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pwiz
analysis
spectrum_processing
SpectrumList_PrecursorRefine.hpp
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//
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// $Id: SpectrumList_PrecursorRefine.hpp 1191 2009-08-14 19:33:05Z chambm $
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//
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//
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// Original author: Chris Paulse <cpaulse@systemsbiology.org>
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//
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// Copyright 2008 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 _SPECTRUMLIST_PRECURSORREREFINE_HPP_
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#define _SPECTRUMLIST_PRECURSORREREFINE_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include "
pwiz/data/msdata/SpectrumListWrapper.hpp
"
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namespace
pwiz {
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namespace
analysis {
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/// SpectrumList wrapper that recalculates precursor info on spectrum() requests
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class
PWIZ_API_DECL
SpectrumList_PrecursorRefine
:
public
msdata::SpectrumListWrapper
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{
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public
:
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struct
PWIZ_API_DECL
PrecursorInfo
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{
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double
mz
;
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double
intensity
;
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double
charge
;
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double
score
;
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PrecursorInfo
() :
mz
(0), intensity(0), charge(0), score(0) {}
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};
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/// constructor needs the full MSData object for instrument info;
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/// SpectrumList_PrecursorRefine holds a reference to the original SpectrumListPtr
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SpectrumList_PrecursorRefine
(
const
msdata::MSData
& msd);
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~
SpectrumList_PrecursorRefine
();
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/// \name SpectrumList interface
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//@{
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virtual
msdata::SpectrumPtr
spectrum(
size_t
index,
bool
getBinaryData =
false
)
const
;
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//@}
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private
:
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double
RefineMassVal(
double
initialEstimate,
size_t
index)
const
;
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struct
Impl;
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boost::shared_ptr<Impl>
impl_
;
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SpectrumList_PrecursorRefine
(
SpectrumList_PrecursorRefine
&);
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SpectrumList_PrecursorRefine
& operator=(
SpectrumList_PrecursorRefine
&);
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mutable
int
numRefined
;
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mutable
int
numTotal
;
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};
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}
// namespace analysis
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}
// namespace pwiz
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#endif // _SPECTRUMLIST_PRECURSORREREFINE_HPP_
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