OpenMS  3.0.0
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 2002-2022.
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 
65  CVMappingFile();
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 
95  CVMappingFile(const CVMappingFile& rhs);
96 
98  CVMappingFile& operator=(const CVMappingFile& rhs);
99 
101 
103 
105 
106  std::vector<CVMappingRule> rules_;
107 
108  std::vector<CVReference> cv_references_;
109 
110  };
111 
112 } // namespace OpenMS
113 
LogStream.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::TextFile::addLine
void addLine(const StringType &line)
Definition: TextFile.h:112
TextFile.h
XMLFile.h
Size
OpenMS::CVMappingFile
Used to load CvMapping files.
Definition: CVMappingFile.h:58
OpenMS::ControlledVocabulary
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
ControlledVocabulary.h
OpenMS::CVMappingFile::actual_rule_
CVMappingRule actual_rule_
Definition: CVMappingFile.h:104
OpenMS::ControlledVocabulary::CVTerm::obsolete
bool obsolete
Flag that indicates of the term is obsolete.
Definition: ControlledVocabulary.h:86
OpenMS::CVMappingFile::load
void load(const String &filename, CVMappings &cv_mappings, bool strip_namespaces=false)
loads CvMappings from the given file
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::CVMappingRule::SHOULD
Definition: CVMappingRule.h:61
Int
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::CVMappings::getMappingRules
const std::vector< CVMappingRule > & getMappingRules() const
returns the mapping rules
OpenMS::ControlledVocabulary::CVTerm::getXRefTypeName
static String getXRefTypeName(XRefType type)
OpenMS::ControlledVocabulary::getTerms
const std::map< String, CVTerm > & getTerms() const
returns all the terms stored in the CV
OpenMS::ControlledVocabulary::CVTerm::NONE
Definition: ControlledVocabulary.h:75
XMLHandler.h
OpenMS::CVMappingRule::MAY
Definition: CVMappingRule.h:62
OpenMS::CVMappings
Representation of controlled vocabulary mapping rules (for PSI formats)
Definition: CVMappings.h:56
OpenMS::ControlledVocabulary::CVTerm::xref_type
XRefType xref_type
xref value-type for the CV-term
Definition: ControlledVocabulary.h:90
OpenMS::ListUtils::concatenate
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:209
OpenMS::ControlledVocabulary::loadFromOBO
void loadFromOBO(const String &name, const String &filename)
Loads the CV from an OBO file.
OpenMS::ControlledVocabulary::CVTerm::id
String id
Identifier.
Definition: ControlledVocabulary.h:83
OpenMS::ControlledVocabulary::CVTerm::name
String name
if it is a score type, lookup has_order
Definition: ControlledVocabulary.h:82
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::CVMappingRule::MUST
Definition: CVMappingRule.h:60
CVMappingRule.h
CVMappings.h
OpenMS::ControlledVocabulary::CVTerm::synonyms
StringList synonyms
List of synonyms.
Definition: ControlledVocabulary.h:88
OpenMS::CVMappingRule::OR
Definition: CVMappingRule.h:68
OpenMS::CVMappingRule
Representation of a CV Mapping rule used by CVMappings.
Definition: CVMappingRule.h:53
OpenMS::ControlledVocabulary::getTerm
const CVTerm & getTerm(const String &id) const
Returns a term specified by ID.
OpenMS::CVMappingFile::rules_
std::vector< CVMappingRule > rules_
Definition: CVMappingFile.h:106
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
CVMappingFile.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::CVMappingRule::AND
Definition: CVMappingRule.h:69
OpenMS::ControlledVocabulary::CVTerm
Representation of a CV term.
Definition: ControlledVocabulary.h:60
OpenMS::ControlledVocabulary::CVTerm::units
std::set< String > units
unit accession ids, defined by relationship has units
Definition: ControlledVocabulary.h:92
OpenMS::CVMappingFile::tag_
String tag_
Definition: CVMappingFile.h:100
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::CVMappingFile::strip_namespaces_
bool strip_namespaces_
Definition: CVMappingFile.h:102
OpenMS::ControlledVocabulary::CVTerm::description
String description
Term description.
Definition: ControlledVocabulary.h:87
CVMappingTerm.h
OpenMS::CVMappingRule::XOR
Definition: CVMappingRule.h:70
OpenMS::TextFile::store
void store(const String &filename)
Writes the data to a file.
OpenMS::CVMappingFile::cv_references_
std::vector< CVReference > cv_references_
Definition: CVMappingFile.h:108
OpenMS::ControlledVocabulary::getAllChildTerms
void getAllChildTerms(std::set< String > &terms, const String &parent_id) const
Writes all child terms recursively into terms.
TOPPBase.h
OpenMS::ControlledVocabulary::CVTerm::xref_binary
StringList xref_binary
xref binary-data-type for the CV-term (list of all allowed data value types for the current binary da...
Definition: ControlledVocabulary.h:91
OpenMS::ControlledVocabulary::exists
bool exists(const String &id) const
Returns true if the term is in the CV. Returns false otherwise.
StringListUtils.h
OpenMS::ControlledVocabulary::CVTerm::children
std::set< String > children
The child IDs.
Definition: ControlledVocabulary.h:85