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pwiz::tradata Namespace Reference

Namespaces

 examples
 
 IO
 
 References
 functions for resolving references from objects into the internal MSData lists
 

Classes

struct  Compound
 Chemical compound other than a peptide for which one or more transitions. More...
 
struct  Configuration
 Instrument configuration used in the validation or optimization of the transitions. More...
 
struct  Contact
 
class  DefaultReaderList
 default Reader list More...
 
struct  DiffConfig
 configuration struct for diffs More...
 
struct  Evidence
 Information about empirical mass spectrometer observations of the peptide. More...
 
struct  Instrument
 Instrument on which transitions are validated. More...
 
struct  Interpretation
 A possible interpration of the product ion for a transition. More...
 
struct  Modification
 A molecule modification specification. More...
 
struct  Peptide
 Peptide for which one or more transitions are intended to identify. More...
 
struct  Precursor
 Precursor (Q1) of the transition. More...
 
struct  Prediction
 Information about a prediction for a suitable transition using some software. More...
 
struct  Product
 Product (Q3) of the transition. More...
 
struct  Protein
 
struct  Publication
 
class  Reader
 interface for file readers More...
 
class  ReaderFail
 
class  ReaderList
 Reader container (composite pattern). More...
 
struct  RetentionTime
 
class  Serializer_traML
 TraData <-> traML stream serialization. More...
 
struct  Software
 
struct  Target
 A peptide or compound that is to be included or excluded from a target list of precursor m/z values. More...
 
struct  TargetList
 List of precursor m/z targets to include or exclude. More...
 
class  TextWriter
 
struct  TraData
 
struct  TraDataFile
 TraData object plus file I/O. More...
 
struct  Transition
 
struct  Validation
 Information about the state of validation of a transition on a given instrument model. More...
 
struct  Version
 

Typedefs

typedef boost::shared_ptr< ReaderReaderPtr
 
typedef boost::shared_ptr< ContactContactPtr
 
typedef boost::shared_ptr< SoftwareSoftwarePtr
 
typedef boost::shared_ptr< InstrumentInstrumentPtr
 
typedef boost::shared_ptr< ProteinProteinPtr
 
typedef boost::shared_ptr< PeptidePeptidePtr
 
typedef boost::shared_ptr< CompoundCompoundPtr
 
typedef boost::shared_ptr< TraDataTraDataPtr
 

Functions

PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const data::Diff< TraData, DiffConfig > &diff)
 
PWIZ_API_DECL ReaderList operator+ (const ReaderPtr &lhs, const ReaderPtr &rhs)
 returns a list containing the lhs and rhs as readers More...
 
PWIZ_API_DECL std::vector< CVdefaultCVList ()
 returns a default list of CVs used in an TraML document; currently includes PSI-MS, Unit Ontology, and UNIMOD More...
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, TraDataFile::Format format)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const TraDataFile::WriteConfig &config)
 

Typedef Documentation

§ ReaderPtr

typedef boost::shared_ptr<Reader> pwiz::tradata::ReaderPtr

Definition at line 95 of file Reader.hpp.

§ ContactPtr

typedef boost::shared_ptr<Contact> pwiz::tradata::ContactPtr

Definition at line 57 of file TraData.hpp.

§ SoftwarePtr

typedef boost::shared_ptr<Software> pwiz::tradata::SoftwarePtr

Definition at line 88 of file TraData.hpp.

§ InstrumentPtr

typedef boost::shared_ptr<Instrument> pwiz::tradata::InstrumentPtr

Definition at line 143 of file TraData.hpp.

§ ProteinPtr

typedef boost::shared_ptr<Protein> pwiz::tradata::ProteinPtr

Definition at line 184 of file TraData.hpp.

§ PeptidePtr

typedef boost::shared_ptr<Peptide> pwiz::tradata::PeptidePtr

Definition at line 236 of file TraData.hpp.

§ CompoundPtr

typedef boost::shared_ptr<Compound> pwiz::tradata::CompoundPtr

Definition at line 254 of file TraData.hpp.

§ TraDataPtr

typedef boost::shared_ptr<TraData> pwiz::tradata::TraDataPtr

Definition at line 406 of file TraData.hpp.

Function Documentation

§ operator<<() [1/3]

PWIZ_API_DECL std::ostream& pwiz::tradata::operator<< ( std::ostream &  os,
const data::Diff< TraData, DiffConfig > &  diff 
)

§ operator+()

PWIZ_API_DECL ReaderList pwiz::tradata::operator+ ( const ReaderPtr lhs,
const ReaderPtr rhs 
)

returns a list containing the lhs and rhs as readers

Referenced by pwiz::tradata::ReaderList::getType().

§ defaultCVList()

PWIZ_API_DECL std::vector<CV> pwiz::tradata::defaultCVList ( )

returns a default list of CVs used in an TraML document; currently includes PSI-MS, Unit Ontology, and UNIMOD

§ operator<<() [2/3]

PWIZ_API_DECL std::ostream& pwiz::tradata::operator<< ( std::ostream &  os,
TraDataFile::Format  format 
)

§ operator<<() [3/3]

PWIZ_API_DECL std::ostream& pwiz::tradata::operator<< ( std::ostream &  os,
const TraDataFile::WriteConfig config 
)