35 #ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H 
   36 #define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H 
  111     void clear(
bool clear_meta_data);
 
  117     void setCVs(
const std::vector<CV> & cvs);
 
  119     const std::vector<CV> & getCVs() 
const;
 
  121     void addCV(
const CV & cv);
 
  124     void setContacts(
const std::vector<Contact> & contacts);
 
  126     const std::vector<Contact> & getContacts() 
const;
 
  128     void addContact(
const Contact & contact);
 
  131     void setPublications(
const std::vector<Publication> & publications);
 
  133     const std::vector<Publication> & getPublications() 
const;
 
  135     void addPublication(
const Publication & publication);
 
  138     void setTargetCVTerms(
const CVTermList & cv_terms);
 
  142     void addTargetCVTerm(
const CVTerm & cv_term);
 
  147     void setInstruments(
const std::vector<Instrument> & instruments);
 
  149     const std::vector<Instrument> & getInstruments() 
const;
 
  151     void addInstrument(
const Instrument & instrument);
 
  154     void setSoftware(
const std::vector<Software> & software);
 
  156     const std::vector<Software> & getSoftware() 
const;
 
  158     void addSoftware(
const Software & software);
 
  161     void setProteins(
const std::vector<Protein> & proteins);
 
  163     const std::vector<Protein> & getProteins() 
const;
 
  167     void addProtein(
const Protein & protein);
 
  170     void setCompounds(
const std::vector<Compound> & rhs);
 
  172     const std::vector<Compound> & getCompounds() 
const;
 
  174     void addCompound(
const Compound & rhs);
 
  176     void setPeptides(
const std::vector<Peptide> & rhs);
 
  178     const std::vector<Peptide> & getPeptides() 
const;
 
  182     void addPeptide(
const Peptide & rhs);
 
  185     void setTransitions(
const std::vector<ReactionMonitoringTransition> & transitions);
 
  188     const std::vector<ReactionMonitoringTransition> & getTransitions() 
const;
 
  193     void setIncludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
 
  195     const std::vector<IncludeExcludeTarget> & getIncludeTargets() 
const;
 
  199     void setExcludeTargets(
const std::vector<IncludeExcludeTarget> & targets);
 
  201     const std::vector<IncludeExcludeTarget> & getExcludeTargets() 
const;
 
  206     void setSourceFiles(
const std::vector<SourceFile> & source_files);
 
  209     const std::vector<SourceFile> & getSourceFiles() 
const;
 
  212     void addSourceFile(
const SourceFile & source_file);
 
  220     void sortTransitionsByProductMZ();
 
  225     void createProteinReferenceMap_();
 
  227     void createPeptideReferenceMap_();
 
  266   namespace TargetedExperimentHelper
 
  273 #endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H 
CVTermList targets_
Definition: TargetedExperiment.h:237
A more convenient string class. 
Definition: String.h:56
std::vector< IncludeExcludeTarget > include_targets_
Definition: TargetedExperiment.h:249
Representation of controlled vocabulary term list. 
Definition: CVTermList.h:54
Definition: TargetedExperimentHelper.h:374
TargetedExperimentHelper::Peptide Peptide
Definition: TargetedExperiment.h:61
ProteinReferenceMapType protein_reference_map_
Definition: TargetedExperiment.h:255
std::vector< Protein > proteins_
Definition: TargetedExperiment.h:241
Description of a file location, used to store the origin of (meta) data. 
Definition: SourceFile.h:47
std::vector< Peptide > peptides_
Definition: TargetedExperiment.h:245
Description of the software used for processing. 
Definition: Software.h:49
Class to hold strings, numeric values, lists of strings and lists of numeric values. 
Definition: DataValue.h:57
bool peptide_reference_map_dirty_
Definition: TargetedExperiment.h:261
std::vector< SourceFile > source_files_
Definition: TargetedExperiment.h:253
std::vector< Compound > compounds_
Definition: TargetedExperiment.h:243
std::map< String, const Peptide * > PeptideReferenceMapType
Definition: TargetedExperiment.h:68
std::vector< Contact > contacts_
Definition: TargetedExperiment.h:231
std::vector< Instrument > instruments_
Definition: TargetedExperiment.h:235
TargetedExperimentHelper::Prediction Prediction
Definition: TargetedExperiment.h:65
TargetedExperimentHelper::Protein Protein
Definition: TargetedExperiment.h:58
Representation of controlled vocabulary term. 
Definition: CVTerm.h:51
std::vector< CV > cvs_
Definition: TargetedExperiment.h:229
Definition: TargetedExperimentHelper.h:172
std::map< String, const Protein * > ProteinReferenceMapType
Definition: TargetedExperiment.h:67
bool protein_reference_map_dirty_
Definition: TargetedExperiment.h:257
Definition: TargetedExperimentHelper.h:76
This class stores a SRM/MRM transition. 
Definition: IncludeExcludeTarget.h:53
std::vector< ReactionMonitoringTransition > transitions_
Definition: TargetedExperiment.h:247
PeptideReferenceMapType peptide_reference_map_
Definition: TargetedExperiment.h:259
std::vector< IncludeExcludeTarget > exclude_targets_
Definition: TargetedExperiment.h:251
This class stores an prediction of an SRM/MRM transition. 
Definition: TargetedExperiment.h:53
Definition: TargetedExperimentHelper.h:402
Definition: TargetedExperimentHelper.h:133
TargetedExperimentHelper::Instrument Instrument
Definition: TargetedExperiment.h:64
Definition: TargetedExperimentHelper.h:430
std::vector< Software > software_
Definition: TargetedExperiment.h:239
TargetedExperimentHelper::Publication Publication
Definition: TargetedExperiment.h:63
Definition: TargetedExperimentHelper.h:102
TargetedExperimentHelper::Contact Contact
Definition: TargetedExperiment.h:62
TargetedExperimentHelper::Compound Compound
Definition: TargetedExperiment.h:60
std::vector< Publication > publications_
Definition: TargetedExperiment.h:233
TargetedExperimentHelper::CV CV
Definition: TargetedExperiment.h:57
Definition: TargetedExperimentHelper.h:211
This class stores a SRM/MRM transition. 
Definition: ReactionMonitoringTransition.h:53
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: TargetedExperiment.h:59