35 #ifndef OPENMS_ANALYSIS_OPENSWATH_TRANSITIONTSVREADER_H 36 #define OPENMS_ANALYSIS_OPENSWATH_TRANSITIONTSVREADER_H 135 static const char* strarray_[];
147 void getTSVHeader_(
const std::string& line,
char& delimiter, std::vector<std::string> header, std::map<std::string, int>& header_dict);
156 void readUnstructuredTSVInput_(
const char* filename,
FileTypes::Type filetype, std::vector<TSVTransition>& transition_list);
202 void resolveMixedSequenceGroups_(std::vector<TSVTransition>& transition_list);
210 void addModification_(std::vector<TargetedExperiment::Peptide::Modification>& mods,
225 void updateMembers_();
Type
Actual file types enum.
Definition: FileTypes.h:59
double fragment_mzdelta
Definition: TransitionTSVReader.h:124
bool override_group_label_check_
Definition: TransitionTSVReader.h:92
double CE
Definition: TransitionTSVReader.h:111
int fragment_modification
Definition: TransitionTSVReader.h:125
A more convenient string class.
Definition: String.h:57
bool identifying_transition
Definition: TransitionTSVReader.h:129
String Annotation
Definition: TransitionTSVReader.h:117
String site_identifying_transition
Definition: TransitionTSVReader.h:130
String label_type
Definition: TransitionTSVReader.h:121
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Typedefs.
Definition: TransitionTSVReader.h:95
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: TransitionTSVReader.h:96
This class can convert TraML and TSV files into each other.
Definition: TransitionTSVReader.h:84
String site_identifying_class
Definition: TransitionTSVReader.h:131
Representation of a modification.
Definition: ResidueModification.h:65
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
double precursor
Definition: TransitionTSVReader.h:107
double library_intensity
Definition: TransitionTSVReader.h:112
String ProteinName
Definition: TransitionTSVReader.h:116
int decoy
Definition: TransitionTSVReader.h:114
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: TransitionTSVReader.h:97
String group_id
Definition: TransitionTSVReader.h:113
String uniprot_id
Definition: TransitionTSVReader.h:127
int precursor_charge
Definition: TransitionTSVReader.h:119
String fragment_type
Definition: TransitionTSVReader.h:126
String peptide_group_label
Definition: TransitionTSVReader.h:120
bool quantifying_transition
Definition: TransitionTSVReader.h:132
int fragment_nr
Definition: TransitionTSVReader.h:123
double product
Definition: TransitionTSVReader.h:108
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
Internal structure to represent a transition.
Definition: TransitionTSVReader.h:105
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
String transition_name
Definition: TransitionTSVReader.h:110
String PeptideSequence
Definition: TransitionTSVReader.h:115
bool detecting_transition
Definition: TransitionTSVReader.h:128
String retentionTimeInterpretation_
Members.
Definition: TransitionTSVReader.h:91
Definition: TargetedExperimentHelper.h:102
double rt_calibrated
Definition: TransitionTSVReader.h:109
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
static const std::vector< std::string > header_names_
Definition: TransitionTSVReader.h:137
int fragment_charge
Definition: TransitionTSVReader.h:122
Definition: TransitionExperiment.h:179
String FullPeptideName
Definition: TransitionTSVReader.h:118
Definition: TargetedExperimentHelper.h:211
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:55