIdentified, // MS:1001240 Non-identified ion
543 Unannotated, // no stored annotation
544 SizeOfResidueType
545 };
546 */
547
548 typedef Residue::ResidueType IonType;
549
550 unsigned char ordinal;
551 unsigned char rank;
552 IonType iontype;
553
554 // Constructor
555 Interpretation() :
556 CVTermListInterface(),
557 ordinal(0),
558 rank(0),
559 iontype(Residue::Unannotated) // Unannotated does not imply any MS OBO term
560 {
561 }
562
566 bool operator==(const Interpretation & rhs) const
567 {
568 return CVTermListInterface::operator==(rhs) &&
569 ordinal == rhs.ordinal &&
570 rank == rhs.rank &&
571 iontype == rhs.iontype;
572 }
573
574 bool operator!=(const Interpretation & rhs) const
575 {
576 return !(operator==(rhs));
577 }
579
580 };
581
588 struct OPENMS_DLLAPI TraMLProduct :
589 public CVTermListInterface
590 {
591 TraMLProduct() :
592 CVTermListInterface(),
593 charge_(0),
594 charge_set_(false),
595 mz_(0)
596 {
597 }
598
599 bool operator==(const TraMLProduct & rhs) const
600 {
601 return CVTermListInterface::operator==(rhs) &&
602 charge_ == rhs.charge_ &&
603 charge_set_ == rhs.charge_set_ &&
604 mz_ == rhs.mz_ &&
605 configuration_list_ == rhs.configuration_list_ &&
606 interpretation_list_ == rhs.interpretation_list_;
607 }
608
609 void setChargeState(int charge)
610 {
611 charge_ = charge;
612 charge_set_ = true;
613 }
614
616 bool hasCharge() const
617 {
618 return charge_set_;
619 }
620
621 int getChargeState() const
622 {
623 OPENMS_PRECONDITION(charge_set_, "Cannot return charge which was never set")
624 return charge_;
625 }
626
627 double getMZ() const
628 {
629 return mz_;
630 }
631
632 void setMZ(double mz)
633 {
634 mz_ = mz;
635 }
636
637 const std::vector<Configuration> & getConfigurationList() const
638 {
639 return configuration_list_;
640 }
641
642 void addConfiguration(const Configuration& configuration)
643 {
644 configuration_list_.push_back(configuration);
645 }
646
647 const std::vector<Interpretation> & getInterpretationList() const
648 {
649 return interpretation_list_;
650 }
651
652 void addInterpretation(const Interpretation& interpretation)
653 {
654 interpretation_list_.push_back(interpretation);
655 }
656
657 void resetInterpretations()
658 {
659 return interpretation_list_.clear();
660 }
661
662 private:
663 int charge_;
664 bool charge_set_;
665 double mz_;
666 std::vector<Configuration> configuration_list_;
667 std::vector<Interpretation> interpretation_list_;
668
669 };
670
672 OPENMS_DLLAPI OpenMS::AASequence getAASequence(const Peptide& peptide);
673
675 OPENMS_DLLAPI void setModification(int location, int max_size, String modification, OpenMS::AASequence & aas);
676
677 }
678
679 } // namespace OpenMS
680
OpenMS::TargetedExperimentHelper::Contact::id
String id
Definition: TargetedExperimentHelper.h:458
OpenMS::TargetedExperimentHelper::PeptideCompound::drift_time_
double drift_time_
Definition: TargetedExperimentHelper.h:323
OpenMS::TargetedExperimentHelper::Instrument::operator==
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:486
OpenMS::TargetedExperimentHelper::TraMLProduct::getMZ
double getMZ() const
Definition: TargetedExperimentHelper.h:627
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TargetedExperimentHelper::Peptide::Modification::mono_mass_delta
double mono_mass_delta
Definition: TargetedExperimentHelper.h:379
OpenMS::TargetedExperimentHelper::TraMLProduct::addInterpretation
void addInterpretation(const Interpretation &interpretation)
Definition: TargetedExperimentHelper.h:652
OpenMS::TargetedExperimentHelper::Configuration::validations
std::vector< CVTermList > validations
Definition: TargetedExperimentHelper.h:69
OpenMS::TargetedExperimentHelper::Peptide::peptide_group_label_
String peptide_group_label_
Definition: TargetedExperimentHelper.h:441
OpenMS::TargetedExperimentHelper::TraMLProduct::operator==
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:599
OpenMS::TargetedExperimentHelper::TraMLProduct::setChargeState
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:609
OpenMS::TargetedExperimentHelper::Peptide::Modification::unimod_id
Int32 unimod_id
Definition: TargetedExperimentHelper.h:381
OpenMS::TargetedExperimentHelper::TraMLProduct::resetInterpretations
void resetInterpretations()
Definition: TargetedExperimentHelper.h:657
OpenMS::TargetedExperimentHelper::Prediction::Prediction
Prediction()
Definition: TargetedExperimentHelper.h:498
OpenMS::TargetedExperimentHelper::CV::id
String id
Definition: TargetedExperimentHelper.h:83
OpenMS::TargetedExperimentHelper::TraMLProduct::getConfigurationList
const std::vector< Configuration > & getConfigurationList() const
Definition: TargetedExperimentHelper.h:637
OpenMS::TargetedExperimentHelper::Peptide::getPeptideGroupLabel
String getPeptideGroupLabel() const
Get the peptide group label.
