OpenMS  2.6.0
CVMappingFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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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:144
OpenMS::TextFile::addLine
void addLine(const StringType &line)
Definition: TextFile.h:112
TextFile.h
XMLFile.h
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:151
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Flag that indicates of the term is obsolete.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:59
OpenMS::CVMappingRule::SHOULD
Definition: CVMappingRule.h:61
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::CVMappings::getMappingRules
const std::vector< CVMappingRule > & getMappingRules() const
returns the mapping rules
OpenMS::ControlledVocabulary::CVTerm::getXRefTypeName
static String getXRefTypeName(XRefType type)
OpenMS::ControlledVocabulary::CVTerm::NONE
Definition: ControlledVocabulary.h:75
OpenMS::ControlledVocabulary::getAllChildTerms
void getAllChildTerms(std::set< String > &terms, const String &parent) const
Writes all child terms recursively into terms.
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:193
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:46
OpenMS::CVMappingRule::MUST
Definition: CVMappingRule.h:60
CVMappingRule.h
CVMappings.h
OpenMS::ControlledVocabulary::CVTerm::synonyms
StringList synonyms
List of synonyms.
Definition: ControlledVocabulary.h:88
int
OpenMS::CVMappingRule::OR
Definition: CVMappingRule.h:68
OpenMS::ControlledVocabulary::getTerms
const Map< String, CVTerm > & getTerms() const
returns all the terms stored in the CV
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:73
OpenMS::CVMappingRule::AND
Definition: CVMappingRule.h:69
OpenMS::Map::ConstIterator
Base::const_iterator ConstIterator
Definition: Map.h:81
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::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::CVMappingFile::cv_references_
std::vector< CVReference > cv_references_
Definition: CVMappingFile.h:108
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