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pwiz::tradata Namespace Reference

Namespaces

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

Classes

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

Typedefs

typedef boost::shared_ptr< ReaderReaderPtr
typedef boost::shared_ptr
< Contact
ContactPtr
typedef boost::shared_ptr
< Software
SoftwarePtr
typedef boost::shared_ptr
< Instrument
InstrumentPtr
typedef boost::shared_ptr
< Protein
ProteinPtr
typedef boost::shared_ptr
< Peptide
PeptidePtr
typedef boost::shared_ptr
< Compound
CompoundPtr
typedef boost::shared_ptr
< TraData
TraDataPtr

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
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
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

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

Definition at line 95 of file Reader.hpp.

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

Definition at line 57 of file TraData.hpp.

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

Definition at line 88 of file TraData.hpp.

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

Definition at line 143 of file TraData.hpp.

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

Definition at line 184 of file TraData.hpp.

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

Definition at line 236 of file TraData.hpp.

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

Definition at line 254 of file TraData.hpp.

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

Definition at line 406 of file TraData.hpp.


Function Documentation

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

returns a list containing the lhs and rhs as readers

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

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