50 #include <boost/numeric/conversion/cast.hpp> 61 namespace TargetedExperimentHelper
103 return id == cv.
id &&
179 retention_time_unit(
RTUnit::SIZE_OF_RTUNIT),
180 retention_time_type(
RTType::SIZE_OF_RTTYPE),
181 retention_time_set_(false),
191 software_ref(rhs.software_ref),
192 retention_time_unit(rhs.retention_time_unit),
193 retention_time_type(rhs.retention_time_type),
194 retention_time_set_(rhs.retention_time_set_),
195 retention_time_(rhs.retention_time_)
229 return retention_time_set_;
233 retention_time_ = rt;
234 retention_time_set_ =
true;
239 return retention_time_;
277 charge_(rhs.charge_),
278 charge_set_(rhs.charge_set_),
279 drift_time_(rhs.drift_time_)
343 return (!rts.empty() && rts[0].isRTset());
352 if (!hasRetentionTime())
355 "No retention time information available");
357 return rts[0].getRT();
363 if (!hasRetentionTime())
366 "No retention time information available");
368 return rts[0].retention_time_type;
374 if (!hasRetentionTime())
377 "No retention time information available");
379 return rts[0].retention_time_unit;
384 std::vector<RetentionTime>
rts;
405 theoretical_mass(0.0)
411 molecular_formula(rhs.molecular_formula),
412 smiles_string(rhs.smiles_string),
413 theoretical_mass(rhs.theoretical_mass)
480 protein_refs(rhs.protein_refs),
481 evidence(rhs.evidence),
482 sequence(rhs.sequence),
484 peptide_group_label_(rhs.peptide_group_label_)
522 void setPeptideGroupLabel(
const String & label)
525 peptide_group_label_ = label;
531 return peptide_group_label_;
538 std::vector<Modification>
mods;
711 ordinal(rhs.ordinal),
819 return configuration_list_;
824 return configuration_list_.push_back(configuration);
829 return interpretation_list_;
834 return interpretation_list_.push_back(interpretation);
839 return interpretation_list_.clear();
bool operator==(const Compound &rhs) const
Definition: TargetedExperimentHelper.h:429
double retention_time_
Definition: TargetedExperimentHelper.h:249
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:610
void addConfiguration(const Configuration configuration)
Definition: TargetedExperimentHelper.h:822
Peptide(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:478
String peptide_group_label_
Definition: TargetedExperimentHelper.h:541
int getChargeState() const
Definition: TargetedExperimentHelper.h:801
double getDriftTime() const
Return the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:333
bool operator==(const Protein &rhs) const
Definition: TargetedExperimentHelper.h:122
virtual ~RetentionTime()
Definition: TargetedExperimentHelper.h:199
CVTermList evidence
Definition: TargetedExperimentHelper.h:536
A more convenient string class.
Definition: String.h:57
const std::vector< Interpretation > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:827
RetentionTime::RTUnit getRetentionTimeUnit() const
Get compound or peptide retentiontime unit (minute/seconds)
Definition: TargetedExperimentHelper.h:372
Interpretation(const Interpretation &rhs)
Definition: TargetedExperimentHelper.h:709
double avg_mass_delta
Definition: TargetedExperimentHelper.h:459
Protein & operator=(const Protein &rhs)
Definition: TargetedExperimentHelper.h:129
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:789
String smiles_string
Definition: TargetedExperimentHelper.h:438
Compound & operator=(const Compound &rhs)
Definition: TargetedExperimentHelper.h:417
Configuration & operator=(const Configuration &rhs)
Definition: TargetedExperimentHelper.h:71
String URI
Definition: TargetedExperimentHelper.h:99
void setMZ(double mz)
Definition: TargetedExperimentHelper.h:812
RTUnit
Definition: TargetedExperimentHelper.h:157
Definition: TargetedExperimentHelper.h:572
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:106
Compound()
Definition: TargetedExperimentHelper.h:404
String instrument_ref
Definition: TargetedExperimentHelper.h:68
std::vector< Interpretation > interpretation_list_
Procution ion interpretation.
