ProteoWizard
PeptideID_pepXML.hpp
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1 //
2 // $Id$
3 //
4 //
5 // Original author: Robert Burke <robert.burke@cshs.org>
6 //
7 // Copyright 2007 Spielberg Family Center for Applied Proteomics
8 // Cedars-Sinai Medical Center, Los Angeles, California 90048
9 //
10 // Licensed under the Apache License, Version 2.0 (the "License");
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12 // You may obtain a copy of the License at
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17 // distributed under the License is distributed on an "AS IS" BASIS,
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22 
23 #ifndef _PEPTIDEID_PEPXML_HPP_
24 #define _PEPTIDEID_PEPXML_HPP_
25 
27 #include <map>
28 #include <boost/shared_ptr.hpp>
29 
30 #include "PeptideID.hpp"
31 
32 namespace pwiz {
33 namespace peptideid {
34 
35 /// This class allows access to identified proteins in PeptideProphet files.
36 
37 /// A PeptideID_pepXML object is contructed with either the path to a
38 /// PeptideProphet format file (*.pep.xml), or an std::istream open to
39 /// the beginning of a pep.xml file.
40 
42 {
43 public:
44  /// Constructor taking path to input file in std::string.
45  PeptideID_pepXml(const std::string& filename);
46 
47  /// Constructor taking path to input file from const char*.
48  PeptideID_pepXml(const char* filename);
49 
50  /// Constructor taking std::istream as input.
51  PeptideID_pepXml(std::istream* in);
52 
53  /// Destructor.
54  virtual ~PeptideID_pepXml() {}
55 
56  /// Returns the Record object associated with the given nativeID.
57 
58  /// A range_error is thrown if the nativeID isn't associated with
59  /// a Record.
60  virtual Record record(const Location& location) const;
61 
62  virtual std::multimap<double, boost::shared_ptr<PeptideID::Record> >::const_iterator
63  record(double retention_time_sec) const;
64 
65  virtual Iterator begin() const;
66  virtual Iterator end() const;
67 
68 private:
69  class Impl;
70  boost::shared_ptr<Impl> pimpl;
71 
72 };
73 
74 } // namespace peptideid
75 } // namespace pwiz
76 
77 #endif // _PEPTIDEID_PEPXML_HPP_
pwiz::peptideid::PeptideID_pepXml::PeptideID_pepXml
PeptideID_pepXml(const std::string &filename)
Constructor taking path to input file in std::string.
pwiz
Definition: ChromatogramList_Filter.hpp:36
pwiz::peptideid::PeptideID::Location
Definition: PeptideID.hpp:47
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition: Export.hpp:32
pwiz::peptideid::PeptideID_pepXml::pimpl
boost::shared_ptr< Impl > pimpl
Definition: PeptideID_pepXML.hpp:69
Export.hpp
pwiz::peptideid::PeptideID_pepXml::~PeptideID_pepXml
virtual ~PeptideID_pepXml()
Destructor.
Definition: PeptideID_pepXML.hpp:54
pwiz::peptideid::PeptideID
This is an interface for classes that allow access to data sources of identified peptides.
Definition: PeptideID.hpp:43
pwiz::peptideid::PeptideID::Iterator
Iterator for.
Definition: PeptideID.hpp:94
pwiz::peptideid::PeptideID_pepXml::PeptideID_pepXml
PeptideID_pepXml(const char *filename)
Constructor taking path to input file from const char*.
pwiz::peptideid::PeptideID_pepXml::PeptideID_pepXml
PeptideID_pepXml(std::istream *in)
Constructor taking std::istream as input.
pwiz::peptideid::PeptideID_pepXml::record
virtual std::multimap< double, boost::shared_ptr< PeptideID::Record > >::const_iterator record(double retention_time_sec) const
pwiz::peptideid::PeptideID_pepXml::begin
virtual Iterator begin() const
pwiz::peptideid::PeptideID::Record
Definition: PeptideID.hpp:59
pwiz::peptideid::PeptideID_pepXml
This class allows access to identified proteins in PeptideProphet files.
Definition: PeptideID_pepXML.hpp:42
pwiz::peptideid::PeptideID_pepXml::record
virtual Record record(const Location &location) const
Returns the Record object associated with the given nativeID.
PeptideID.hpp
pwiz::peptideid::PeptideID_pepXml::end
virtual Iterator end() const