pwiz::proteome Namespace Reference

Namespaces
namespace	AminoAcid
	scope for types related to amino acids
namespace	examples

Classes
struct	PeptideDatabaseFormula
struct	PeptideDatabaseRecord
class	PeptideDatabase
class	DefaultReaderList
	default Reader list More...
struct	DiffConfig
	configuration struct for diffs More...
class	DigestedPeptide
	peptide subclass that contains extra metadata provided by digestion More...
class	Digestion
	enumerates the peptides from proteolytic digestion of a polypeptide or protein; More...
class	Modification
	represents a post-translational modification (PTM) modification formula or masses must be provided at instantiation More...
class	ModificationList
	represents a list of modifications on a single amino acid More...
class	ModificationMap
	maps peptide/protein sequence indexes (0-based) to a modification list More...
class	Peptide
	represents a peptide or polypeptide (a sequence of amino acids) More...
class	Fragmentation
	provides fragment ion masses for a peptide More...
class	ProteinListCache
	adds a level of flexible MRU caching to a ProteinList processor chain More...
class	ProteinListWrapper
	Inheritable pass-through implementation for wrapping a ProteinList. More...
struct	Protein
class	IndexList
class	ProteinList
struct	ProteinListSimple
struct	ProteomeData
struct	ProteomeDataFile
	ProteomeData object plus file I/O. More...
class	Reader
	interface for file readers More...
class	ReaderFail
class	ReaderList
	Reader container (composite pattern). More...
class	Reader_FASTA
	FASTA -> ProteomeData stream serialization. More...
class	Serializer_FASTA
	ProteomeData <-> FASTA stream serialization. More...
class	TextWriter
struct	Version
class	IPIFASTADatabase
	class for accessing data in ipi.*.fasta files More...

Typedefs
typedef boost::shared_ptr < Protein >	ProteinPtr
typedef boost::shared_ptr < ProteinList >	ProteinListPtr
typedef boost::shared_ptr< Reader >	ReaderPtr

Functions
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const PeptideDatabaseFormula &formula)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const PeptideDatabaseRecord &record)
PWIZ_API_DECL bool	operator== (const PeptideDatabaseFormula &r, const PeptideDatabaseFormula &s)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const data::Diff< ProteomeData, DiffConfig > &diff)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, ProteomeDataFile::Format format)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const ProteomeDataFile::WriteConfig &config)
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::ostream &	operator<< (std::ostream &os, const Reader_FASTA::Config &config)
PWIZ_API_DECL std::ostream &	operator<< (std::ostream &os, const IPIFASTADatabase::Record &record)

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Typedef Documentation

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

Definition at line 48 of file ProteomeData.hpp.

typedef boost::shared_ptr<ProteinList> pwiz::proteome::ProteinListPtr

Definition at line 73 of file ProteomeData.hpp.

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

Definition at line 89 of file Reader.hpp.

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Function Documentation

PWIZ_API_DECL std::ostream& pwiz::proteome::operator<<	(	std::ostream &	os,
		const PeptideDatabaseFormula &	formula
	)

PWIZ_API_DECL std::ostream& pwiz::proteome::operator<<	(	std::ostream &	os,
		const PeptideDatabaseRecord &	record
	)

PWIZ_API_DECL bool pwiz::proteome::operator==	(	const PeptideDatabaseFormula &	r,
		const PeptideDatabaseFormula &	s
	)

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

PWIZ_API_DECL std::ostream& pwiz::proteome::operator<<	(	std::ostream &	os,
		ProteomeDataFile::Format	format
	)

PWIZ_API_DECL std::ostream& pwiz::proteome::operator<<	(	std::ostream &	os,
		const ProteomeDataFile::WriteConfig &	config
	)

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

returns a list containing the lhs and rhs as readers

PWIZ_API_DECL std::ostream& pwiz::proteome::operator<<	(	std::ostream &	os,
		const Reader_FASTA::Config &	config
	)

PWIZ_API_DECL std::ostream& pwiz::proteome::operator<<	(	std::ostream &	os,
		const IPIFASTADatabase::Record &	record
	)