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Tagger.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 2002-2020.
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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: Eugen Netz $
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// $Authors: Timo Sachsenberg, Eugen Netz $
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// --------------------------------------------------------------------------
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#pragma once
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#include <
OpenMS/DATASTRUCTURES/ListUtils.h
>
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#include <map>
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namespace
OpenMS
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{
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class
MSSpectrum;
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class
OPENMS_DLLAPI
Tagger
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{
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public
:
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Tagger
(
size_t
min_tag_length,
double
ppm,
size_t
max_tag_length = 65535,
size_t
min_charge = 1,
size_t
max_charge = 1,
const
StringList
& fixed_mods =
StringList
(),
const
StringList
& var_mods =
StringList
());
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void
getTag(
const
std::vector<double>& mzs, std::vector<std::string>& tags)
const
;
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void
getTag(
const
MSSpectrum
& spec, std::vector<std::string>& tags)
const
;
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void
setMaxCharge(
size_t
max_charge);
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private
:
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double
min_gap_
;
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double
max_gap_
;
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double
ppm_
;
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size_t
min_tag_length_
;
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size_t
max_tag_length_
;
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size_t
min_charge_
;
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size_t
max_charge_
;
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std::map<double, char>
mass2aa_
;
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char
getAAByMass_(
double
m)
const
;
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void
getTag_(std::string& tag,
const
std::vector<double>& mzs,
const
size_t
i, std::vector<std::string>& tags,
const
size_t
charge)
const
;
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};
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}
OpenMS::Tagger::min_charge_
size_t min_charge_
minimal fragment charge
Definition:
Tagger.h:111
OpenMS::Tagger
Calculate sequence tags from m/z values.
Definition:
Tagger.h:52
OpenMS::Tagger::max_tag_length_
size_t max_tag_length_
maximum tag length
Definition:
Tagger.h:110
OpenMS::Tagger::max_charge_
size_t max_charge_
maximal fragment charge
Definition:
Tagger.h:112
OpenMS::Tagger::min_tag_length_
size_t min_tag_length_
minimum tag length
Definition:
Tagger.h:109
OpenMS::Tagger::ppm_
double ppm_
tolerance
Definition:
Tagger.h:108
ListUtils.h
OpenMS::Tagger::max_gap_
double max_gap_
will be set to highest residue mass in ResidueDB
Definition:
Tagger.h:107
OpenMS::Tagger::mass2aa_
std::map< double, char > mass2aa_
mapping of residue masses to their one letter codes
Definition:
Tagger.h:113
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
OpenMS::Tagger::min_gap_
double min_gap_
will be set to smallest residue mass in ResidueDB
Definition:
Tagger.h:106
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition:
ListUtils.h:70
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition:
MSSpectrum.h:67
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