23 #include <boost/numeric/conversion/cast.hpp>
34 namespace TargetedExperimentHelper
124 retention_time_unit(
RTUnit::SIZE_OF_RTUNIT),
125 retention_time_type(
RTType::SIZE_OF_RTTYPE),
126 retention_time_set_(false),
143 software_ref == rhs.software_ref &&
144 retention_time_unit == rhs.retention_time_unit &&
145 retention_time_type == rhs.retention_time_type &&
146 retention_time_set_ == rhs.retention_time_set_ &&
147 retention_time_ == rhs.retention_time_;
152 return retention_time_set_;
156 retention_time_ = rt;
157 retention_time_set_ =
true;
162 return retention_time_;
198 charge_ == rhs.charge_ &&
199 charge_set_ == rhs.charge_set_;
239 return (!rts.empty() && rts[0].isRTset());
248 if (!hasRetentionTime())
251 "No retention time information available");
253 return rts[0].getRT();
259 if (!hasRetentionTime())
262 "No retention time information available");
264 return rts[0].retention_time_type;
270 if (!hasRetentionTime())
273 "No retention time information available");
275 return rts[0].retention_time_unit;
280 std::vector<RetentionTime>
rts;
284 bool charge_set_{
false};
285 double drift_time_{-1};
300 theoretical_mass(0.0)
312 molecular_formula == rhs.molecular_formula &&
313 smiles_string == rhs.smiles_string &&
314 theoretical_mass == rhs.theoretical_mass;
361 protein_refs == rhs.protein_refs &&
362 evidence == rhs.evidence &&
363 sequence == rhs.sequence &&
365 peptide_group_label_ == rhs.peptide_group_label_;
381 peptide_group_label_ = label;
387 return peptide_group_label_;
394 std::vector<Modification>
mods;
588 return configuration_list_;
593 configuration_list_.push_back(configuration);
598 return interpretation_list_;
603 interpretation_list_.push_back(interpretation);
608 return interpretation_list_.clear();
613 bool charge_set_{
false};
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:33
bool operator==(const CVTermListInterface &rhs) const
equality operator
Representation of controlled vocabulary term list.
Definition: CVTermList.h:28
bool operator==(const CVTermList &cv_term_list) const
equality operator
A method or algorithm argument contains illegal values.
Definition: Exception.h:616
Representation of an amino acid residue.
Definition: Residue.h:40
ResidueType
Definition: Residue.h:152
A more convenient string class.
Definition: String.h:34
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:296
String molecular_formula
Definition: TargetedExperimentHelper.h:317
double theoretical_mass
Definition: TargetedExperimentHelper.h:319
Compound(const Compound &)=default
Compound(Compound &&) noexcept=default
String smiles_string
Definition: TargetedExperimentHelper.h:318
Compound()
Definition: TargetedExperimentHelper.h:299
Base class to represent either a peptide or a compound.
Definition: TargetedExperimentHelper.h:185
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:280
bool hasRetentionTime() const
Check whether compound or peptide has an annotated retention time.
Definition: TargetedExperimentHelper.h:237
double getRetentionTime() const
Gets compound or peptide retention time.
Definition: TargetedExperimentHelper.h:246
PeptideCompound(const PeptideCompound &)=default
String id
Definition: TargetedExperimentHelper.h:279
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:216
bool operator==(const PeptideCompound &rhs) const
Definition: TargetedExperimentHelper.h:193
PeptideCompound(PeptideCompound &&) noexcept=default
void setChargeState(int charge)
Set the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:203
RetentionTime::RTType getRetentionTimeType() const
Get compound or peptide retentiontime type.
Definition: TargetedExperimentHelper.h:257
PeptideCompound()=default
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:210
RetentionTime::RTUnit getRetentionTimeUnit() const
Get compound or peptide retentiontime unit (minute/seconds)
Definition: TargetedExperimentHelper.h:268
double getDriftTime() const
Return the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:229
void setDriftTime(double dt)
Set the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:223
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:333
String getPeptideGroupLabel() const
Get the peptide group label.
Definition: TargetedExperimentHelper.h:385
String sequence
Definition: TargetedExperimentHelper.h:393
Peptide(const Peptide &)=default
CVTermList evidence
Definition: TargetedExperimentHelper.h:392
std::vector< Modification > mods
Definition: TargetedExperimentHelper.h:394
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:391
void setPeptideGroupLabel(const String &label)
Set the peptide group label.
