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Pep2MzIdent.hpp
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//
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// $Id: Pep2MzIdent.hpp 2820 2011-06-27 22:51:16Z chambm $
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//
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// Original author: Robert Burke <robert.burke@proteowizard.org>
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//
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// Copyright 2009 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 _PEP2MZIDENT_HPP_
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#define _PEP2MZIDENT_HPP_
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#include "
IdentData.hpp
"
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#include "
KwCVMap.hpp
"
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#include "
pwiz/data/misc/MinimumPepXML.hpp
"
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#include "
pwiz/data/common/CVTranslator.hpp
"
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#include "
pwiz/utility/misc/Export.hpp
"
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#include <vector>
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namespace
pwiz{
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namespace
identdata{
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using namespace
pwiz::data::pepxml;
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typedef
boost::shared_ptr<IdentData>
IdentDataPtr
;
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/// Translates data from a MinimumPepXML object into a IdentData
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/// object tree when a translation is known. The IdentData object
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/// initializes a cvList with the "MS" and "UO" elements.
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///
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/// The translate method is used to copy data. The clear method resets
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/// the IdentData object, null's out the MSMSPipelineAnalysis.
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class
PWIZ_API_DECL
Pep2MzIdent
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{
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public
:
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/// Initialized the member variables. Also adds the "MS" and "UO"
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/// CV's to the cvList.
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Pep2MzIdent
(
const
MSMSPipelineAnalysis
& mspa,
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IdentDataPtr
result =
IdentDataPtr
(
new
IdentData
()));
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/// Resets the member variables.
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void
clear();
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bool
operator()(
const
MSMSPipelineAnalysis
& pepxml,
IdentDataPtr
mzid);
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/// Translates all known tags in the pepXML object tree into the
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/// IdentData object tree. The resulting IdentDataPtr is returned.
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IdentDataPtr
translate
();
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/// Clears fields and then sets the _mspa field to the address of
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/// mspa.
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void
setMspa(
const
MSMSPipelineAnalysis
& mspa);
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/// Returns the IdentDataPtr object. If a translation has not been
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/// done, or if clear has been called, then an empty IdentData
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/// will be return in the IdentDataPtr object.
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IdentDataPtr
getIdentData()
const
;
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void
setDebug(
bool
debug);
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bool
getDebug()
const
;
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void
setVerbose(
bool
verbose);
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bool
getVerbose()
const
;
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void
addParamMap(std::vector<CVMapPtr>& map);
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void
setParamMap(std::vector<CVMapPtr>& map);
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const
std::vector<CVMapPtr>& getParamMap()
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 identdata
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}
// namespace pwiz
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#endif
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