35 #ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENTHELPER_H 36 #define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENTHELPER_H 51 #include <boost/numeric/conversion/cast.hpp> 61 namespace TargetedExperimentHelper
89 fullname(new_fullname),
103 return id == cv.
id &&
154 software_ref(rhs.software_ref)
188 theoretical_mass(0.0),
198 molecular_formula(rhs.molecular_formula),
199 smiles_string(rhs.smiles_string),
200 theoretical_mass(rhs.theoretical_mass),
201 charge_(rhs.charge_),
202 charge_set_(rhs.charge_set_)
255 std::vector<RetentionTime>
rts;
299 protein_refs(rhs.protein_refs),
300 evidence(rhs.evidence),
301 sequence(rhs.sequence),
303 charge_(rhs.charge_),
304 charge_set_(rhs.charge_set_),
305 peptide_group_label_(rhs.peptide_group_label_)
371 void setPeptideGroupLabel(
const String & label)
374 peptide_group_label_ = label;
380 return peptide_group_label_;
388 if (rts.empty() || rts[0].getCVTerms()[
"MS:1000896"].empty())
391 "No retention time information (CV term 1000896) available");
393 return rts[0].getCVTerms()[
"MS:1000896"][0].getValue().toString().toDouble();
396 std::vector<RetentionTime>
rts;
401 std::vector<Modification>
mods;
570 ordinal(rhs.ordinal),
672 return configuration_list_;
677 return configuration_list_.push_back(configuration);
682 return interpretation_list_;
687 return interpretation_list_.push_back(interpretation);
692 return interpretation_list_.clear();
714 #endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENTHELPER_H
bool operator==(const Compound &rhs) const
Definition: TargetedExperimentHelper.h:222
bool operator==(const Instrument &rhs) const
Definition: TargetedExperimentHelper.h:475
void addConfiguration(const Configuration configuration)
Definition: TargetedExperimentHelper.h:675
Peptide(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:295
String peptide_group_label_
Definition: TargetedExperimentHelper.h:406
int getChargeState() const
Definition: TargetedExperimentHelper.h:654
bool operator==(const Protein &rhs) const
Definition: TargetedExperimentHelper.h:122
virtual ~RetentionTime()
Definition: TargetedExperimentHelper.h:158
CVTermList evidence
Definition: TargetedExperimentHelper.h:399
A more convenient string class.
Definition: String.h:57
const std::vector< Interpretation > & getInterpretationList() const
Definition: TargetedExperimentHelper.h:680
Interpretation(const Interpretation &rhs)
Definition: TargetedExperimentHelper.h:568
double avg_mass_delta
Definition: TargetedExperimentHelper.h:274
Protein & operator=(const Protein &rhs)
Definition: TargetedExperimentHelper.h:129
Representation of controlled vocabulary term list.
Definition: CVTermList.h:53
void setChargeState(int charge)
Definition: TargetedExperimentHelper.h:642
bool hasCharge() const
Whether peptide has set charge state.
Definition: TargetedExperimentHelper.h:349
String smiles_string
Definition: TargetedExperimentHelper.h:257
Compound & operator=(const Compound &rhs)
Definition: TargetedExperimentHelper.h:206
Configuration & operator=(const Configuration &rhs)
Definition: TargetedExperimentHelper.h:71
String URI
Definition: TargetedExperimentHelper.h:99
void setMZ(double mz)
Definition: TargetedExperimentHelper.h:665
Definition: TargetedExperimentHelper.h:437
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:107
Compound()
Definition: TargetedExperimentHelper.h:186
String instrument_ref
Definition: TargetedExperimentHelper.h:68
std::vector< Interpretation > interpretation_list_
Definition: TargetedExperimentHelper.h:700
String software_ref
Definition: TargetedExperimentHelper.h:501
bool operator==(const TraMLProduct &rhs) const
Definition: TargetedExperimentHelper.h:618
TraMLProduct & operator=(const TraMLProduct &rhs)
Definition: TargetedExperimentHelper.h:628
Prediction & operator=(const Prediction &rhs)
Definition: TargetedExperimentHelper.h:511
Definition: TargetedExperimentHelper.h:524
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:108
String fullname
Definition: TargetedExperimentHelper.h:97
Peptide & operator=(const Peptide &rhs)
Definition: TargetedExperimentHelper.h:309
bool operator==(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:579
int getChargeState() const
Return the compound charge state.
Definition: TargetedExperimentHelper.h:248
CVTermList & operator=(const CVTermList &rhs)
Assignment operator.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
TraMLProduct()
Definition: TargetedExperimentHelper.h:610
bool hasCharge() const
Whether product has set charge state.
Definition: TargetedExperimentHelper.h:649
double mono_mass_delta
Definition: TargetedExperimentHelper.h:275
bool operator==(const Publication &rhs) const
Definition: TargetedExperimentHelper.h:447
Representation of a residue.
