OpenMS  2.8.0
CVMappingFile.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: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/FORMAT/XMLFile.h>
41 
42 #include <vector>
43 
44 namespace OpenMS
45 {
46  class String;
47 
58  class OPENMS_DLLAPI CVMappingFile :
59  protected Internal::XMLHandler,
60  public Internal::XMLFile
61  {
62 public:
63 
66 
68  ~CVMappingFile() override;
69 
79  void load(const String& filename, CVMappings& cv_mappings, bool strip_namespaces = false);
80 
81 protected:
82 
83  // Docu in base class
84  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
85 
86  // Docu in base class
87  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
88 
89  // Docu in base class
90  void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
91 
92 private:
93 
96 
99 
101 
103 
105 
106  std::vector<CVMappingRule> rules_;
107 
108  std::vector<CVReference> cv_references_;
109 
110  };
111 
112 } // namespace OpenMS
113 
Used to load CvMapping files.
Definition: CVMappingFile.h:61
CVMappingFile & operator=(const CVMappingFile &rhs)
Not implemented.
String tag_
Definition: CVMappingFile.h:100
~CVMappingFile() override
Destructor.
CVMappingFile(const CVMappingFile &rhs)
Not implemented.
CVMappingFile()
Default constructor.
std::vector< CVReference > cv_references_
Definition: CVMappingFile.h:108
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
std::vector< CVMappingRule > rules_
Definition: CVMappingFile.h:106
bool strip_namespaces_
Definition: CVMappingFile.h:102
void characters(const XMLCh *const chars, const XMLSize_t) override
CVMappingRule actual_rule_
Definition: CVMappingFile.h:104
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
void load(const String &filename, CVMappings &cv_mappings, bool strip_namespaces=false)
loads CvMappings from the given file
Representation of a CV Mapping rule used by CVMappings.
Definition: CVMappingRule.h:54
Representation of controlled vocabulary mapping rules (for PSI formats)
Definition: CVMappings.h:57
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
Base class for XML handlers.
Definition: XMLHandler.h:325
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47