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OpenMS
2.5.0
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50 #include <boost/numeric/conversion/cast.hpp>
61 namespace TargetedExperimentHelper
154 retention_time_unit(
RTUnit::SIZE_OF_RTUNIT),
155 retention_time_type(
RTType::SIZE_OF_RTTYPE),
156 retention_time_set_(false),
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_;
182 return retention_time_set_;
186 retention_time_ = rt;
187 retention_time_set_ =
true;
192 return retention_time_;
236 charge_ == rhs.charge_ &&
237 charge_set_ == rhs.charge_set_;
277 return (!rts.empty() && rts[0].isRTset());
286 if (!hasRetentionTime())
289 "No retention time information available");
291 return rts[0].getRT();
297 if (!hasRetentionTime())
300 "No retention time information available");
302 return rts[0].retention_time_type;
308 if (!hasRetentionTime())
311 "No retention time information available");
313 return rts[0].retention_time_unit;
318 std::vector<RetentionTime>
rts;
339 theoretical_mass(0.0)
351 molecular_formula == rhs.molecular_formula &&
352 smiles_string == rhs.smiles_string &&
353 theoretical_mass == rhs.theoretical_mass;
405 protein_refs == rhs.protein_refs &&
406 evidence == rhs.evidence &&
407 sequence == rhs.sequence &&
409 peptide_group_label_ == rhs.peptide_group_label_;
422 void setPeptideGroupLabel(
const String & label)
425 peptide_group_label_ = label;
431 return peptide_group_label_;
438 std::vector<Modification>
mods;
639 return configuration_list_;
644 configuration_list_.push_back(configuration);
649 return interpretation_list_;
654 interpretation_list_.push_back(interpretation);
659 return interpretation_list_.clear();
Definition: TargetedExperimentHelper.h:375
String software_ref
Definition: TargetedExperimentHelper.h:510
bool operator==(const CVTermList &cv_term_list) const
equality operator
Definition: TargetedExperimentHelper.h:478
void setDriftTime(double dt)
Set the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:261
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:318
void addConfiguration(const Configuration &configuration)
Definition: TargetedExperimentHelper.h:642
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
double theoretical_mass
Definition: TargetedExperimentHelper.h:358
bool isRTset() const
Definition: TargetedExperimentHelper.h:180
bool hasCharge() const
Whether product has set charge state.
Definition: TargetedExperimentHelper.h:616
double mz_
Product ion m/z.
Definition: TargetedExperimentHelper.h:665
bool retention_time_set_
Definition: TargetedExperimentHelper.h:201
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
RTUnit retention_time_unit
Definition: TargetedExperimentHelper.h:196
void addInterpretation(const Interpretation &interpretation)
Definition: TargetedExperimentHelper.h:652
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:435
const std::vector< Interpretation > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:647
A more convenient string class.
Definition: String.h:58
double getDriftTime() const
Return the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:267
int charge_
Definition: TargetedExperimentHelper.h:321
Protein()
Definition: TargetedExperimentHelper.h:101
std::vector< Modification > mods
Definition: TargetedExperimentHelper.h:438
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:503
String getPeptideGroupLabel() const
Get the peptide group label.
Definition: TargetedExperimentHelper.h:429
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:136
IonType iontype
which type of ion (b/y/z/ ...), see Residue::ResidueType
Definition: TargetedExperimentHelper.h:552
String id
Definition: TargetedExperimentHelper.h:475
bool operator==(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:566
RetentionTime::RTType getRetentionTimeType() const
Get compound or peptide retentiontime type.
Definition: TargetedExperimentHelper.h:295
bool operator==(const PeptideCompound &rhs) const
Definition: TargetedExperimentHelper.h:231
String id
Definition: TargetedExperimentHelper.h:106
String URI
Definition: TargetedExperimentHelper.h:86
double drift_time_
Definition: TargetedExperimentHelper.h:323
String molecular_formula
Definition: TargetedExperimentHelper.h:356
Base class to represent either a peptide or a compound.
Definition: TargetedExperimentHelper.h:213
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:609
String fullname
Definition: TargetedExperimentHelper.h:84
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool operator==(const Protein &rhs) const
Definition: TargetedExperimentHelper.h:109
double retention_time_
Definition: TargetedExperimentHelper.h:202
String sequence
Definition: TargetedExperimentHelper.h:437
bool charge_set_
Whether product ion charge is set or not.
Definition: TargetedExperimentHelper.h:664
String sequence
Definition: TargetedExperimentHelper.h:107
Representation of a residue.
Definition: Residue.h:61
bool hasRetentionTime() const
Check whether compound or peptide has an annotated retention time.