Definition: Residue.h:62
Int32 location
Definition: TargetedExperimentHelper.h:276
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:587
std::vector< Configuration > configuration_list_
Definition: TargetedExperimentHelper.h:699
RetentionTime & operator=(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:162
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:396
std::vector< RetentionTime > rts
Definition: TargetedExperimentHelper.h:255
Peptide()
Definition: TargetedExperimentHelper.h:288
bool hasCharge() const
Whether compound has set charge state.
Definition: TargetedExperimentHelper.h:242
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:649
unsigned char ordinal
Definition: TargetedExperimentHelper.h:554
IonType iontype
Definition: TargetedExperimentHelper.h:556
bool operator==(const RetentionTime &rhs) const
Definition: TargetedExperimentHelper.h:172
int charge_
Definition: TargetedExperimentHelper.h:404
Definition: TargetedExperimentHelper.h:64
std::vector< CVTermList > validations
Definition: TargetedExperimentHelper.h:69
String id
Definition: TargetedExperimentHelper.h:397
Definition: TargetedExperimentHelper.h:607
void setChargeState(int charge)
Set the peptide charge state.
Definition: TargetedExperimentHelper.h:235
OPENMS_INT32_TYPE Int32
Signed integer type (32bit)
Definition: Types.h:57
Instrument()
Definition: TargetedExperimentHelper.h:468
double theoretical_mass
Definition: TargetedExperimentHelper.h:258
bool charge_set_
Definition: TargetedExperimentHelper.h:697
Instrument & operator=(const Instrument &rhs)
Definition: TargetedExperimentHelper.h:481
bool charge_set_
Definition: TargetedExperimentHelper.h:262
String id
Definition: TargetedExperimentHelper.h:96
bool operator==(const Prediction &rhs) const
Definition: TargetedExperimentHelper.h:504
String contact_ref
Definition: TargetedExperimentHelper.h:502
Publication & operator=(const Publication &rhs)
Definition: TargetedExperimentHelper.h:453
String sequence
Definition: TargetedExperimentHelper.h:120
String getPeptideGroupLabel() const
Get the peptide group label.
Definition: TargetedExperimentHelper.h:378
RetentionTime()
Definition: TargetedExperimentHelper.h:147
Definition: TargetedExperimentHelper.h:181
std::vector< Modification > mods
Definition: TargetedExperimentHelper.h:401
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:398
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:59
void setChargeState(int charge)
Set the peptide charge state.
Definition: TargetedExperimentHelper.h:342
String id
Definition: TargetedExperimentHelper.h:445
Prediction()
Definition: TargetedExperimentHelper.h:496
Definition: TargetedExperimentHelper.h:85
double getMZ() const
Definition: TargetedExperimentHelper.h:660
String sequence
Definition: TargetedExperimentHelper.h:400
Definition: TargetedExperimentHelper.h:271
bool operator==(const CV &cv) const
Definition: TargetedExperimentHelper.h:101
const std::vector< Configuration > & getConfigurationList() const
Definition: TargetedExperimentHelper.h:670
ResidueType
Definition: Residue.h:144
Interpretation()
Definition: TargetedExperimentHelper.h:559
void addInterpretation(const Interpretation interpretation)
Definition: TargetedExperimentHelper.h:685
int getChargeState() const
Return the peptide charge state.
Definition: TargetedExperimentHelper.h:355
String id
Definition: TargetedExperimentHelper.h:119
Residue::ResidueType IonType
Definition: TargetedExperimentHelper.h:552
double getRetentionTime() const
Definition: TargetedExperimentHelper.h:384
void resetInterpretations()
Definition: TargetedExperimentHelper.h:690
bool operator==(const CVTermListInterface &rhs) const
equality operator
RetentionTime(const RetentionTime &rhs)
Definition: TargetedExperimentHelper.h:152
Modification()
Definition: TargetedExperimentHelper.h:279
Definition: TargetedExperimentHelper.h:465
String id
Definition: TargetedExperimentHelper.h:254
Definition: TargetedExperimentHelper.h:142
String id
Definition: TargetedExperimentHelper.h:473
bool operator==(const CVTermList &cv_term_list) const
equality operator
Definition: TargetedExperimentHelper.h:493
double mz_
Definition: TargetedExperimentHelper.h:698
Definition: TargetedExperimentHelper.h:111
int charge_
Definition: TargetedExperimentHelper.h:261
String contact_ref
Definition: TargetedExperimentHelper.h:67
Int32 unimod_id
Definition: TargetedExperimentHelper.h:277
String software_ref
Definition: TargetedExperimentHelper.h:178
bool operator!=(const Interpretation &rhs) const
Definition: TargetedExperimentHelper.h:599
Compound(const Compound &rhs)
Definition: TargetedExperimentHelper.h:194
String molecular_formula
Definition: TargetedExperimentHelper.h:256
Publication()
Definition: TargetedExperimentHelper.h:440
bool operator==(const Peptide &rhs) const
Definition: TargetedExperimentHelper.h:327
String version
Definition: TargetedExperimentHelper.h:98
bool charge_set_
Definition: TargetedExperimentHelper.h:405
int charge_
Definition: TargetedExperimentHelper.h:696
unsigned char rank
Definition: TargetedExperimentHelper.h:555
Definition: TargetedExperimentHelper.h:266