Base class for XML handlers. More...
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
 
  
 | Classes | |
| class | EndParsingSoftly | 
| Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed).  More... | |
| Public Types | |
| enum | ActionMode { LOAD, STORE } | 
| Action to set the current mode (for error messages)  More... | |
| Public Member Functions | |
| XMLHandler (const String &filename, const String &version) | |
| Default constructor.  More... | |
| virtual | ~XMLHandler () | 
| Destructor.  More... | |
| void | reset () | 
| Release internal memory used for parsing (call.  More... | |
| void | fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | 
| Fatal error handler. Throws a ParseError exception.  More... | |
| void | error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | 
| Error handler for recoverable errors.  More... | |
| void | warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | 
| Warning handler.  More... | |
| virtual void | characters (const XMLCh *const chars, const XMLSize_t length) | 
| Parsing method for character data.  More... | |
| virtual void | startElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) | 
| Parsing method for opening tags.  More... | |
| virtual void | endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) | 
| Parsing method for closing tags.  More... | |
| virtual void | writeTo (std::ostream &) | 
| Writes the contents to a stream.  More... | |
| String | errorString () | 
| Returns the last error description.  More... | |
| Reimplemented XERCES-C error handlers | |
| These methods forward the error message to our own error handlers below. | |
| void | fatalError (const xercesc::SAXParseException &exception) | 
| void | error (const xercesc::SAXParseException &exception) | 
| void | warning (const xercesc::SAXParseException &exception) | 
| Protected Member Functions | |
| bool | equal_ (const XMLCh *a, const XMLCh *b) | 
| Returns if two xerces strings are equal.  More... | |
| General MetaInfo handling (for idXML, featureXML, consensusXML) | |
| void | writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | 
| Writes the content of MetaInfoInterface to the file.  More... | |
| String conversion | |
| Int | asInt_ (const String &in) | 
| Conversion of a String to an integer value.  More... | |
| Int | asInt_ (const XMLCh *in) | 
| Conversion of a Xerces string to an integer value.  More... | |
| UInt | asUInt_ (const String &in) | 
| Conversion of a String to an unsigned integer value.  More... | |
| double | asDouble_ (const String &in) | 
| Conversion of a String to a double value.  More... | |
| float | asFloat_ (const String &in) | 
| Conversion of a String to a float value.  More... | |
| bool | asBool_ (const String &in) | 
| Conversion of a string to a boolean value.  More... | |
| DateTime | asDateTime_ (String date_string) | 
| Conversion of a xs:datetime string to a DataTime value.  More... | |
| Accessing attributes | |
| char * | attributeAsString_ (const xercesc::Attributes &a, const char *name) const | 
| Converts an attribute to a String.  More... | |
| Int | attributeAsInt_ (const xercesc::Attributes &a, const char *name) const | 
| Converts an attribute to a Int.  More... | |
| DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const | 
| Converts an attribute to a DoubleReal.  More... | |
| DoubleList | attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const | 
| Converts an attribute to a DoubleList.  More... | |
| IntList | attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const | 
| Converts an attribute to an IntList.  More... | |
| StringList | attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const | 
| Converts an attribute to an StringList.  More... | |
| bool | optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the String value if the attribute is present.  More... | |
| bool | optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the Int value if the attribute is present.  More... | |
| bool | optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the UInt value if the attribute is present.  More... | |
| bool | optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the DoubleReal value if the attribute is present.  More... | |
| bool | optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the DoubleList value if the attribute is present.  More... | |
| bool | optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the StringList value if the attribute is present.  More... | |
| bool | optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const char *name) const | 
| Assigns the attribute content to the IntList value if the attribute is present.  More... | |
| char * | attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const | 
| Converts an attribute to a String.  More... | |
| Int | attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const | 
