OpenMS
2.4.0
OpenMS
FORMAT
HANDLERS
MzMLSqliteSwathHandler.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: Hannes Roest $
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// $Authors: Hannes Roest
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// --------------------------------------------------------------------------
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#pragma once
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#include <
OpenMS/CONCEPT/Types.h
>
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#include <
OpenMS/DATASTRUCTURES/String.h
>
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#include <
OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h
>
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// forward declarations
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struct
sqlite3;
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namespace
OpenMS
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{
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namespace
Internal
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{
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class
OPENMS_DLLAPI
MzMLSqliteSwathHandler
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{
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public
:
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MzMLSqliteSwathHandler
(
String
filename) :
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filename_(filename)
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{}
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std::vector<OpenSwath::SwathMap> readSwathWindows();
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std::vector<int> readMS1Spectra();
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std::vector<int> readSpectraForWindow(
OpenSwath::SwathMap
swath_map);
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protected
:
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sqlite3* openDB();
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String
filename_
;
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/*
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* These are spectra and chromatogram ids that are global for a specific
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* database file. Keeping track of them allows us to append spectra and
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* chromatograms multiple times to a database.
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*/
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Int
spec_id_
;
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Int
chrom_id_
;
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};
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}
// namespace Internal
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}
// namespace OpenMS
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OpenMS::Internal::MzMLSqliteSwathHandler::chrom_id_
Int chrom_id_
Definition:
MzMLSqliteSwathHandler.h:109
Types.h
SwathMap.h
OpenMS::String
A more convenient string class.
Definition:
String.h:57
OpenMS::Internal::MzMLSqliteSwathHandler::filename_
String filename_
Definition:
MzMLSqliteSwathHandler.h:101
OpenMS::Int
int Int
Signed integer type.
Definition:
Types.h:102
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
OpenMS::Internal::MzMLSqliteSwathHandler
Sqlite handler for SWATH data sets.
Definition:
MzMLSqliteSwathHandler.h:59
OpenSwath::SwathMap
Data structure to hold one SWATH map with information about upper / lower isolation window and whethe...
Definition:
SwathMap.h:45
String.h
OpenMS::Internal::MzMLSqliteSwathHandler::MzMLSqliteSwathHandler
MzMLSqliteSwathHandler(String filename)
Constructor.
Definition:
MzMLSqliteSwathHandler.h:69
OpenMS::Internal::MzMLSqliteSwathHandler::spec_id_
Int spec_id_
Definition:
MzMLSqliteSwathHandler.h:108
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