ProteoWizard
pwiz
analysis
peptideid
PeptideID_pepXML.hpp
Go to the documentation of this file.
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//
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// $Id$
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//
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//
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// Original author: Robert Burke <robert.burke@cshs.org>
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//
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// Copyright 2007 Spielberg Family Center for Applied Proteomics
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// Cedars-Sinai Medical Center, Los Angeles, California 90048
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//
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// Licensed under the Apache License, Version 2.0 (the "License");
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// you may not use this file except in compliance with the License.
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// You may obtain a copy of the License at
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//
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// http://www.apache.org/licenses/LICENSE-2.0
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//
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// Unless required by applicable law or agreed to in writing, software
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// distributed under the License is distributed on an "AS IS" BASIS,
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// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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// See the License for the specific language governing permissions and
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// limitations under the License.
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//
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#ifndef _PEPTIDEID_PEPXML_HPP_
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#define _PEPTIDEID_PEPXML_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include <map>
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#include <boost/shared_ptr.hpp>
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#include "
PeptideID.hpp
"
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namespace
pwiz
{
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namespace
peptideid {
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/// This class allows access to identified proteins in PeptideProphet files.
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/// A PeptideID_pepXML object is contructed with either the path to a
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/// PeptideProphet format file (*.pep.xml), or an std::istream open to
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/// the beginning of a pep.xml file.
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class
PWIZ_API_DECL
PeptideID_pepXml
:
public
PeptideID
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{
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public
:
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/// Constructor taking path to input file in std::string.
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PeptideID_pepXml
(
const
std::string& filename);
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/// Constructor taking path to input file from const char*.
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PeptideID_pepXml
(
const
char
* filename);
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/// Constructor taking std::istream as input.
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PeptideID_pepXml
(std::istream* in);
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/// Destructor.
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virtual
~PeptideID_pepXml
() {}
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/// Returns the Record object associated with the given nativeID.
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/// A range_error is thrown if the nativeID isn't associated with
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/// a Record.
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virtual
Record
record
(
const
Location& location)
const
;
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virtual
std::multimap<double, boost::shared_ptr<PeptideID::Record> >::const_iterator
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record
(
double
retention_time_sec)
const
;
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virtual
Iterator begin()
const
;
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virtual
Iterator end()
const
;
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private
:
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class
Impl;
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boost::shared_ptr<Impl>
pimpl
;
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};
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}
// namespace peptideid
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}
// namespace pwiz
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#endif // _PEPTIDEID_PEPXML_HPP_
pwiz
Definition:
ChromatogramList_Filter.hpp:36
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:42
pwiz::peptideid::PeptideID_pepXml
This class allows access to identified proteins in PeptideProphet files.
Definition:
PeptideID_pepXML.hpp:41
pwiz::proteome::AminoAcid::Info::record
const PWIZ_API_DECL Record & record(Type type)
returns the amino acid's Record by type
PeptideID.hpp
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