ProteoWizard
pwiz
analysis
spectrum_processing
SpectrumList_PeakPicker.hpp
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//
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// $Id$
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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_PEAKPICKER_HPP_
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#define _SPECTRUMLIST_PEAKPICKER_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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#include "
pwiz/analysis/common/LocalMaximumPeakDetector.hpp
"
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#include "
pwiz/analysis/common/CwtPeakDetector.hpp
"
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namespace
pwiz
{
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namespace
analysis {
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/// SpectrumList implementation to replace peak profiles with picked peaks
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class
PWIZ_API_DECL
SpectrumList_PeakPicker
:
public
msdata::SpectrumListWrapper
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{
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public
:
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SpectrumList_PeakPicker
(
const
msdata::SpectrumListPtr
& inner,
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PeakDetectorPtr
algorithm,
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bool
preferVendorPeakPicking,
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const
util::IntegerSet
& msLevelsToPeakPick);
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static
bool
accept(
const
msdata::SpectrumListPtr
& inner);
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virtual
msdata::SpectrumPtr
spectrum(
size_t
index,
msdata::DetailLevel
detailLevel)
const
;
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virtual
msdata::SpectrumPtr
spectrum(
size_t
index,
bool
getBinaryData =
false
)
const
;
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const
util::IntegerSet
&
msLevels
()
const
{
return
msLevelsToPeakPick_; }
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private
:
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PeakDetectorPtr
algorithm_
;
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const
util::IntegerSet
msLevelsToPeakPick_
;
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int
mode_
;
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};
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class
PWIZ_API_DECL
NoVendorPeakPickingException
:
public
std::runtime_error
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{
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public
:
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NoVendorPeakPickingException
() : std::runtime_error(
"[PeakDetector::NoVendorPeakPickingException]"
) {}
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};
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}
// namespace analysis
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}
// namespace pwiz
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#endif // _SPECTRUMLIST_PEAKPICKER_HPP_
pwiz::analysis::SpectrumList_PeakPicker
SpectrumList implementation to replace peak profiles with picked peaks.
Definition:
SpectrumList_PeakPicker.hpp:39
pwiz::msdata::SpectrumListPtr
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition:
MSData.hpp:711
pwiz::analysis::SpectrumList_PeakPicker::msLevelsToPeakPick_
const util::IntegerSet msLevelsToPeakPick_
Definition:
SpectrumList_PeakPicker.hpp:58
pwiz::analysis::NoVendorPeakPickingException::NoVendorPeakPickingException
NoVendorPeakPickingException()
Definition:
SpectrumList_PeakPicker.hpp:65
pwiz
Definition:
ChromatogramList_Filter.hpp:36
pwiz::msdata::SpectrumListWrapper
Inheritable pass-through implementation for wrapping a SpectrumList.
Definition:
SpectrumListWrapper.hpp:37
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition:
Export.hpp:32
Export.hpp
pwiz::analysis::SpectrumList_PeakPicker::msLevels
const util::IntegerSet & msLevels() const
Definition:
SpectrumList_PeakPicker.hpp:54
pwiz::msdata::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition:
MSData.hpp:573
pwiz::analysis::SpectrumList_PeakPicker::algorithm_
PeakDetectorPtr algorithm_
Definition:
SpectrumList_PeakPicker.hpp:57
LocalMaximumPeakDetector.hpp
pwiz::analysis::SpectrumList_PeakPicker::mode_
int mode_
Definition:
SpectrumList_PeakPicker.hpp:59
CwtPeakDetector.hpp
pwiz::msdata::DetailLevel
DetailLevel
Definition:
MSData.hpp:630
IntegerSet.hpp
pwiz::analysis::NoVendorPeakPickingException
Definition:
SpectrumList_PeakPicker.hpp:62
pwiz::util::IntegerSet
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
Definition:
IntegerSet.hpp:37
SpectrumListWrapper.hpp
pwiz::analysis::PeakDetectorPtr
boost::shared_ptr< PeakDetector > PeakDetectorPtr
Definition:
PeakDetector.hpp:57
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