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OpenMS
ANALYSIS
RNPXL
RNPxlModificationsGenerator.h
Go to the documentation of this file.
1
// --------------------------------------------------------------------------
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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.
10
// * Redistributions in binary form must reproduce the above copyright
11
// notice, this list of conditions and the following disclaimer in the
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// documentation and/or other materials provided with the distribution.
13
// * 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
15
// without specific prior written permission.
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
18
// 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;
25
// 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
27
// 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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35
#pragma once
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#include <
OpenMS/KERNEL/StandardTypes.h
>
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#include <
OpenMS/DATASTRUCTURES/String.h
>
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#include <
OpenMS/DATASTRUCTURES/ListUtils.h
>
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#include <
OpenMS/CHEMISTRY/EmpiricalFormula.h
>
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#include <vector>
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#include <map>
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#include <set>
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#include <iostream>
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namespace
OpenMS
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{
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class
AASequence;
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struct
OPENMS_DLLAPI
RNPxlModificationMassesResult
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{
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std::map<String, double>
mod_masses
;
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std::map<String, std::set<String> >
mod_combinations
;
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};
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class
OPENMS_DLLAPI
RNPxlModificationsGenerator
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{
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public
:
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static
RNPxlModificationMassesResult
initModificationMassesRNA(
StringList
target_nucleotides,
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StringList
nt_groups,
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std::set<char> can_xl,
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StringList
mappings,
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StringList
modifications,
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String
sequence_restriction,
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bool
cysteine_adduct,
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Int
max_length = 4);
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private
:
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static
bool
notInSeq(
String
res_seq,
String
query);
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static
void
generateTargetSequences(
const
String
& res_seq,
Size
param_pos,
const
std::map<
char
, std::vector<char> >& map_source2target,
StringList
& target_sequences);
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};
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}
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OpenMS::RNPxlModificationMassesResult::mod_combinations
std::map< String, std::set< String > > mod_combinations
empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities)
Definition:
RNPxlModificationsGenerator.h:53
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition:
Types.h:127
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition:
ListUtils.h:70
int
ListUtils.h
OpenMS::RNPxlModificationMassesResult::mod_masses
std::map< String, double > mod_masses
empirical formula -> mass
Definition:
RNPxlModificationsGenerator.h:52
OpenMS::RNPxlModificationsGenerator
Definition:
RNPxlModificationsGenerator.h:56
OpenMS::RNPxlModificationMassesResult
Definition:
RNPxlModificationsGenerator.h:50
OpenMS::String
A more convenient string class.
Definition:
String.h:58
StandardTypes.h
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
EmpiricalFormula.h
String.h
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