| Converts an attribute to a Int.  More... | |
| DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const | 
| Converts an attribute to a DoubleReal.  More... | |
| DoubleList | attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const | 
| Converts an attribute to a DoubleList.  More... | |
| IntList | attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const | 
| Converts an attribute to a IntList.  More... | |
| StringList | attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const | 
| Converts an attribute to a StringList.  More... | |
| bool | optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the String value if the attribute is present.  More... | |
| bool | optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the Int value if the attribute is present.  More... | |
| bool | optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the UInt value if the attribute is present.  More... | |
| bool | optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the DoubleReal value if the attribute is present.  More... | |
| bool | optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the DoubleList value if the attribute is present.  More... | |
| bool | optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the IntList value if the attribute is present.  More... | |
| bool | optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const XMLCh *name) const | 
| Assigns the attribute content to the StringList value if the attribute is present.  More... | |
| Protected Attributes | |
| String | error_message_ | 
| Error message of the last error.  More... | |
| String | file_ | 
| File name.  More... | |
| String | version_ | 
| Schema version.  More... | |
| StringManager | sm_ | 
| Helper class for string conversion.  More... | |
| std::vector< String > | open_tags_ | 
| Stack of open XML tags.  More... | |
| Private Member Functions | |
| XMLHandler () | |
| Not implemented.  More... | |
| String | expectList_ (const char *str) const | 
| controlled vocabulary handling methods | |
| std::vector< std::vector < String > > | cv_terms_ | 
| Array of CV term lists (one sublist denotes one term and it's children)  More... | |
| SignedSize | cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0) | 
Base class for XML handlers.
| enum ActionMode | 
| XMLHandler | ( | const String & | filename, | 
| const String & | version | ||
| ) | 
Default constructor.
| 
 | virtual | 
Destructor.
| 
 | private | 
Not implemented.
| 
 | inlineprotected | 
Conversion of a string to a boolean value.
'true', 'false', '1' and '0' are accpeted. 
 For all other values a parse error is produced. 
Conversion of a xs:datetime string to a DataTime value.
References DateTime::set(), String::substr(), and String::trim().
Conversion of a String to a double value.
References String::toDouble().
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 | inlineprotected | 
Conversion of a String to a float value.
References String::toFloat().
Conversion of a String to an integer value.
References String::toInt().
| 
 | inlineprotected | 
Conversion of a Xerces string to an integer value.
Conversion of a String to an unsigned integer value.
References String::toInt().
| 
 | inlineprotected | 
Converts an attribute to a DoubleReal.
| 
 | inlineprotected | 
Converts an attribute to a DoubleReal.
| 
 | inlineprotected | 
Converts an attribute to a DoubleList.
References DoubleList::create(), and String::substr().
| 
 | inlineprotected | 
Converts an attribute to a DoubleList.
References DoubleList::create(), and String::substr().
| 
 | inlineprotected | 
Converts an attribute to a Int.
| 
 | inlineprotected | 
Converts an attribute to a Int.
| 
 | inlineprotected | 
Converts an attribute to an IntList.
References IntList::create(), and String::substr().
| 
 | inlineprotected | 
Converts an attribute to a IntList.
References IntList::create(), and String::substr().
| 
 | inlineprotected | 
Converts an attribute to a String.
| 
 | inlineprotected | 
Converts an attribute to a String.
| 
 | inlineprotected | 
Converts an attribute to an StringList.
References StringList::create(), and String::substr().
| 
 | inlineprotected | 
Converts an attribute to a StringList.
References StringList::create(), and String::substr().
| 
 | virtual | 
Parsing method for character data.
Reimplemented in QcMLFile, MzMLHandler< MapType >, SemanticValidator, FeatureXMLFile, MzXMLHandler< MapType >, MzDataHandler< MapType >, ConsensusXMLFile, OMSSAXMLFile, XTandemXMLFile, MzIdentMLHandler, CVMappingFile, TraMLHandler, MascotXMLHandler, MzQuantMLHandler, XTandemInfileXMLHandler, ToolDescriptionHandler, PTMXMLHandler, and UnimodXMLHandler.
| 
 | inlineprotected | 
Converts term to the index of the term in the cv_terms_ entry section If the term is not found, result_on_error is returned (0 by default) 
References OPENMS_PRECONDITION.
| 
 | virtual | 
Parsing method for closing tags.