Definition: TargetedExperimentHelper.h:429
AASequence.h
StandardDeclarations.h
OpenMS::Residue
Representation of a residue.
Definition: Residue.h:61
OpenMS::TargetedExperimentHelper::Interpretation::rank
unsigned char rank
MS:1000926 : product interpretation rank (e.g. 1 for the most likely rank)
Definition: TargetedExperimentHelper.h:551
OpenMS::TargetedExperimentHelper::Peptide::Peptide
Peptide()
Definition: TargetedExperimentHelper.h:392
OpenMS::CVTermList::operator==
bool operator==(const CVTermList &cv_term_list) const
equality operator
OpenMS::TargetedExperimentHelper::RetentionTime
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
OpenMS::TargetedExperimentHelper::RetentionTime::isRTset
bool isRTset() const
Definition: TargetedExperimentHelper.h:180
OpenMS::TargetedExperimentHelper::TraMLProduct::mz_
double mz_
Product ion m/z.
Definition: TargetedExperimentHelper.h:665
Exception.h
Residue.h
OpenMS::TargetedExperimentHelper::Instrument::id
String id
Definition: TargetedExperimentHelper.h:492
OpenMS::TargetedExperimentHelper::Interpretation::operator==
bool operator==(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:566
OpenMS::TargetedExperimentHelper::RetentionTime::retention_time_unit
RTUnit retention_time_unit
Definition: TargetedExperimentHelper.h:196
StandardTypes.h
OpenMS::TargetedExperimentHelper::PeptideCompound::getChargeState
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:254
OpenMS::TargetedExperimentHelper::Contact
Definition: TargetedExperimentHelper.h:444
OpenMS::TargetedExperimentHelper::Prediction::software_ref
String software_ref
Definition: TargetedExperimentHelper.h:510
OpenMS::Int32
OPENMS_INT32_TYPE Int32
Signed integer type (32bit)
Definition: Types.h:56
OpenMS::TargetedExperimentHelper::TraMLProduct::getInterpretationList
const std::vector< Interpretation > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:647
Types.h
OpenMS::TargetedExperimentHelper::PeptideCompound::getDriftTime
double getDriftTime() const
Return the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:267
OpenMS::TargetedExperimentHelper::Configuration::contact_ref
String contact_ref
Definition: TargetedExperimentHelper.h:67
OpenMS::TargetedExperimentHelper::Peptide::Modification::avg_mass_delta
double avg_mass_delta
Definition: TargetedExperimentHelper.h:378
OpenMS::TargetedExperimentHelper::PeptideCompound::operator==
bool operator==(const PeptideCompound &rhs) const
Definition: TargetedExperimentHelper.h:231
OpenMS::CVTermListInterface::operator==
bool operator==(const CVTermListInterface &rhs) const
equality operator
OpenMS::TargetedExperimentHelper::TraMLProduct::getChargeState
int getChargeState() const
Definition: TargetedExperimentHelper.h:621
OpenMS::TargetedExperimentHelper::Prediction::operator==
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:503
OpenMS::TargetedExperimentHelper::Configuration
Definition: TargetedExperimentHelper.h:64
OpenMS::TargetedExperimentHelper::TraMLProduct::interpretation_list_
std::vector< Interpretation > interpretation_list_
Product ion interpretation.
Definition: TargetedExperimentHelper.h:667
OpenMS::TargetedExperimentHelper::Peptide::evidence
CVTermList evidence
Definition: TargetedExperimentHelper.h:436
CVTerm.h
OpenMS::TargetedExperimentHelper::PeptideCompound::getRetentionTime
double getRetentionTime() const
Gets compound or peptide retention time.
