35 #ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENTHELPER_H
36 #define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENTHELPER_H
42 #include <boost/numeric/conversion/cast.hpp>
52 namespace TargetedExperimentHelper
145 software_ref(rhs.software_ref)
208 std::vector<RetentionTime>
rts;
234 protein_refs(rhs.protein_refs),
235 evidence(rhs.evidence),
236 sequence(rhs.sequence),
238 charge_(rhs.charge_),
239 peptide_group_label_(rhs.peptide_group_label_)
295 void setPeptideGroupLabel(
const String & label)
298 peptide_group_label_ = label;
304 return peptide_group_label_;
312 if (rts.empty() || rts[0].getCVTerms()[
"MS:1000896"].empty())
315 "No retention time information (CV term 1000896) available");
317 return rts[0].getCVTerms()[
"MS:1000896"][0].getValue().toString().toDouble();
320 std::vector<RetentionTime>
rts;
325 std::vector<Modification>
mods;
488 return configuration_list_;
493 return configuration_list_.push_back(configuration);
498 cv_terms_ = cv_terms;
503 return interpretation_list_;
508 return interpretation_list_.push_back(interpretation);
513 return interpretation_list_.clear();
532 #endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENTHELPER_H
void addConfiguration(const Configuration configuration)
Definition: TargetedExperimentHelper.h:491
Peptide(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:230
String peptide_group_label_
Definition: TargetedExperimentHelper.h:329
virtual ~RetentionTime()
Definition: TargetedExperimentHelper.h:149
CVTermList evidence
Definition: TargetedExperimentHelper.h:323
A more convenient string class.
Definition: String.h:57
double avg_mass_delta
Definition: TargetedExperimentHelper.h:219
Protein & operator=(const Protein &rhs)
Definition: TargetedExperimentHelper.h:120
Representation of controlled vocabulary term list.
Definition: CVTermList.h:54
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:476
Compound & operator=(const Compound &rhs)
Definition: TargetedExperimentHelper.h:189
Configuration & operator=(const Configuration &rhs)
Definition: TargetedExperimentHelper.h:62
int location
Definition: TargetedExperimentHelper.h:220
String URI
Definition: TargetedExperimentHelper.h:90
const std::vector< Configuration > & getConfigurationList() const
Definition: TargetedExperimentHelper.h:486
Definition: TargetedExperimentHelper.h:360
Compound()
Definition: TargetedExperimentHelper.h:177
String instrument_ref
Definition: TargetedExperimentHelper.h:59
String software_ref
Definition: TargetedExperimentHelper.h:424
TraMLProduct & operator=(const TraMLProduct &rhs)
Definition: TargetedExperimentHelper.h:464
std::vector< CVTermList > interpretation_list_
Definition: TargetedExperimentHelper.h:519
Prediction & operator=(const Prediction &rhs)
Definition: TargetedExperimentHelper.h:434
OpenMS::AASequence getAASequence(const Peptide &peptide)
helper function that converts a Peptide object to a AASequence object
String getPeptideGroupLabel() const
Get the peptide group label.
Definition: TargetedExperimentHelper.h:302
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
String fullname
Definition: TargetedExperimentHelper.h:88
Peptide & operator=(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:243
CVTermList & operator=(const CVTermList &rhs)
Assignment operator.
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:398
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
void addInterpretation(const CVTermList interpretation)
Definition: TargetedExperimentHelper.h:506
TraMLProduct()
Definition: TargetedExperimentHelper.h:450
double mono_mass_delta
Definition: TargetedExperimentHelper.h:221
CV(const String &new_id, const String &new_fullname, const String &new_version, const String &new_URI)
Definition: TargetedExperimentHelper.h:78
int getChargeState() const
Return the peptide charge state.
Definition: TargetedExperimentHelper.h:280
std::vector< Configuration > configuration_list_
Definition: TargetedExperimentHelper.h:518
RetentionTime & operator=(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:153
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:320
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:208
Peptide()
Definition: TargetedExperimentHelper.h:224
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
Protein()
Definition: TargetedExperimentHelper.h:105
A method or algorithm argument contains illegal values.
Definition: Exception.h:634
int charge_
Definition: TargetedExperimentHelper.h:328
bool operator==(const Protein &rhs) const
Definition: TargetedExperimentHelper.h:113
Definition: TargetedExperimentHelper.h:55
std::vector< CVTermList > validations
Definition: TargetedExperimentHelper.h:60
String id
Definition: TargetedExperimentHelper.h:321
Definition: TargetedExperimentHelper.h:447
Instrument()
Definition: TargetedExperimentHelper.h:391
void replaceCVTerms(Map< String, std::vector< CVTerm > > &cv_terms)
Definition: TargetedExperimentHelper.h:496
bool operator==(const CVTermList &cv_term_list) const
equality operator
Instrument & operator=(const Instrument &rhs)
Definition: TargetedExperimentHelper.h:404
String id
Definition: TargetedExperimentHelper.h:87
String contact_ref
Definition: TargetedExperimentHelper.h:425
Publication & operator=(const Publication &rhs)
Definition: TargetedExperimentHelper.h:376
String sequence
Definition: TargetedExperimentHelper.h:111
RetentionTime()
Definition: TargetedExperimentHelper.h:138
bool operator==(const RetentionTime &rhs) const
Definition: TargetedExperimentHelper.h:163
Definition: TargetedExperimentHelper.h:172
std::vector< Modification > mods
Definition: TargetedExperimentHelper.h:325
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:322
void setChargeState(int charge)
Set the peptide charge state.
Definition: TargetedExperimentHelper.h:274
String id
Definition: TargetedExperimentHelper.h:368
Prediction()
Definition: TargetedExperimentHelper.h:419
Definition: TargetedExperimentHelper.h:76
String sequence
Definition: TargetedExperimentHelper.h:324
Definition: TargetedExperimentHelper.h:216
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:92
String id
Definition: TargetedExperimentHelper.h:110
int getChargeState() const
Definition: TargetedExperimentHelper.h:481
void resetInterpretations()
Definition: TargetedExperimentHelper.h:511
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:370
RetentionTime(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:143
Definition: TargetedExperimentHelper.h:388
String id
Definition: TargetedExperimentHelper.h:207
Definition: TargetedExperimentHelper.h:133
String id
Definition: TargetedExperimentHelper.h:396
Definition: TargetedExperimentHelper.h:416
Definition: TargetedExperimentHelper.h:102
String contact_ref
Definition: TargetedExperimentHelper.h:58
bool operator==(const Compound &rhs) const
Definition: TargetedExperimentHelper.h:200
String software_ref
Definition: TargetedExperimentHelper.h:169
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:427
double getRetentionTime() const
Definition: TargetedExperimentHelper.h:308
Compound(const Compound &rhs)
Definition: TargetedExperimentHelper.h:182
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
Publication()
Definition: TargetedExperimentHelper.h:363
String version
Definition: TargetedExperimentHelper.h:89
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:456
bool operator==(const Peptide &rhs) const
Definition: TargetedExperimentHelper.h:260
int charge_
Definition: TargetedExperimentHelper.h:517
Definition: TargetedExperimentHelper.h:211
const std::vector< CVTermList > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:501