ProteoWizard
pwiz
data
identdata
Serializer_protXML.hpp
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//
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// $Id$
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//
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//
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// Original author: Brian Pratt <brian.pratt .@. insilicos.com>
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// after Serializer_pepXML by Matt Chambers <matt.chambers .@. vanderbilt.edu>
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//
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// Copyright 2012 Spielberg Family Center for Applied Proteomics
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// University of Southern California, Los Angeles, California 90033
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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 _SERIALIZER_PROTXML_HPP_
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#define _SERIALIZER_PROTXML_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include "
IdentData.hpp
"
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#include "
pwiz/utility/misc/IterationListener.hpp
"
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namespace
pwiz
{
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namespace
identdata {
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/// MZIDData <-> pepXML stream serialization
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class
PWIZ_API_DECL
Serializer_protXML
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{
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public
:
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/// Serializer_protXML configuration
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struct
PWIZ_API_DECL
Config
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{
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bool
readSpectrumQueries
;
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Config
(
bool
readSpectrumQueries =
true
) : readSpectrumQueries(readSpectrumQueries) {}
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};
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Serializer_protXML
(
const
Config
& config =
Config
()) : config_(config) {}
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/// write MZIDData object to ostream as pepXML
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void
write
(std::ostream& os,
const
IdentData
& mzid,
const
std::string& filepath,
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const
pwiz::util::IterationListenerRegistry
* = 0)
const
;
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/// read in MZIDData object from a protXML istream
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void
read
(boost::shared_ptr<std::istream> is,
IdentData
& mzid,
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std::vector<std::string> *sourceFilesPtr,
// if non-null, just read the SourceFiles info and return it here
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const
pwiz::util::IterationListenerRegistry
* = 0)
const
;
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private
:
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const
Config
config_
;
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Serializer_protXML
(
Serializer_protXML
&);
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Serializer_protXML
& operator=(
Serializer_protXML
&);
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};
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}
// namespace identdata
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}
// namespace pwiz
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#endif // _SERIALIZER_PROTXML_HPP_
IterationListener.hpp
pwiz
Definition:
ChromatogramList_Filter.hpp:36
pwiz::identdata::Serializer_protXML::Serializer_protXML
Serializer_protXML(const Config &config=Config())
Definition:
Serializer_protXML.hpp:50
pwiz::identdata::Serializer_protXML::Config::Config
Config(bool readSpectrumQueries=true)
Definition:
Serializer_protXML.hpp:47
pwiz::identdata::Serializer_protXML::Config::readSpectrumQueries
bool readSpectrumQueries
Definition:
Serializer_protXML.hpp:45
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition:
Export.hpp:32
pwiz::identdata::IO::write
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
Export.hpp
IdentData.hpp
pwiz::util::IterationListenerRegistry
handles registration of IterationListeners and broadcast of update messages
Definition:
IterationListener.hpp:65
pwiz::identdata::IdentData
Implementation of the MzIdentMLType from the mzIdentML schema.
Definition:
IdentData.hpp:993
pwiz::identdata::Serializer_protXML::Config
Serializer_protXML configuration.
Definition:
Serializer_protXML.hpp:43
pwiz::identdata::Serializer_protXML
MZIDData <-> pepXML stream serialization.
Definition:
Serializer_protXML.hpp:38
pwiz::identdata::IO::read
PWIZ_API_DECL void read(std::istream &is, CV &cv)
pwiz::identdata::Serializer_protXML::config_
const Config config_
Definition:
Serializer_protXML.hpp:62
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