Reimplemented in QcMLFile, MzMLHandler< MapType >, SemanticValidator, FeatureXMLFile, ProtXMLFile, IdXMLFile, PepXMLFile, MzXMLHandler< MapType >, MzDataHandler< MapType >, ConsensusXMLFile, OMSSAXMLFile, XTandemXMLFile, MzIdentMLHandler, CVMappingFile, TraMLHandler, PepXMLFileMascot, MascotXMLHandler, MzQuantMLHandler, XTandemInfileXMLHandler, ToolDescriptionHandler, PTMXMLHandler, UnimodXMLHandler, and ParamXMLHandler.
| 
 | inlineprotected | 
Returns if two xerces strings are equal.
| void error | ( | const xercesc::SAXParseException & | exception | ) | 
| void error | ( | ActionMode | mode, | 
| const String & | msg, | ||
| UInt | line = 0, | ||
| UInt | column = 0 | ||
| ) | const | 
Error handler for recoverable errors.
| String errorString | ( | ) | 
Returns the last error description.
| 
 | inlineprivate | 
References String::hasPrefix(), and String::hasSuffix().
| void fatalError | ( | const xercesc::SAXParseException & | exception | ) | 
| void fatalError | ( | ActionMode | mode, | 
| const String & | msg, | ||
| UInt | line = 0, | ||
| UInt | column = 0 | ||
| ) | const | 
Fatal error handler. Throws a ParseError exception.
| 
 | inlineprotected | 
Assigns the attribute content to the DoubleReal value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the DoubleReal value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the DoubleList value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the DoubleList value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the Int value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the Int value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the IntList value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the IntList value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the String value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the String value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the StringList value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the StringList value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the UInt value if the attribute is present.
| 
 | inlineprotected | 
Assigns the attribute content to the UInt value if the attribute is present.
| void reset | ( | ) | 
Release internal memory used for parsing (call.
| 
 | virtual | 
Parsing method for opening tags.
Reimplemented in QcMLFile, MzMLHandler< MapType >, SemanticValidator, FeatureXMLFile, ProtXMLFile, IdXMLFile, PepXMLFile, MzXMLHandler< MapType >, MzDataHandler< MapType >, ConsensusXMLFile, OMSSAXMLFile, XTandemXMLFile, MzIdentMLHandler, TransformationXMLFile, CVMappingFile, TraMLHandler, PepXMLFileMascot, MascotXMLHandler, MzQuantMLHandler, XTandemInfileXMLHandler, ToolDescriptionHandler, MzMLValidator, PTMXMLHandler, UnimodXMLHandler, and ParamXMLHandler.
| void warning | ( | const xercesc::SAXParseException & | exception | ) | 
Referenced by MzDataHandler< MapType >::writeCVS_().
| void warning | ( | ActionMode | mode, | 
| const String & | msg, | ||
| UInt | line = 0, | ||
| UInt | column = 0 | ||
| ) | const | 
Warning handler.
| 
 | inlinevirtual | 
Writes the contents to a stream.
Reimplemented in MzMLHandler< MapType >, MzXMLHandler< MapType >, MzDataHandler< MapType >, MzIdentMLHandler, TraMLHandler, MzQuantMLHandler, ToolDescriptionHandler, and PTMXMLHandler.
| 
 | protected | 
Writes the content of MetaInfoInterface to the file.
| 
 | protected | 
Array of CV term lists (one sublist denotes one term and it's children)
Referenced by MzDataHandler< MapType >::init_(), MzXMLHandler< MapType >::init_(), and MzDataHandler< MapType >::writeCVS_().
| 
 | mutableprotected | 
Error message of the last error.
| 
 | protected | 
Stack of open XML tags.
This member is used only in those XML parsers that need this information.
| 
 | protected | 
Helper class for string conversion.
| 
 | protected | 
Schema version.
Referenced by MzMLHandler< MapType >::MzMLHandler().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:38 using doxygen 1.8.5 |