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82 const std::string& _version);
347 namespace IO {
struct HandlerTraData;}
402 friend struct IO::HandlerTraData;
413 #endif // _TRADATA_HPP_
std::vector< ProteinPtr > proteinPtrs
Reference to zero or more proteins which this peptide is intended to identify.
List of precursor m/z targets to include or exclude.
std::string id
String label for this target.
boost::shared_ptr< Compound > CompoundPtr
std::vector< InstrumentPtr > instrumentPtrs
List of instruments on which transitions are validated.
bool empty() const
returns true iff all members are empty
RetentionTime retentionTime
Information about predicted or calibrated retention time.
bool empty() const
returns true iff contain no params
bool empty() const
returns true iff all members are empty and contain no params
bool empty() const
returns true iff contains no params
Product (Q3) of the transition.
Precursor precursor
Precursor (Q1) of the target.
std::vector< Target > targetIncludeList
List of precursor m/z targets to include.
A possible interpration of the product ion for a transition.
boost::shared_ptr< TraData > TraDataPtr
Precursor precursor
Precursor (Q1) of the transition.
SoftwarePtr softwarePtr
Reference to a software package from which this prediction is derived.
TraData & operator=(const TraData &)
Chemical compound other than a peptide for which one or more transitions.
std::string id
Identifier for the software to be used for referencing within a document.
std::vector< Target > targetExcludeList
List of precursor m/z targets to exclude.
Information about empirical mass spectrometer observations of the peptide.
RetentionTime retentionTime
Information about predicted or calibrated retention time.
PeptidePtr peptidePtr
Reference to a peptide for which this target is the trigger.
A peptide or compound that is to be included or excluded from a target list of precursor m/z values.
represents a post-translational modification (PTM) modification formula or masses must be provided at...
ContactPtr contactPtr
Reference to a contact person originating this information.
std::vector< ContactPtr > contactPtrs
List of contacts referenced in the generation or validation of transitions.
std::vector< CV > cvs
List of controlled vocabularies used in a TraML document note: one of the <cv> elements in this list ...
bool empty() const
returns true iff all members are empty and contain no params
represents a peptide or polypeptide (a sequence of amino acids)
std::vector< Configuration > configurationList
List of insutrument configurations used in the validation or optimization of the transitions.
std::vector< RetentionTime > retentionTimes
List of retention time information entries.
bool empty() const
returns true iff contain no params
double monoisotopicMassDelta
Atomic mass delta when assuming only the most common isotope of elements in Daltons.
std::vector< Modification > modifications
List of modifications on this peptide.
std::string id
String label for this transition.
bool empty() const
returns true iff contains no params
std::vector< Publication > publications
List of publications from which the transitions were collected or wherein they are published.
std::string version
Version of the software program described.
std::string id
Identifier for the compound to be used for referencing within a document.
bool empty() const
returns true iff all members are empty and contain no params
bool empty() const
returns true iff all members are empty and contain no params
Information about a prediction for a suitable transition using some software.
PWIZ_API_DECL std::vector< CV > defaultCVList()
returns a default list of CVs used in an TraML document; currently includes PSI-MS,...
Instrument(const std::string &id="")
std::string sequence
Amino acid sequence of the peptide being described.
std::string id
Identifier for the peptide to be used for referencing within a document.
Instrument on which transitions are validated.
The base class for elements that may contain cvParams, userParams, or paramGroup references.
std::vector< Interpretation > interpretationList
List of possible interprations of fragment ions for a transition.
bool empty() const
returns true iff all members are empty and contain no params
boost::shared_ptr< Software > SoftwarePtr
Protein(const std::string &id="")
std::vector< RetentionTime > retentionTimes
List of retention time information entries.
Software(const std::string &_id, const CVParam &_param, const std::string &_version)
bool empty() const
returns true iff all members are empty and contain no params
bool empty() const
returns true iff all members are empty and contain no params
std::string id
Identifier for the instrument to be used for referencing within a document.
bool empty() const
returns true iff all members are empty and contain no params
std::vector< Transition > transitions
List of transitions.
std::vector< ProteinPtr > proteinPtrs
List of proteins for which one or more transitions are intended to identify.
Peptide(const std::string &id="")
bool empty() const
returns true iff all members are empty and contain no params
SoftwarePtr softwarePtr
Software used to determine the retention time.
CompoundPtr compoundPtr
Reference to a compound for which this target is the trigger.
Compound(const std::string &id="")
std::string id
Identifier for the protein to be used for referencing within a document.
TargetList targets
List of precursor m/z targets to include or exclude.
bool empty() const
returns true iff all members are empty and contain no params
const std::string & version() const
returns the version of this traML document; for a document created programmatically,...
int location
Location of the modification within the peptide sequence, counted from the N-terminus,...
boost::shared_ptr< Protein > ProteinPtr
bool empty() const
returns true iff all members are empty and contain no params
double averageMassDelta
Atomic mass delta when considering the natural distribution of isotopes in Daltons.
Product product
Product (Q3) of the transition.
std::vector< CompoundPtr > compoundPtrs
Information about the state of validation of a transition on a given instrument model.
Software(const std::string &_id="")
std::vector< Configuration > configurationList
List of instrument configurations used in the validation or optimization of the target.
bool empty() const
returns true iff contains no params
std::string sequence
Amino acid sequence of the protein.
Prediction prediction
Information about a prediction for a suitable transition using some software.
Precursor (Q1) of the transition.
std::string id
Identifier for the publication to be used for referencing within a document.
boost::shared_ptr< Contact > ContactPtr
Instrument configuration used in the validation or optimization of the transitions.
std::vector< SoftwarePtr > softwarePtrs
List of software packages used in the generation of one of more transitions described in the document...
represents a tag-value pair, where the tag comes from the controlled vocabulary
bool empty() const
returns true iff all members are empty and contain no params
boost::shared_ptr< Instrument > InstrumentPtr
ContactPtr contactPtr
Reference to a contact person that generated this prediction.
boost::shared_ptr< Peptide > PeptidePtr
std::string id
for internal use: not currently in the schema
PeptidePtr peptidePtr
Reference to a peptide which this transition is intended to identify.
CompoundPtr compoundPtr
Reference to a compound for this transition.
bool empty() const
returns true iff all members are zero and contain no params
std::vector< PeptidePtr > peptidePtrs
List of compounds (including peptides) for which one or more transitions are intended to identify.
std::vector< Validation > validations
InstrumentPtr instrumentPtr
Reference to an instrument for which this configuration information is appropriate.