50 #include <boost/numeric/conversion/cast.hpp> 61 namespace TargetedExperimentHelper
76 fullname(new_fullname),
154 retention_time_unit(
RTUnit::SIZE_OF_RTUNIT),
155 retention_time_type(
RTType::SIZE_OF_RTTYPE),
156 retention_time_set_(false),
182 return retention_time_set_;
186 retention_time_ = rt;
187 retention_time_set_ =
true;
192 return retention_time_;
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)
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();
RTUnit
Definition: TargetedExperimentHelper.h:132
RetentionTime()
Definition: TargetedExperimentHelper.h:151
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:469
Definition: TargetedExperimentHelper.h:495
String contact_ref
Definition: TargetedExperimentHelper.h:511
Protein()
Definition: TargetedExperimentHelper.h:101
Definition: TargetedExperimentHelper.h:444
OpenMS::AASequence getAASequence(const Peptide &peptide)
helper function that converts a Peptide object to a AASequence object
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:609
RetentionTime::RTType getRetentionTimeType() const
Get compound or peptide retentiontime type.
Definition: TargetedExperimentHelper.h:295
String molecular_formula
Definition: TargetedExperimentHelper.h:356
Contact()
Definition: TargetedExperimentHelper.h:447
bool operator==(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:566
void setDriftTime(double dt)
Set the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:261
int charge_
Definition: TargetedExperimentHelper.h:321
IonType iontype
which type of ion (b/y/z/ ...), see Residue::ResidueType
Definition: TargetedExperimentHelper.h:552
bool operator==(const Protein &rhs) const
Definition: TargetedExperimentHelper.h:109
Int32 unimod_id
Definition: TargetedExperimentHelper.h:381
String id
Definition: TargetedExperimentHelper.h:317
bool operator==(const RetentionTime &rhs) const
Definition: TargetedExperimentHelper.h:170
double mono_mass_delta
Definition: TargetedExperimentHelper.h:379
Int32 location
Definition: TargetedExperimentHelper.h:380
bool operator==(const Compound &rhs) const
Definition: TargetedExperimentHelper.h:348
bool hasRetentionTime() const
Check whether compound or peptide has an annotated retention time.
Definition: TargetedExperimentHelper.h:275
double avg_mass_delta
Definition: TargetedExperimentHelper.h:378
Residue::ResidueType IonType
Interpretation IonType.
Definition: TargetedExperimentHelper.h:548
int charge_
Product ion charge.
Definition: TargetedExperimentHelper.h:663
String fullname
Definition: TargetedExperimentHelper.h:84
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:318
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:248
double getMZ() const
Definition: TargetedExperimentHelper.h:627
RTType
Definition: TargetedExperimentHelper.h:140
String sequence
Definition: TargetedExperimentHelper.h:107
Representation of a residue.
Definition: Residue.h:61
const std::vector< Interpretation > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:647
Product ion interpretation.
Definition: TargetedExperimentHelper.h:520
OPENMS_INT32_TYPE Int32
Signed integer type (32bit)
Definition: Types.h:56
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:435
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:599
double mz_
Product ion m/z.
Definition: TargetedExperimentHelper.h:665
String id
Definition: TargetedExperimentHelper.h:475
unsigned char ordinal
MS:1000903 : product ion series ordinal (e.g. 8 for a y8 ion)
Definition: TargetedExperimentHelper.h:550
Interpretation()
Definition: TargetedExperimentHelper.h:555
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:136
String version
Definition: TargetedExperimentHelper.h:85
RetentionTime::RTUnit getRetentionTimeUnit() const
Get compound or peptide retentiontime unit (minute/seconds)
Definition: TargetedExperimentHelper.h:306
bool operator==(const CVTermList &cv_term_list) const
equality operator
bool charge_set_
Definition: TargetedExperimentHelper.h:322
Compound()
Definition: TargetedExperimentHelper.h:338
unsigned char rank
MS:1000926 : product interpretation rank (e.g. 1 for the most likely rank)
Definition: TargetedExperimentHelper.h:551
Publication()
Definition: TargetedExperimentHelper.h:464
bool hasCharge() const
Whether product has set charge state.
