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Serializer_pepXML.hpp
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//
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// $Id: Serializer_pepXML.hpp 3148 2011-11-23 17:23:35Z chambm $
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//
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//
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// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
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//
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// Copyright 2010 Vanderbilt University - Nashville, TN 37232
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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_PEPXML_HPP_
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#define _SERIALIZER_PEPXML_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_pepXML
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{
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public
:
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/// Serializer_pepXML 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_pepXML
(
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 pepXML istream
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void
read
(boost::shared_ptr<std::istream> is,
IdentData
& mzid,
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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_pepXML
(
Serializer_pepXML
&);
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Serializer_pepXML
& operator=(
Serializer_pepXML
&);
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};
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struct
PWIZ_API_DECL
PepXMLSpecificity
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{
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std::string cut, no_cut,
sense
;
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};
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/// converts an identdata::Enzyme into a pepXML cut/no_cut/sense tuple
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PWIZ_API_DECL
PepXMLSpecificity
pepXMLSpecificity
(
const
Enzyme
& ez);
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/// strips charge state from known conventions of the pepXML spectrum attribute;
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/// used to find a unique identifier for a spectrum in order to merge charge states
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PWIZ_API_DECL
std::string
stripChargeFromConventionalSpectrumId
(
const
std::string&
id
);
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}
// namespace identdata
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}
// namespace pwiz
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#endif // _SERIALIZER_PEPXML_HPP_
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