Definition: TargetedExperimentHelper.h:847
String software_ref
Definition: TargetedExperimentHelper.h:636
void setDriftTime(double dt)
Set the peptide or compound ion mobility drift time.
Definition: TargetedExperimentHelper.h:327
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:765
TraMLProduct & operator=(const TraMLProduct &rhs)
Definition: TargetedExperimentHelper.h:775
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Prediction & operator=(const Prediction &rhs)
Definition: TargetedExperimentHelper.h:646
Product ion interpretation.
Definition: TargetedExperimentHelper.h:665
OpenMS::AASequence getAASequence(const Peptide &peptide)
helper function that converts a Peptide object to a AASequence object
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
String fullname
Definition: TargetedExperimentHelper.h:97
Peptide & operator=(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:488
bool operator==(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:720
CVTermList & operator=(const CVTermList &rhs)
Assignment operator.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
TraMLProduct()
Definition: TargetedExperimentHelper.h:757
bool hasCharge() const
Whether product has set charge state.
Definition: TargetedExperimentHelper.h:796
double mono_mass_delta
Definition: TargetedExperimentHelper.h:460
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:582
Representation of a residue.
Definition: Residue.h:61
Int32 location
Definition: TargetedExperimentHelper.h:461
bool isRTset() const
Definition: TargetedExperimentHelper.h:227
CV(const String &new_id, const String &new_fullname, const String &new_version, const String &new_URI)
Definition: TargetedExperimentHelper.h:87
Interpretation & operator=(const Interpretation &rhs)
Definition: TargetedExperimentHelper.h:728
RetentionTime::RTType getRetentionTimeType() const
Get compound or peptide retentiontime type.
Definition: TargetedExperimentHelper.h:361
std::vector< Configuration > configuration_list_
Product ion configurations used.
Definition: TargetedExperimentHelper.h:846
RetentionTime & operator=(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:203
bool charge_set_
Definition: TargetedExperimentHelper.h:388
Peptide()
Definition: TargetedExperimentHelper.h:473
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
CVTermListInterface & operator=(const CVTermListInterface &rhs)
Assignment operator.
Protein()
Definition: TargetedExperimentHelper.h:114
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
unsigned char ordinal
MS:1000903 : product ion series ordinal (e.g. 8 for a y8 ion)
Definition: TargetedExperimentHelper.h:695
IonType iontype
which type of ion (b/y/z/ ...), see Residue::ResidueType
Definition: TargetedExperimentHelper.h:697
bool operator==(const RetentionTime &rhs) const
Definition: TargetedExperimentHelper.h:217
Definition: TargetedExperimentHelper.h:64
std::vector< CVTermList > validations
Definition: TargetedExperimentHelper.h:69
double getRT() const
Definition: TargetedExperimentHelper.h:236
Represents a product ion.
Definition: TargetedExperimentHelper.h:754
OPENMS_INT32_TYPE Int32
Signed integer type (32bit)
Definition: Types.h:56
Instrument()
Definition: TargetedExperimentHelper.h:603
double theoretical_mass
Definition: TargetedExperimentHelper.h:439
bool charge_set_
Whether product ion charge is set or not.
Definition: TargetedExperimentHelper.h:844
int charge_
Definition: TargetedExperimentHelper.h:387
Instrument & operator=(const Instrument &rhs)
Definition: TargetedExperimentHelper.h:616
void setRT(double rt)
Definition: TargetedExperimentHelper.h:231
String id
Definition: TargetedExperimentHelper.h:96
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:639
String contact_ref
Definition: TargetedExperimentHelper.h:637
Publication & operator=(const Publication &rhs)
Definition: TargetedExperimentHelper.h:588
String sequence
Definition: TargetedExperimentHelper.h:120
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:314
PeptideCompound()
Definition: TargetedExperimentHelper.h:265
String getPeptideGroupLabel() const
Get the peptide group label.
