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;
228 peptide_group_label_ = -1;
232 static std::vector<String> * init_peptide_group_labels_ = 0;
233 if (init_peptide_group_labels_ == 0)
235 init_peptide_group_labels_ =
new std::vector<String>;
237 peptide_group_labels_ = init_peptide_group_labels_;
244 protein_refs(rhs.protein_refs),
245 evidence(rhs.evidence),
246 sequence(rhs.sequence),
248 charge_(rhs.charge_),
249 peptide_group_label_(rhs.peptide_group_label_),
250 peptide_group_labels_(rhs.peptide_group_labels_)
298 for (
Size i = 0; i < peptide_group_labels_->size(); i++)
300 if ((*peptide_group_labels_)[i] == label)
302 peptide_group_label_ = (
Int)i;
308 peptide_group_label_ = (
Int)peptide_group_labels_->size();
309 peptide_group_labels_->push_back(label);
314 if (peptide_group_label_ == -1)
318 return (*peptide_group_labels_)[peptide_group_label_];
325 if (rts.empty() || rts[0].getCVTerms()[
"MS:1000896"].empty())
328 "No retention time information (CV term 1000896) available");
330 return rts[0].getCVTerms()[
"MS:1000896"][0].getValue().toString().toDouble();
333 std::vector<RetentionTime>
rts;
338 std::vector<Modification>
mods;
502 return configuration_list_;
507 return configuration_list_.push_back(configuration);
512 cv_terms_ = cv_terms;
517 return interpretation_list_;
522 return interpretation_list_.push_back(interpretation);
541 #endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENTHELPER_H
void addConfiguration(const Configuration configuration)
Definition: TargetedExperimentHelper.h:505
Peptide(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:240
virtual ~RetentionTime()
Definition: TargetedExperimentHelper.h:149
CVTermList evidence
Definition: TargetedExperimentHelper.h:336
A more convenient string class.
Definition: String.h:56
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:490
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:500
Definition: TargetedExperimentHelper.h:374
Compound()
Definition: TargetedExperimentHelper.h:177
String instrument_ref
Definition: TargetedExperimentHelper.h:59
String software_ref
Definition: TargetedExperimentHelper.h:438
TraMLProduct & operator=(const TraMLProduct &rhs)
Definition: TargetedExperimentHelper.h:478
std::vector< CVTermList > interpretation_list_
Definition: TargetedExperimentHelper.h:528
Prediction & operator=(const Prediction &rhs)
Definition: TargetedExperimentHelper.h:448
OpenMS::AASequence getAASequence(const Peptide &peptide)
helper function that converts a Peptide object to a AASequence object
String getPeptideGroupLabel() const
Definition: TargetedExperimentHelper.h:312
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
String fullname
Definition: TargetedExperimentHelper.h:88
Peptide & operator=(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:254
CVTermList & operator=(const CVTermList &rhs)
Assignment operator.
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:412
std::vector< String > * peptide_group_labels_
Definition: TargetedExperimentHelper.h:343
void addInterpretation(const CVTermList interpretation)
Definition: TargetedExperimentHelper.h:520
TraMLProduct()
Definition: TargetedExperimentHelper.h:464
CV(const String &new_id, const String &new_fullname, const String &new_version, const String &new_URI)
Definition: TargetedExperimentHelper.h:78
int getChargeState() const
Definition: TargetedExperimentHelper.h:291
std::vector< Configuration > configuration_list_
Definition: TargetedExperimentHelper.h:527
RetentionTime & operator=(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:153
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:333
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 modifiction 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:341
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:334
Definition: TargetedExperimentHelper.h:461
Instrument()
Definition: TargetedExperimentHelper.h:405
void replaceCVTerms(Map< String, std::vector< CVTerm > > &cv_terms)
Definition: TargetedExperimentHelper.h:510
bool operator==(const CVTermList &cv_term_list) const
equality operator
Instrument & operator=(const Instrument &rhs)
Definition: TargetedExperimentHelper.h:418
Int peptide_group_label_
Definition: TargetedExperimentHelper.h:342
String id
Definition: TargetedExperimentHelper.h:87
String contact_ref
Definition: TargetedExperimentHelper.h:439
Publication & operator=(const Publication &rhs)
Definition: TargetedExperimentHelper.h:390
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:338
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:335
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:286
String id
Definition: TargetedExperimentHelper.h:382
Prediction()
Definition: TargetedExperimentHelper.h:433
Definition: TargetedExperimentHelper.h:76
void setPeptideGroupLabel(const String &label)
Definition: TargetedExperimentHelper.h:296
String sequence
Definition: TargetedExperimentHelper.h:337
Definition: TargetedExperimentHelper.h:216
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:92
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
String id
Definition: TargetedExperimentHelper.h:110
int getChargeState() const
Definition: TargetedExperimentHelper.h:495
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:384
RetentionTime(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:143
Definition: TargetedExperimentHelper.h:402
String id
Definition: TargetedExperimentHelper.h:207
Definition: TargetedExperimentHelper.h:133
String id
Definition: TargetedExperimentHelper.h:410
Definition: TargetedExperimentHelper.h:430
Definition: TargetedExperimentHelper.h:102
String contact_ref
Definition: TargetedExperimentHelper.h:58
bool operator==(const Compound &rhs) const
Definition: TargetedExperimentHelper.h:200
DoubleReal mono_mass_delta
Definition: TargetedExperimentHelper.h:221
DoubleReal avg_mass_delta
Definition: TargetedExperimentHelper.h:219
String software_ref
Definition: TargetedExperimentHelper.h:169
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:441
double getRetentionTime() const
Definition: TargetedExperimentHelper.h:321
int Int
Signed integer type.
Definition: Types.h:100
Compound(const Compound &rhs)
Definition: TargetedExperimentHelper.h:182
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
Publication()
Definition: TargetedExperimentHelper.h:377
String version
Definition: TargetedExperimentHelper.h:89
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:470
bool operator==(const Peptide &rhs) const
Definition: TargetedExperimentHelper.h:272
int charge_
Definition: TargetedExperimentHelper.h:526
Definition: TargetedExperimentHelper.h:211
const std::vector< CVTermList > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:515