OpenMS
2.4.0
OpenMS
ANALYSIS
RNPXL
RNPxlDeisotoper.h
Go to the documentation of this file.
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// --------------------------------------------------------------------------
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// OpenMS -- Open-Source Mass Spectrometry
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// --------------------------------------------------------------------------
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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//
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// This software is released under a three-clause BSD license:
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above copyright
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// notice, this list of conditions and the following disclaimer in the
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// documentation and/or other materials provided with the distribution.
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// * Neither the name of any author or any participating institution
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// may be used to endorse or promote products derived from this software
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// without specific prior written permission.
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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// --------------------------------------------------------------------------
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// $Maintainer: Timo Sachsenberg $
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// $Authors: Timo Sachsenberg $
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// --------------------------------------------------------------------------
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#pragma once
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#include <
OpenMS/KERNEL/StandardTypes.h
>
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#include <
OpenMS/CONCEPT/Types.h
>
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#include <
OpenMS/CONCEPT/Constants.h
>
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namespace
OpenMS
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{
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class
MSSpectrum;
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class
OPENMS_DLLAPI
Deisotoper
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{
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public
:
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/* @brief Detect isotopic clusters in a fragment spectrum.
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* @param [spectra] Input spectra (sorted by m/z)
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* @param [min_charge] The minimum charge considered
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* @param [max_charge] The maximum charge considered
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* @param [fragment_tolerance] The tolerance used to match isotopic peaks
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* @oaram [fragment_unit_ppm] Whether ppm or m/z is used as tolerance
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* @param [keep_only_deisotoped] Only monoisotopic peaks of fragments with isotopic pattern are retained
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* @param [min_isopeaks] The minimum number of isotopic peaks (at least 2) required for an isotopic cluster
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* @param [max_isopeaks] The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster
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* @param [make_single_charged] Convert deisotoped monoisotopic peak to single charge
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* @param [annotate_charge] Annotate the charge to the peaks in the IntegerDataArray: "charge" (0 for unknown charge)
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* Note: If make_single_charged is selected, the original charge (>=1) gets annotated.
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*/
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static
void
deisotopeAndSingleCharge(
MSSpectrum
& spectra,
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double
fragment_tolerance,
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bool
fragment_unit_ppm,
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int
min_charge = 1,
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int
max_charge = 3,
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bool
keep_only_deisotoped =
false
,
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unsigned
int
min_isopeaks = 3,
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unsigned
int
max_isopeaks = 10,
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bool
make_single_charged =
true
,
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bool
annotate_charge =
false
);
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};
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}
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Types.h
Constants.h
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
OpenMS::Deisotoper
Definition:
RNPxlDeisotoper.h:46
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition:
MSSpectrum.h:66
StandardTypes.h
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