ProteoWizard
PeptideID_pepXML.hpp
Go to the documentation of this file.
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");
11// you may not use this file except in compliance with the License.
12// You may obtain a copy of the License at
13//
14// http://www.apache.org/licenses/LICENSE-2.0
15//
16// Unless required by applicable law or agreed to in writing, software
17// distributed under the License is distributed on an "AS IS" BASIS,
18// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19// See the License for the specific language governing permissions and
20// limitations under the License.
21//
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
32namespace pwiz {
33namespace 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{
43public:
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
68private:
69 class Impl;
70 boost::shared_ptr<Impl> pimpl;
71
72};
73
74} // namespace peptideid
75} // namespace pwiz
76
77#endif // _PEPTIDEID_PEPXML_HPP_
#define PWIZ_API_DECL
Definition Export.hpp:32
This class allows access to identified proteins in PeptideProphet files.
virtual std::multimap< double, boost::shared_ptr< PeptideID::Record > >::const_iterator record(double retention_time_sec) const
boost::shared_ptr< Impl > pimpl
virtual Record record(const Location &location) const
Returns the Record object associated with the given nativeID.
PeptideID_pepXml(const std::string &filename)
Constructor taking path to input file in std::string.
virtual Iterator end() const
PeptideID_pepXml(const char *filename)
Constructor taking path to input file from const char*.
virtual Iterator begin() const
PeptideID_pepXml(std::istream *in)
Constructor taking std::istream as input.
This is an interface for classes that allow access to data sources of identified peptides.
Definition PeptideID.hpp:43