ProteoWizard
pwiz
analysis
spectrum_processing
MS2Deisotoper.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: Chris Paulse <cpaulse <a.t> systemsbiology.org>
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//
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// Copyright 2009 Institute for Systems Biology, Seattle, WA
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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 _MS2DEISOTOPER_HPP_
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#define _MS2DEISOTOPER_HPP_
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#include "
pwiz/analysis/common/DataFilter.hpp
"
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#include "
pwiz/utility/chemistry/MZTolerance.hpp
"
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typedef
struct
{
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int
charge
;
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std::vector <int>
indexList
;
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}
isoChain
;
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namespace
pwiz
{
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namespace
analysis {
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using
chemistry::MZTolerance;
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// Deisotope high resolution ms2 spectra
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struct
PWIZ_API_DECL
MS2Deisotoper
:
public
SpectrumDataFilter
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{
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/// PrecursorMassFilter's parameters
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struct
PWIZ_API_DECL
Config
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{
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Config
(
MZTolerance
tol =
MZTolerance
(0.5),
bool
hires_ =
false
,
bool
poisson_ =
false
,
int
maxCharge_ = 3,
int
minCharge_ = 1)
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: matchingTolerance(tol), hires(hires_), poisson(poisson_), maxCharge(maxCharge_), minCharge(minCharge_) {}
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MZTolerance
matchingTolerance
;
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bool
hires
;
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bool
poisson
;
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int
maxCharge
;
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int
minCharge
;
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};
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MS2Deisotoper
(
const
MS2Deisotoper::Config
params_) : params(params_) {}
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virtual
void
operator () (
const
pwiz::msdata::SpectrumPtr
&)
const
;
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virtual
void
describe
(
pwiz::msdata::ProcessingMethod
&)
const
;
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const
MS2Deisotoper::Config
params
;
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};
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}
// namespace analysis
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}
// namespace pwiz
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#endif
// _MS2DEISOTOPER_HPP_
DataFilter.hpp
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition
Export.hpp:32
MZTolerance.hpp
pwiz::msdata::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition
MSData.hpp:573
pwiz
Definition
ChromatogramList_Filter.hpp:36
isoChain
Definition
MS2Deisotoper.hpp:30
isoChain::charge
int charge
Definition
MS2Deisotoper.hpp:31
isoChain::indexList
std::vector< int > indexList
Definition
MS2Deisotoper.hpp:32
pwiz::analysis::MS2Deisotoper::Config
PrecursorMassFilter's parameters.
Definition
MS2Deisotoper.hpp:48
pwiz::analysis::MS2Deisotoper::Config::poisson
bool poisson
Definition
MS2Deisotoper.hpp:54
pwiz::analysis::MS2Deisotoper::Config::hires
bool hires
Definition
MS2Deisotoper.hpp:53
pwiz::analysis::MS2Deisotoper::Config::Config
Config(MZTolerance tol=MZTolerance(0.5), bool hires_=false, bool poisson_=false, int maxCharge_=3, int minCharge_=1)
Definition
MS2Deisotoper.hpp:49
pwiz::analysis::MS2Deisotoper::Config::maxCharge
int maxCharge
Definition
MS2Deisotoper.hpp:55
pwiz::analysis::MS2Deisotoper::Config::matchingTolerance
MZTolerance matchingTolerance
Definition
MS2Deisotoper.hpp:52
pwiz::analysis::MS2Deisotoper::Config::minCharge
int minCharge
Definition
MS2Deisotoper.hpp:56
pwiz::analysis::MS2Deisotoper
Definition
MS2Deisotoper.hpp:45
pwiz::analysis::MS2Deisotoper::params
const MS2Deisotoper::Config params
Definition
MS2Deisotoper.hpp:63
pwiz::analysis::MS2Deisotoper::MS2Deisotoper
MS2Deisotoper(const MS2Deisotoper::Config params_)
Definition
MS2Deisotoper.hpp:59
pwiz::analysis::MS2Deisotoper::describe
virtual void describe(pwiz::msdata::ProcessingMethod &) const
pwiz::analysis::SpectrumDataFilter
Definition
DataFilter.hpp:36
pwiz::chemistry::MZTolerance
struct for expressing m/z tolerance in either amu or ppm
Definition
MZTolerance.hpp:39
pwiz::msdata::ProcessingMethod
Description of the default peak processing method. This element describes the base method used in the...
Definition
MSData.hpp:255
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