ProteoWizard
Namespaces | Classes | Typedefs | Functions
pwiz::proteome Namespace Reference

Namespaces

 AminoAcid
 scope for types related to amino acids
 
 examples
 

Classes

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  Fragmentation
 provides fragment ion masses for a peptide More...
 
class  IndexList
 
class  IPIFASTADatabase
 class for accessing data in ipi.*.fasta files 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...
 
struct  Protein
 
class  ProteinList
 
class  ProteinListCache
 adds a level of flexible MRU caching to a ProteinList processor chain More...
 
struct  ProteinListSimple
 
class  ProteinListWrapper
 Inheritable pass-through implementation for wrapping a ProteinList. More...
 
struct  ProteomeData
 
struct  ProteomeDataFile
 ProteomeData object plus file I/O. More...
 
class  Reader
 interface for file readers More...
 
class  Reader_FASTA
 FASTA -> ProteomeData stream serialization. More...
 
class  ReaderFail
 
class  ReaderList
 Reader container (composite pattern). More...
 
class  Serializer_FASTA
 ProteomeData <-> FASTA stream serialization. More...
 
class  TextWriter
 
struct  Version
 

Typedefs

typedef boost::shared_ptr< ProteinProteinPtr
 
typedef boost::shared_ptr< ProteinListProteinListPtr
 
typedef boost::shared_ptr< ReaderReaderPtr
 

Functions

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 More...
 
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)
 

Typedef Documentation

§ ProteinPtr

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

Definition at line 48 of file ProteomeData.hpp.

§ ProteinListPtr

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

Definition at line 73 of file ProteomeData.hpp.

§ ReaderPtr

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

Definition at line 89 of file Reader.hpp.

Function Documentation

§ operator<<() [1/5]

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

§ operator<<() [2/5]

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

§ operator<<() [3/5]

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

§ operator+()

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

returns a list containing the lhs and rhs as readers

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

§ operator<<() [4/5]

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

§ operator<<() [5/5]

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