Definition: TargetedExperimentHelper.h:529
RetentionTime()
Definition: TargetedExperimentHelper.h:176
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:399
Base class to represent either a peptide or a compound.
Definition: TargetedExperimentHelper.h:260
double getRetentionTime() const
Gets compound or peptide retention time.
Definition: TargetedExperimentHelper.h:350
std::vector< Modification > mods
Definition: TargetedExperimentHelper.h:538
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:535
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:58
String id
Definition: TargetedExperimentHelper.h:383
String id
Definition: TargetedExperimentHelper.h:580
bool hasRetentionTime() const
Check whether compound or peptide has an annotated retention time.
Definition: TargetedExperimentHelper.h:341
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:384
double drift_time_
Definition: TargetedExperimentHelper.h:389
Prediction()
Definition: TargetedExperimentHelper.h:631
Definition: TargetedExperimentHelper.h:85
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:320
PeptideCompound(const PeptideCompound &rhs)
Definition: TargetedExperimentHelper.h:273
double getMZ() const
Definition: TargetedExperimentHelper.h:807
String sequence
Definition: TargetedExperimentHelper.h:537
Definition: TargetedExperimentHelper.h:456
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:101
const std::vector< Configuration > & getConfigurationList() const
Definition: TargetedExperimentHelper.h:817
ResidueType
Definition: Residue.h:150
Interpretation()
Definition: TargetedExperimentHelper.h:700
void addInterpretation(const Interpretation interpretation)
Definition: TargetedExperimentHelper.h:832
String id
Definition: TargetedExperimentHelper.h:119
Residue::ResidueType IonType
Interpretation IonType.
Definition: TargetedExperimentHelper.h:693
RTType
Definition: TargetedExperimentHelper.h:165
void resetInterpretations()
Definition: TargetedExperimentHelper.h:837
bool operator==(const CVTermListInterface &rhs) const
equality operator
RetentionTime(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:189
Modification()
Definition: TargetedExperimentHelper.h:464
Definition: TargetedExperimentHelper.h:600
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:152
String id
Definition: TargetedExperimentHelper.h:608
bool operator==(const CVTermList &cv_term_list) const
equality operator
Definition: TargetedExperimentHelper.h:628
double mz_
Product ion m/z.
Definition: TargetedExperimentHelper.h:845
Definition: TargetedExperimentHelper.h:111
String contact_ref
Definition: TargetedExperimentHelper.h:67
Int32 unimod_id
Definition: TargetedExperimentHelper.h:462
RTType retention_time_type
Definition: TargetedExperimentHelper.h:244
void setChargeState(int charge)
Set the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:307
String software_ref
Definition: TargetedExperimentHelper.h:242
bool operator!=(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:740
bool retention_time_set_
Definition: TargetedExperimentHelper.h:248
Compound(const Compound &rhs)
Definition: TargetedExperimentHelper.h:409
String molecular_formula
Definition: TargetedExperimentHelper.h:437
Publication()
Definition: TargetedExperimentHelper.h:575
bool operator==(const Peptide &rhs) const
Definition: TargetedExperimentHelper.h:502
String version
Definition: TargetedExperimentHelper.h:98
bool operator==(const PeptideCompound &rhs) const
Definition: TargetedExperimentHelper.h:297
int charge_
Product ion charge.
Definition: TargetedExperimentHelper.h:843
unsigned char rank
MS:1000926 : product interpretation rank (e.g. 1 for the most likely rank)
Definition: TargetedExperimentHelper.h:696
PeptideCompound & operator=(const PeptideCompound &rhs)
Definition: TargetedExperimentHelper.h:283
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:451
RTUnit retention_time_unit
Definition: TargetedExperimentHelper.h:243