129 library_intensity(-1),
131 fragment_charge(
"NA"),
133 fragment_mzdelta(-1),
135 fragment_modification(0),
136 detecting_transition(true),
137 identifying_transition(false),
138 quantifying_transition(true)
144 return CompoundName.empty();
179 void updateMembers_()
override;
192 static const char* strarray_[];
204 void getTSVHeader_(
const std::string& line,
char& delimiter, std::vector<std::string> header, std::map<std::string, int>& header_dict);
213 void readUnstructuredTSVInput_(
const char* filename,
FileTypes::Type filetype, std::vector<TSVTransition>& transition_list);
215 void spectrastRTExtract(
const String str_inp,
double & value,
bool & spectrast_legacy);
235 void resolveMixedSequenceGroups_(std::vector<TSVTransition>& transition_list);
244 void interpretRetentionTime_(std::vector<TargetedExperiment::RetentionTime>& retention_times,
const OpenMS::DataValue rt_value);
252 void addModification_(std::vector<TargetedExperiment::Peptide::Modification>& mods,
Type
Actual file types enum.
Definition: FileTypes.h:58
bool detecting_transition
Definition: TransitionTSVFile.h:119
String SMILES
Definition: TransitionTSVFile.h:107
String fragment_charge
Definition: TransitionTSVFile.h:112
String fragment_type
Definition: TransitionTSVFile.h:117
A more convenient string class.
Definition: String.h:57
String precursor_charge
Definition: TransitionTSVFile.h:109
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Typedefs.
Definition: TransitionTSVFile.h:188
String transition_name
Definition: TransitionTSVFile.h:97
String Annotation
Definition: TransitionTSVFile.h:104
Representation of a modification.
Definition: ResidueModification.h:76
double fragment_mzdelta
Definition: TransitionTSVFile.h:114
String CompoundName
Definition: TransitionTSVFile.h:106
String uniprot_id
Definition: TransitionTSVFile.h:118
int fragment_modification
Definition: TransitionTSVFile.h:116
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
String peptide_group_label
Definition: TransitionTSVFile.h:110
int fragment_nr
Definition: TransitionTSVFile.h:113
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
double product
Definition: TransitionTSVFile.h:95
double rt_calibrated
Definition: TransitionTSVFile.h:96
String FullPeptideName
Definition: TransitionTSVFile.h:105
Internal structure to represent a transition.
Definition: TransitionTSVFile.h:92
String PeptideSequence
Definition: TransitionTSVFile.h:102
bool isPeptide()
Definition: TransitionTSVFile.h:142
TSVTransition()
Definition: TransitionTSVFile.h:124
double drift_time
Definition: TransitionTSVFile.h:115
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: TransitionTSVFile.h:189
double library_intensity
Definition: TransitionTSVFile.h:99
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: TransitionTSVFile.h:190
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:399
bool decoy
Definition: TransitionTSVFile.h:101
bool force_invalid_mods_
Definition: TransitionTSVFile.h:185
String label_type
Definition: TransitionTSVFile.h:111
String ProteinName
Definition: TransitionTSVFile.h:103
This class can convert TraML and TSV files into each other.
Definition: TransitionTSVFile.h:80
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:61
bool identifying_transition
Definition: TransitionTSVFile.h:120
String SumFormula
Definition: TransitionTSVFile.h:108
bool quantifying_transition
Definition: TransitionTSVFile.h:121
Definition: TargetedExperimentHelper.h:111
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
String retentionTimeInterpretation_
Members.
Definition: TransitionTSVFile.h:183
String group_id
Definition: TransitionTSVFile.h:100
double CE
Definition: TransitionTSVFile.h:98
static const std::vector< std::string > header_names_
Definition: TransitionTSVFile.h:194
std::vector< String > peptidoforms
Definition: TransitionTSVFile.h:122
Definition: TransitionExperiment.h:206
bool override_group_label_check_
Definition: TransitionTSVFile.h:184
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:451
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
double precursor
Definition: TransitionTSVFile.h:94