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pwiz
analysis
spectrum_processing
SpectrumList_ChargeStateCalculator.hpp
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//
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// $Id: SpectrumList_ChargeStateCalculator.hpp 4092 2012-11-08 17:44:45Z kaipot $
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//
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//
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// Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
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//
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// Copyright 2008 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 _SPECTRUMLIST_CHARGESTATECALCULATOR_HPP_
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#define _SPECTRUMLIST_CHARGESTATECALCULATOR_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include "
pwiz/utility/misc/IntegerSet.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 implementation that assigns (probable) charge states to tandem mass spectra
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class
PWIZ_API_DECL
SpectrumList_ChargeStateCalculator
:
public
msdata::SpectrumListWrapper
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{
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public
:
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SpectrumList_ChargeStateCalculator
(
const
msdata::SpectrumListPtr
& inner,
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bool
overrideExistingChargeState =
true
,
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int
maxMultipleCharge = 3,
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int
minMultipleCharge = 2,
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double
intensityFractionBelowPrecursorForSinglyCharged = 0.9,
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bool
makeMS2 =
false
);
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/// accepts any tandem mass spectrum
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static
bool
accept
(
const
msdata::SpectrumListPtr
& inner) {
return
true
;}
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/// charge calculation requires binary data to function, so returned spectra will always provide the binary data
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virtual
msdata::SpectrumPtr
spectrum(
size_t
index,
bool
getBinaryData =
true
)
const
;
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private
:
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bool
override_
;
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int
maxCharge_
;
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int
minCharge_
;
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double
fraction_
;
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bool
makeMS2_
;
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};
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}
// namespace analysis
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}
// namespace pwiz
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#endif // _SPECTRUMLIST_CHARGESTATECALCULATOR_HPP_
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