Definition: TargetedExperimentHelper.h:616
double drift_time_
Definition: TargetedExperimentHelper.h:323
const std::vector< Configuration > & getConfigurationList() const
Definition: TargetedExperimentHelper.h:637
String instrument_ref
Definition: TargetedExperimentHelper.h:68
Definition: TargetedExperimentHelper.h:64
bool isRTset() const
Definition: TargetedExperimentHelper.h:180
void setRT(double rt)
Definition: TargetedExperimentHelper.h:184
std::vector< Modification > mods
Definition: TargetedExperimentHelper.h:438
CV(const String &new_id, const String &new_fullname, const String &new_version, const String &new_URI)
Definition: TargetedExperimentHelper.h:74
bool operator==(const Contact &rhs) const
Definition: TargetedExperimentHelper.h:452
String id
Definition: TargetedExperimentHelper.h:492
String contact_ref
Definition: TargetedExperimentHelper.h:67
CVTermList & operator=(const CVTermList &rhs) &=default
Assignment operator.
String sequence
Definition: TargetedExperimentHelper.h:437
String peptide_group_label_
Definition: TargetedExperimentHelper.h:441
void setChargeState(int charge)
Set the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:241
PeptideCompound()
Definition: TargetedExperimentHelper.h:218
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
std::vector< Interpretation > interpretation_list_
Product ion interpretation.
Definition: TargetedExperimentHelper.h:667
Definition: TargetedExperimentHelper.h:98
String URI
Definition: TargetedExperimentHelper.h:86
String id
Definition: TargetedExperimentHelper.h:83
int getChargeState() const
Definition: TargetedExperimentHelper.h:621
bool operator==(const Peptide &rhs) const
Definition: TargetedExperimentHelper.h:402
String software_ref
Definition: TargetedExperimentHelper.h:195
void addConfiguration(const Configuration &configuration)
Definition: TargetedExperimentHelper.h:642
Definition: TargetedExperimentHelper.h:478
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:57
double retention_time_
Definition: TargetedExperimentHelper.h:202
Definition: TargetedExperimentHelper.h:375
String id
Definition: TargetedExperimentHelper.h:458
double theoretical_mass
Definition: TargetedExperimentHelper.h:358
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
double getRT() const
Definition: TargetedExperimentHelper.h:189
Represents a product ion.
Definition: TargetedExperimentHelper.h:588
RTType retention_time_type
Definition: TargetedExperimentHelper.h:197
bool retention_time_set_
Definition: TargetedExperimentHelper.h:201
bool operator!=(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:574
void setMZ(double mz)
Definition: TargetedExperimentHelper.h:632
void addInterpretation(const Interpretation &interpretation)
Definition: TargetedExperimentHelper.h:652
ResidueType
Definition: Residue.h:150
Prediction()
Definition: TargetedExperimentHelper.h:498
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:503
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
String getPeptideGroupLabel() const
Get the peptide group label.
Definition: TargetedExperimentHelper.h:429
Peptide()
Definition: TargetedExperimentHelper.h:392
A more convenient string class.
Definition: String.h:58
std::vector< Configuration > configuration_list_
Product ion configurations used.
Definition: TargetedExperimentHelper.h:666
Instrument()
Definition: TargetedExperimentHelper.h:481
void resetInterpretations()
Definition: TargetedExperimentHelper.h:657
Base class to represent either a peptide or a compound.
Definition: TargetedExperimentHelper.h:213
Definition: TargetedExperimentHelper.h:72
TraMLProduct()
Definition: TargetedExperimentHelper.h:591
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:254
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:486
String software_ref
Definition: TargetedExperimentHelper.h:510
double getDriftTime() const
Return the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:267
Definition: TargetedExperimentHelper.h:461
String smiles_string
Definition: TargetedExperimentHelper.h:357
bool operator==(const PeptideCompound &rhs) const
Definition: TargetedExperimentHelper.h:231
String id
Definition: TargetedExperimentHelper.h:106
RTUnit retention_time_unit
Definition: TargetedExperimentHelper.h:196
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:88
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
bool operator==(const CVTermListInterface &rhs) const
equality operator
std::vector< CVTermList > validations
Definition: TargetedExperimentHelper.h:69
Modification()
Definition: TargetedExperimentHelper.h:383
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
CVTermList evidence
Definition: TargetedExperimentHelper.h:436
bool charge_set_
Whether product ion charge is set or not.
Definition: TargetedExperimentHelper.h:664
double getRetentionTime() const
Gets compound or peptide retention time.
Definition: TargetedExperimentHelper.h:284