Definition: TargetedExperimentHelper.h:284
OpenMS::TargetedExperimentHelper::Interpretation::iontype
IonType iontype
which type of ion (b/y/z/ ...), see Residue::ResidueType
Definition: TargetedExperimentHelper.h:552
OpenMS::TargetedExperimentHelper::RetentionTime::setRT
void setRT(double rt)
Definition: TargetedExperimentHelper.h:184
OpenMS::TargetedExperimentHelper::Protein::operator==
bool operator==(const Protein &rhs) const
Definition: TargetedExperimentHelper.h:109
OpenMS::TargetedExperimentHelper::Compound::smiles_string
String smiles_string
Definition: TargetedExperimentHelper.h:357
OpenMS::CVTermListInterface
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:57
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::TargetedExperimentHelper::Contact::Contact
Contact()
Definition: TargetedExperimentHelper.h:447
OpenMS::TargetedExperimentHelper::Protein::Protein
Protein()
Definition: TargetedExperimentHelper.h:101
OPENMS_PRECONDITION
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:136
OpenMS::TargetedExperimentHelper::Compound
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
OpenMS::TargetedExperimentHelper::RetentionTime::retention_time_
double retention_time_
Definition: TargetedExperimentHelper.h:202
OpenMS::TargetedExperimentHelper::Protein
Definition: TargetedExperimentHelper.h:98
OpenMS::TargetedExperimentHelper::Contact::operator==
bool operator==(const Contact &rhs) const
Definition: TargetedExperimentHelper.h:452
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
CVTermListInterface.h
OpenMS::TargetedExperimentHelper::Protein::id
String id
Definition: TargetedExperimentHelper.h:106
OpenMS::TargetedExperimentHelper::CV::operator==
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:88
OpenMS::TargetedExperimentHelper::PeptideCompound::setDriftTime
void setDriftTime(double dt)
Set the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:261
OpenMS::TargetedExperimentHelper::Peptide::Modification::location
Int32 location
Definition: TargetedExperimentHelper.h:380
OpenMS::TargetedExperimentHelper::PeptideCompound::charge_
int charge_
Definition: TargetedExperimentHelper.h:321
OpenMS::TargetedExperimentHelper::Instrument
Definition: TargetedExperimentHelper.h:478
OpenMS::TargetedExperimentHelper::TraMLProduct::addConfiguration
void addConfiguration(const Configuration &configuration)
Definition: TargetedExperimentHelper.h:642
OpenMS::TargetedExperimentHelper::RetentionTime::RTType
RTType
Definition: TargetedExperimentHelper.h:140
OpenMS::TargetedExperimentHelper::Peptide::Modification
Definition: TargetedExperimentHelper.h:375
CVTermList.h
OpenMS::TargetedExperimentHelper::Publication::operator==
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:469
OpenMS::TargetedExperimentHelper::PeptideCompound
Base class to represent either a peptide or a compound.
Definition: TargetedExperimentHelper.h:213
OpenMS::TargetedExperimentHelper::RetentionTime::getRT
double getRT() const
Definition: TargetedExperimentHelper.h:189
OpenMS::TargetedExperimentHelper::TraMLProduct::TraMLProduct
TraMLProduct()
Definition: TargetedExperimentHelper.h:591
OpenMS::TargetedExperimentHelper::Interpretation::IonType
Residue::ResidueType IonType
Interpretation IonType.
Definition: TargetedExperimentHelper.h:548
OpenMS::TargetedExperimentHelper::TraMLProduct::hasCharge
bool hasCharge() const
Whether product has set charge state.
Definition: TargetedExperimentHelper.h:616
OpenMS::TargetedExperimentHelper::CV
Definition: TargetedExperimentHelper.h:72
OpenMS::TargetedExperimentHelper::Prediction::contact_ref
String contact_ref
Definition: TargetedExperimentHelper.h:511
OpenMS::TargetedExperimentHelper::RetentionTime::retention_time_type
RTType retention_time_type
Definition: TargetedExperimentHelper.h:197
OpenMS::TargetedExperimentHelper::PeptideCompound::hasRetentionTime
bool hasRetentionTime() const
Check whether compound or peptide has an annotated retention time.
Definition: TargetedExperimentHelper.h:275
OpenMS::TargetedExperimentHelper::TraMLProduct::charge_set_
bool charge_set_
Whether product ion charge is set or not.
Definition: TargetedExperimentHelper.h:664
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::TargetedExperimentHelper::PeptideCompound::rts
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:318
OpenMS::TargetedExperimentHelper::Instrument::Instrument
Instrument()
Definition: TargetedExperimentHelper.h:481
OpenMS::TargetedExperimentHelper::Interpretation::operator!=
bool operator!=(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:574
OpenMS::TargetedExperimentHelper::RetentionTime::software_ref
String software_ref
Definition: TargetedExperimentHelper.h:195
OpenMS::TargetedExperimentHelper::Configuration::instrument_ref
String instrument_ref
Definition: TargetedExperimentHelper.h:68
OpenMS::TargetedExperimentHelper::Peptide::protein_refs
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:435
OpenMS::TargetedExperimentHelper::PeptideCompound::getRetentionTimeType
RetentionTime::RTType getRetentionTimeType() const
Get compound or peptide retentiontime type.
