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