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OpenMS
2.6.0
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158 double precursor = -1;
160 double rt_calibrated = -1;
163 double library_intensity = -1;
179 int fragment_nr = -1;
180 double fragment_mzdelta = -1;
181 double drift_time = -1;
182 int fragment_modification = 0;
185 bool detecting_transition =
true;
186 bool identifying_transition =
false;
187 bool quantifying_transition =
true;
194 return CompoundName.empty() || CompoundName ==
"NA";
229 void updateMembers_()
override;
243 static const char* strarray_[];
259 void getTSVHeader_(
const std::string& line,
char& delimiter, std::map<std::string, int>& header_dict)
const;
268 void readUnstructuredTSVInput_(
const char* filename,
FileTypes::Type filetype, std::vector<TSVTransition>& transition_list);
271 void spectrastRTExtract(
const String str_inp,
double & value,
bool & spectrast_legacy);
298 void resolveMixedSequenceGroups_(std::vector<TSVTransition>& transition_list)
const;
301 void createTransition_(std::vector<TSVTransition>::iterator& tr_it,
305 void createProtein_(
String protein_name,
String uniprot_id,
309 void interpretRetentionTime_(std::vector<TargetedExperiment::RetentionTime>& retention_times,
313 void createPeptide_(std::vector<TSVTransition>::const_iterator tr_it,
317 void createCompound_(std::vector<TSVTransition>::const_iterator tr_it,
321 void addModification_(std::vector<TargetedExperiment::Peptide::Modification>& mods,
std::vector< String > ProteinName
List of protein identifiers.
Definition: TransitionTSVFile.h:167
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:144
String SMILES
SMILES identifier (for metabolomics)
Definition: TransitionTSVFile.h:172
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: TransitionTSVFile.h:241
bool isPeptide() const
Definition: TransitionTSVFile.h:192
Representation of a modification.
Definition: ResidueModification.h:76
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
std::vector< String > peptidoforms
List of peptidoforms.
Definition: TransitionTSVFile.h:188
A more convenient string class.
Definition: String.h:59
String fragment_type
Fragment type (e.g. "y" for a y7 ion)
Definition: TransitionTSVFile.h:183
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: TransitionTSVFile.h:240
bool override_group_label_check_
Definition: TransitionTSVFile.h:235
Definition: TransitionExperiment.h:207
String GeneName
Gene identifier.
Definition: TransitionTSVFile.h:168
String FullPeptideName
Full peptide sequence with UniMod modifications.
Definition: TransitionTSVFile.h:170
String Adducts
Adducts (for metabolomics)
Definition: TransitionTSVFile.h:174
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
Type
Actual file types enum.
Definition: FileTypes.h:58
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
Definition: TargetedExperimentHelper.h:98
Internal structure to represent a transition.
Definition: TransitionTSVFile.h:156
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
String Annotation
Fragment ion annotation.
Definition: TransitionTSVFile.h:169
String CompoundName
Compound name (for metabolomics)
Definition: TransitionTSVFile.h:171
std::vector< String > uniprot_id
List of UniProt identifiers of associated proteins.
Definition: TransitionTSVFile.h:184
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: TransitionTSVFile.h:239
String peptide_group_label
Peptide group identifier (grouping isotopically labelled peptides)
Definition: TransitionTSVFile.h:176
String precursor_charge
Precursor charge state.
Definition: TransitionTSVFile.h:175
bool force_invalid_mods_
Definition: TransitionTSVFile.h:236
String SumFormula
Molecular formula (for metabolomics)
Definition: TransitionTSVFile.h:173
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
String label_type
Type of label that was used (e.g. "heavy" or "light")
Definition: TransitionTSVFile.h:177
static const std::vector< std::string > header_names_
Definition: TransitionTSVFile.h:245
String retentionTimeInterpretation_
Definition: TransitionTSVFile.h:234
String PeptideSequence
Peptide sequence (only AA sequence)
Definition: TransitionTSVFile.h:166