OpenMS  2.8.0
ConsensusXMLFile.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2021.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // 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
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // 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
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Clemens Groepl, Marc Sturm $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/XMLFile.h>
41 
42 namespace OpenMS
43 {
44  class ConsensusMap;
58  class OPENMS_DLLAPI ConsensusXMLFile :
59  public Internal::XMLFile,
60  public ProgressLogger
61  {
62 public:
66  ~ConsensusXMLFile() override;
67 
75  void load(const String& filename, ConsensusMap& map);
76 
84  void store(const String& filename, const ConsensusMap& consensus_map);
85 
88 
90  const PeakFileOptions& getOptions() const;
91 
92 protected:
93 
96  };
97 } // namespace OpenMS
98 
A container for consensus elements.
Definition: ConsensusMap.h:90
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
const PeakFileOptions & getOptions() const
Non-mutable access to the options for loading/storing.
PeakFileOptions options_
Options that can be set.
Definition: ConsensusXMLFile.h:95
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
~ConsensusXMLFile() override
Destructor.
ConsensusXMLFile()
Default constructor.
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
Options for loading files containing peak data.
Definition: PeakFileOptions.h:48
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47