Definition: TargetedExperimentHelper.h:295
OpenMS::TargetedExperimentHelper::Interpretation
Product ion interpretation.
Definition: TargetedExperimentHelper.h:520
OpenMS::TargetedExperimentHelper::Peptide::Modification::Modification
Modification()
Definition: TargetedExperimentHelper.h:383
OpenMS::TargetedExperimentHelper::Publication
Definition: TargetedExperimentHelper.h:461
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
OpenMS::TargetedExperimentHelper::Interpretation::Interpretation
Interpretation()
Definition: TargetedExperimentHelper.h:555
OpenMS::TargetedExperimentHelper::CV::version
String version
Definition: TargetedExperimentHelper.h:85
OpenMS::TargetedExperimentHelper::PeptideCompound::getRetentionTimeUnit
RetentionTime::RTUnit getRetentionTimeUnit() const
Get compound or peptide retentiontime unit (minute/seconds)
Definition: TargetedExperimentHelper.h:306
OpenMS::TargetedExperimentHelper::getAASequence
OpenMS::AASequence getAASequence(const Peptide &peptide)
helper function that converts a Peptide object to a AASequence object
OpenMS::TargetedExperimentHelper::PeptideCompound::charge_set_
bool charge_set_
Definition: TargetedExperimentHelper.h:322
OpenMS::TargetedExperimentHelper::setModification
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
OpenMS::TargetedExperimentHelper::Compound::molecular_formula
String molecular_formula
Definition: TargetedExperimentHelper.h:356
Macros.h
OpenMS::TargetedExperimentHelper::PeptideCompound::id
String id
Definition: TargetedExperimentHelper.h:317
OpenMS::TargetedExperimentHelper::Prediction
Definition: TargetedExperimentHelper.h:495
OpenMS::TargetedExperimentHelper::CV::fullname
String fullname
Definition: TargetedExperimentHelper.h:84
OpenMS::TargetedExperimentHelper::PeptideCompound::hasCharge
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:248
OpenMS::TargetedExperimentHelper::RetentionTime::RetentionTime
RetentionTime()
Definition: TargetedExperimentHelper.h:151
OpenMS::TargetedExperimentHelper::Protein::sequence
String sequence
Definition: TargetedExperimentHelper.h:107
OpenMS::TargetedExperimentHelper::TraMLProduct::configuration_list_
std::vector< Configuration > configuration_list_
Product ion configurations used.
Definition: TargetedExperimentHelper.h:666
OpenMS::TargetedExperimentHelper::Compound::theoretical_mass
double theoretical_mass
Definition: TargetedExperimentHelper.h:358
OpenMS::TargetedExperimentHelper::Peptide::mods
std::vector< Modification > mods
Definition: TargetedExperimentHelper.h:438
OpenMS::TargetedExperimentHelper::CV::CV
CV(const String &new_id, const String &new_fullname, const String &new_version, const String &new_URI)
Definition: TargetedExperimentHelper.h:74
OpenMS::TargetedExperimentHelper::Compound::Compound
Compound()
Definition: TargetedExperimentHelper.h:338
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:150
OpenMS::TargetedExperimentHelper::Publication::id
String id
Definition: TargetedExperimentHelper.h:475
OpenMS::TargetedExperimentHelper::TraMLProduct::charge_
int charge_
Product ion charge.
Definition: TargetedExperimentHelper.h:663
OpenMS::TargetedExperimentHelper::TraMLProduct
Represents a product ion.
Definition: TargetedExperimentHelper.h:588
OpenMS::TargetedExperimentHelper::Interpretation::ordinal
unsigned char ordinal
MS:1000903 : product ion series ordinal (e.g. 8 for a y8 ion)
Definition: TargetedExperimentHelper.h:550
OpenMS::TargetedExperimentHelper::Peptide::sequence
String sequence
Definition: TargetedExperimentHelper.h:437
OpenMS::TargetedExperimentHelper::RetentionTime::RTUnit
RTUnit
Definition: TargetedExperimentHelper.h:132
OpenMS::TargetedExperimentHelper::PeptideCompound::setChargeState
void setChargeState(int charge)
Set the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:241
OpenMS::TargetedExperimentHelper::PeptideCompound::PeptideCompound
PeptideCompound()
Definition: TargetedExperimentHelper.h:218
OpenMS::TargetedExperimentHelper::RetentionTime::retention_time_set_
bool retention_time_set_
Definition: TargetedExperimentHelper.h:201
OpenMS::TargetedExperimentHelper::CV::URI
String URI
Definition: TargetedExperimentHelper.h:86
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::TargetedExperimentHelper::TraMLProduct::setMZ
void setMZ(double mz)
Definition: TargetedExperimentHelper.h:632
OpenMS::TargetedExperimentHelper::Publication::Publication
Publication()
Definition: TargetedExperimentHelper.h:464