ProteoWizard
pwiz
analysis
peakdetect
PeakelPicker.hpp
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//
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// $Id: PeakelPicker.hpp 1191 2009-08-14 19:33:05Z chambm $
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//
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//
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// Original author: Darren Kessner <darren@proteowizard.org>
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//
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// Copyright 2009 Center for Applied Molecular Medicine
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// University of Southern California, Los Angeles, CA
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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 _PEAKELPICKER_HPP_
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#define _PEAKELPICKER_HPP_
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#include "
PeakelPicker.hpp
"
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#include "
MZRTField.hpp
"
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#include "
pwiz/utility/misc/Export.hpp
"
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namespace
pwiz
{
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namespace
analysis {
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///
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/// interface for picking Peakels and arranging into Features;
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/// note: Peakels are actually removed from the PeakelField
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///
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class
PWIZ_API_DECL
PeakelPicker
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{
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public
:
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virtual
void
pick(
PeakelField
& peakels,
FeatureField
& features)
const
= 0;
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virtual
~PeakelPicker
(){}
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};
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///
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/// basic implementation
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///
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class
PWIZ_API_DECL
PeakelPicker_Basic
:
public
PeakelPicker
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{
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public
:
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struct
Config
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{
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std::ostream*
log
;
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size_t
minCharge
;
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size_t
maxCharge
;
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size_t
minMonoisotopicPeakelSize
;
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MZTolerance
mzTolerance
;
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double
rtTolerance
;
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size_t
minPeakelCount
;
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//double intensityThreshold; // ? // some kind of tolerance to match isotope envelope
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//double relativeIntensityTolerance;
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Config
()
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: log(0),
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minCharge(2),
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maxCharge(5),
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minMonoisotopicPeakelSize(3),
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mzTolerance(10,
MZTolerance
::PPM),
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rtTolerance(5),
// seconds
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minPeakelCount(3)
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{}
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};
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PeakelPicker_Basic
(
const
Config
& config =
Config
()) : config_(config) {}
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virtual
void
pick(
PeakelField
& peakels,
FeatureField
& features)
const
;
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private
:
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Config
config_
;
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};
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}
// namespace analysis
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}
// namespace pwiz
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#endif // _PEAKELPICKER_HPP_
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pwiz
Definition:
CwtPeakDetector.hpp:35
MZRTField.hpp
pwiz::analysis::MZRTField
MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT...
Definition:
MZRTField.hpp:94
pwiz::analysis::PeakelPicker_Basic
basic implementation
Definition:
PeakelPicker.hpp:53
PeakelPicker.hpp
pwiz::analysis::PeakelPicker_Basic::Config::minCharge
size_t minCharge
Definition:
PeakelPicker.hpp:60
pwiz::analysis::PeakelPicker_Basic::Config::mzTolerance
MZTolerance mzTolerance
Definition:
PeakelPicker.hpp:63
Export.hpp
pwiz::analysis::PeakelPicker_Basic::Config::log
std::ostream * log
Definition:
PeakelPicker.hpp:59
pwiz::analysis::PeakelPicker::~PeakelPicker
virtual ~PeakelPicker()
Definition:
PeakelPicker.hpp:46
pwiz::analysis::PeakelPicker_Basic::Config::maxCharge
size_t maxCharge
Definition:
PeakelPicker.hpp:61
pwiz::analysis::PeakelPicker_Basic::Config::minPeakelCount
size_t minPeakelCount
Definition:
PeakelPicker.hpp:65
pwiz::analysis::PeakelPicker
interface for picking Peakels and arranging into Features; note: Peakels are actually removed from th...
Definition:
PeakelPicker.hpp:40
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition:
Export.hpp:32
pwiz::analysis::PeakelPicker_Basic::Config::minMonoisotopicPeakelSize
size_t minMonoisotopicPeakelSize
Definition:
PeakelPicker.hpp:62
pwiz::analysis::PeakelPicker_Basic::Config::Config
Config()
Definition:
PeakelPicker.hpp:70
pwiz::chemistry::MZTolerance
struct for expressing m/z tolerance in either amu or ppm
Definition:
MZTolerance.hpp:38
pwiz::analysis::PeakelPicker_Basic::Config
Definition:
PeakelPicker.hpp:57
pwiz::analysis::PeakelPicker_Basic::config_
Config config_
Definition:
PeakelPicker.hpp:86
pwiz::analysis::PeakelPicker_Basic::Config::rtTolerance
double rtTolerance
Definition:
PeakelPicker.hpp:64
pwiz::analysis::PeakelPicker_Basic::PeakelPicker_Basic
PeakelPicker_Basic(const Config &config=Config())
Definition:
PeakelPicker.hpp:81
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