Definition: TargetedExperimentHelper.h:275
std::vector< Configuration > configuration_list_
Product ion configurations used.
Definition: TargetedExperimentHelper.h:666
CV(const String &new_id, const String &new_fullname, const String &new_version, const String &new_URI)
Definition: TargetedExperimentHelper.h:74
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:469
unsigned char ordinal
MS:1000903 : product ion series ordinal (e.g. 8 for a y8 ion)
Definition: TargetedExperimentHelper.h:550
String id
Definition: TargetedExperimentHelper.h:83
CVTermList evidence
Definition: TargetedExperimentHelper.h:436
RTType retention_time_type
Definition: TargetedExperimentHelper.h:197
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:486
Definition: TargetedExperimentHelper.h:98
void resetInterpretations()
Definition: TargetedExperimentHelper.h:657
String instrument_ref
Definition: TargetedExperimentHelper.h:68
void setChargeState(int charge)
Set the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:241
OpenMS::AASequence getAASequence(const Peptide &peptide)
helper function that converts a Peptide object to a AASequence object
String smiles_string
Definition: TargetedExperimentHelper.h:357
Definition: TargetedExperimentHelper.h:495
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:248
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:57
Represents a product ion.
Definition: TargetedExperimentHelper.h:588
Instrument()
Definition: TargetedExperimentHelper.h:481
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
Residue::ResidueType IonType
Interpretation IonType.
Definition: TargetedExperimentHelper.h:548
TraMLProduct()
Definition: TargetedExperimentHelper.h:591
ResidueType
Definition: Residue.h:150
Int32 location
Definition: TargetedExperimentHelper.h:380
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
double getMZ() const
Definition: TargetedExperimentHelper.h:627
bool charge_set_
Definition: TargetedExperimentHelper.h:322
Compound()
Definition: TargetedExperimentHelper.h:338
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
String peptide_group_label_
Definition: TargetedExperimentHelper.h:441
String contact_ref
Definition: TargetedExperimentHelper.h:511
String id
Definition: TargetedExperimentHelper.h:492
Prediction()
Definition: TargetedExperimentHelper.h:498
Definition: TargetedExperimentHelper.h:72
String contact_ref
Definition: TargetedExperimentHelper.h:67
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
double getRT() const
Definition: TargetedExperimentHelper.h:189
double getRetentionTime() const
Gets compound or peptide retention time.
Definition: TargetedExperimentHelper.h:284
void setMZ(double mz)
Definition: TargetedExperimentHelper.h:632
std::vector< CVTermList > validations
Definition: TargetedExperimentHelper.h:69
Definition: TargetedExperimentHelper.h:64
double mono_mass_delta
Definition: TargetedExperimentHelper.h:379
Modification()
Definition: TargetedExperimentHelper.h:383
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
String software_ref
Definition: TargetedExperimentHelper.h:195
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:88
String version
Definition: TargetedExperimentHelper.h:85
Publication()
Definition: TargetedExperimentHelper.h:464
int charge_
Product ion charge.
Definition: TargetedExperimentHelper.h:663
void setRT(double rt)
Definition: TargetedExperimentHelper.h:184
double avg_mass_delta
Definition: TargetedExperimentHelper.h:378
RetentionTime::RTUnit getRetentionTimeUnit() const
Get compound or peptide retentiontime unit (minute/seconds)
Definition: TargetedExperimentHelper.h:306
Definition: TargetedExperimentHelper.h:461
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
const std::vector< Configuration > & getConfigurationList() const
Definition: TargetedExperimentHelper.h:637
Interpretation()
Definition: TargetedExperimentHelper.h:555
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:254
Peptide()
Definition: TargetedExperimentHelper.h:392
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:599
std::vector< Interpretation > interpretation_list_
Product ion interpretation.
Definition: TargetedExperimentHelper.h:667
RetentionTime()
Definition: TargetedExperimentHelper.h:151
int getChargeState() const
Definition: TargetedExperimentHelper.h:621
Int32 unimod_id
Definition: TargetedExperimentHelper.h:381
String id
Definition: TargetedExperimentHelper.h:317
RTType
Definition: TargetedExperimentHelper.h:140
Product ion interpretation.
Definition: TargetedExperimentHelper.h:520
RTUnit
Definition: TargetedExperimentHelper.h:132
bool operator==(const CVTermListInterface &rhs) const
equality operator
PeptideCompound()
Definition: TargetedExperimentHelper.h:218
bool operator!=(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:574
OPENMS_INT32_TYPE Int32
Signed integer type (32bit)
Definition: Types.h:56
unsigned char rank
MS:1000926 : product interpretation rank (e.g. 1 for the most likely rank)
Definition: TargetedExperimentHelper.h:551