Definition: TargetedExperimentHelper.h:379
Peptide(Peptide &&) noexcept=default
String peptide_group_label_
Definition: TargetedExperimentHelper.h:397
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:99
double getRT() const
Definition: TargetedExperimentHelper.h:159
String software_ref
Definition: TargetedExperimentHelper.h:165
RetentionTime(RetentionTime &&) noexcept=default
bool retention_time_set_
Definition: TargetedExperimentHelper.h:171
RetentionTime(const RetentionTime &)=default
RTUnit
Definition: TargetedExperimentHelper.h:103
RTType
Definition: TargetedExperimentHelper.h:111
RetentionTime()
Definition: TargetedExperimentHelper.h:121
RTUnit retention_time_unit
Definition: TargetedExperimentHelper.h:166
RTType retention_time_type
Definition: TargetedExperimentHelper.h:167
double retention_time_
Definition: TargetedExperimentHelper.h:172
bool isRTset() const
Definition: TargetedExperimentHelper.h:150
void setRT(double rt)
Definition: TargetedExperimentHelper.h:154
int32_t Int32
Signed integer type (32bit)
Definition: Types.h:26
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:94
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::AASequence getAASequence(const Peptide &peptide)
helper function that converts a Peptide object to a AASequence object
void setModification(int location, int max_size, const String &modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Definition: TargetedExperimentHelper.h:46
String fullname
Definition: TargetedExperimentHelper.h:57
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:61
String version
Definition: TargetedExperimentHelper.h:58
String id
Definition: TargetedExperimentHelper.h:56
CV(const String &new_id, const String &new_fullname, const String &new_version, const String &new_URI)
Definition: TargetedExperimentHelper.h:47
String URI
Definition: TargetedExperimentHelper.h:59
Definition: TargetedExperimentHelper.h:39
String instrument_ref
Definition: TargetedExperimentHelper.h:41
std::vector< CVTermList > validations
Definition: TargetedExperimentHelper.h:42
String contact_ref
Definition: TargetedExperimentHelper.h:40
Definition: TargetedExperimentHelper.h:436
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:442
String id
Definition: TargetedExperimentHelper.h:448
Instrument()
Definition: TargetedExperimentHelper.h:437
Product ion interpretation.
Definition: TargetedExperimentHelper.h:478
IonType iontype
which type of ion (b/y/z/ ...), see Residue::ResidueType
Definition: TargetedExperimentHelper.h:508
bool operator!=(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:530
Interpretation()
Definition: TargetedExperimentHelper.h:511
Residue::ResidueType IonType
Interpretation IonType.
Definition: TargetedExperimentHelper.h:504
bool operator==(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:522
unsigned char ordinal
MS:1000903 : product ion series ordinal (e.g. 8 for a y8 ion)
Definition: TargetedExperimentHelper.h:506
unsigned char rank
MS:1000926 : product interpretation rank (e.g. 1 for the most likely rank)
Definition: TargetedExperimentHelper.h:507
Definition: TargetedExperimentHelper.h:337
Int32 unimod_id
Definition: TargetedExperimentHelper.h:341
double mono_mass_delta
Definition: TargetedExperimentHelper.h:339
double avg_mass_delta
Definition: TargetedExperimentHelper.h:338
Int32 location
Definition: TargetedExperimentHelper.h:340
Modification()
Definition: TargetedExperimentHelper.h:343
Definition: TargetedExperimentHelper.h:453
String software_ref
Definition: TargetedExperimentHelper.h:466
Prediction()
Definition: TargetedExperimentHelper.h:454
String contact_ref
Definition: TargetedExperimentHelper.h:467
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:459
Definition: TargetedExperimentHelper.h:73
String sequence
Definition: TargetedExperimentHelper.h:83
String id
Definition: TargetedExperimentHelper.h:82
bool operator==(const Protein &rhs) const
Definition: TargetedExperimentHelper.h:75
Definition: TargetedExperimentHelper.h:419
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:425
String id
Definition: TargetedExperimentHelper.h:431
Publication()
Definition: TargetedExperimentHelper.h:420
Represents a product ion.
Definition: TargetedExperimentHelper.h:546
void resetInterpretations()
Definition: TargetedExperimentHelper.h:606
void addConfiguration(const Configuration &configuration)
Definition: TargetedExperimentHelper.h:591
void addInterpretation(const Interpretation &interpretation)
Definition: TargetedExperimentHelper.h:601
const std::vector< Configuration > & getConfigurationList() const
Definition: TargetedExperimentHelper.h:586
void setMZ(double mz)
Definition: TargetedExperimentHelper.h:581
const std::vector< Interpretation > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:596
int getChargeState() const
Definition: TargetedExperimentHelper.h:570
bool charge_set_
Whether product ion charge is set or not.
Definition: TargetedExperimentHelper.h:613
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:558
std::vector< Configuration > configuration_list_
Product ion configurations used.
Definition: TargetedExperimentHelper.h:615
int charge_
Product ion charge.
Definition: TargetedExperimentHelper.h:612
bool hasCharge() const
Whether product has set charge state.
Definition: TargetedExperimentHelper.h:565
std::vector< Interpretation > interpretation_list_
Product ion interpretation.
Definition: TargetedExperimentHelper.h:616
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:548
double mz_
Product ion m/z.
Definition: TargetedExperimentHelper.h:614
double getMZ() const
Definition: TargetedExperimentHelper.h:576