#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
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). | |
UInt | cvStringToEnum_ (UInt section, const String &term, const char *message) |
Converts term to the index of the term in the cv_terms_ entry section . | |
Public Member Functions | |
XMLHandler (const String &filename, const String &version) | |
Default constructor. | |
virtual | ~XMLHandler () |
Destructor. | |
void | fatalError (const String &msg, UInt line=0, UInt column=0) const |
Fatal error handler. Throws a ParseError exception. | |
void | error (const String &msg, UInt line=0, UInt column=0) const |
Error handler for recoverable errors. | |
void | warning (const String &msg, UInt line=0, UInt column=0) const |
Warning handler. | |
virtual void | characters (const XMLCh *const chars, unsigned int length) |
Parsing method for character data. | |
virtual void | startElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) |
Parsing method for opening tags. | |
virtual void | endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) |
Parsing method for closing tags. | |
virtual void | writeTo (std::ostream &) |
Writes the contents to a stream. | |
String | errorString () |
Returns the last error description. | |
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. | |
cvParam and userParam handling methods (for mzData and FeatureXML) | |
void | writeCVS_ (std::ostream &os, DoubleReal value, const String &acc, const String &name, int indent=4) const |
write cvParam containing strings to stream | |
void | writeCVS_ (std::ostream &os, const String &value, const String &acc, const String &name, int indent=4) const |
write cvParam containing strings to stream | |
void | writeCVS_ (std::ostream &os, int value, int map, const String &acc, const String &name, int indent=4) |
write cvParam element to stream | |
void | writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, int indent=4) |
Writing the MetaInfo as UserParam to the file. | |
General MetaInfo handling (for IdXML, FeatureXML, FeaturePairsXML) | |
void | writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const |
Writes the content of MetaInfoInterface to the file. | |
String conversion | |
Int | asInt_ (const String &in) |
Conversion of a String to an integer value. | |
Int | asInt_ (const XMLCh *in) |
Conversion of a Xerces string to an integer value. | |
UInt | asUInt_ (const String &in) |
Conversion of a String to an unsigned integer value. | |
double | asDouble_ (const String &in) |
Conversion of a String to a double value. | |
float | asFloat_ (const String &in) |
Conversion of a String to a float value. | |
bool | asBool_ (const String &in) |
Conversion of a String to a bool value. | |
DateTime | asDateTime_ (const String &in) |
Conversion of a String to a DataTime value. | |
Accessing attributes | |
char * | attributeAsString_ (const xercesc::Attributes &a, const char *name) const |
Converts an attribute to a String. | |
Int | attributeAsInt_ (const xercesc::Attributes &a, const char *name) const |
Converts an attribute to a Int. | |
DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const |
Converts an attribute to a DoubleReal. | |
void | optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const |
Assigns the attribute content to the String value if the attribute is present. | |
void | optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const |
Assigns the attribute content to the Int value if the attribute is present. | |
void | optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const |
Assigns the attribute content to the UInt value if the attribute is present. | |
void | optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const char *name) const |
Assigns the attribute content to the DoubleReal value if the attribute is present. | |
char * | attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const |
Converts an attribute to a String. | |
Int | attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const |
Converts an attribute to a Int. | |
DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const |
Converts an attribute to a DoubleReal. | |
void | optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const |
Assigns the attribute content to the String value if the attribute is present. | |
void | optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const |
Assigns the attribute content to the Int value if the attribute is present. | |
void | optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const |
Assigns the attribute content to the UInt value if the attribute is present. | |
void | optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const XMLCh *name) const |
Assigns the attribute content to the DoubleReal value if the attribute is present. | |
Protected Attributes | |
String | error_message_ |
Error message of the last error. | |
String | file_ |
File name. | |
String | version_ |
Schema version. | |
StringManager | sm_ |
Helper class for string conversion. | |
std::vector< String > | open_tags_ |
Stack of open XML tags. | |
Private Member Functions | |
XMLHandler () | |
Not implemented. | |
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... |
XMLHandler | ( | const String & | filename, | |
const String & | version | |||
) |
Default constructor.
virtual ~XMLHandler | ( | ) | [virtual] |
Destructor.
XMLHandler | ( | ) | [private] |
Not implemented.
void fatalError | ( | const xercesc::SAXParseException & | exception | ) |
void error | ( | const xercesc::SAXParseException & | exception | ) |
void warning | ( | const xercesc::SAXParseException & | exception | ) |
Fatal error handler. Throws a ParseError exception.
Error handler for recoverable errors.
virtual void characters | ( | const XMLCh *const | chars, | |
unsigned int | length | |||
) | [virtual] |
Parsing method for character data.
Reimplemented in ConsensusXMLHandler, FeaturePairsHandler, FeatureXMLHandler, GridHandler, MascotXMLHandler, MzDataExpSettHandler, MzDataHandler, MzXMLHandler, OMSSAXMLHandler, and PTMXMLHandler.
virtual void startElement | ( | const XMLCh *const | uri, | |
const XMLCh *const | localname, | |||
const XMLCh *const | qname, | |||
const xercesc::Attributes & | attrs | |||
) | [virtual] |
Parsing method for opening tags.
Reimplemented in ConsensusXMLHandler, FeaturePairsHandler, FeatureXMLHandler, GridHandler, MascotXMLHandler, MzDataExpSettHandler, MzDataHandler, MzXMLHandler, OMSSAXMLHandler, ParamXMLHandler, PTMXMLHandler, and IdXMLFile.
virtual void endElement | ( | const XMLCh *const | uri, | |
const XMLCh *const | localname, | |||
const XMLCh *const | qname | |||
) | [virtual] |
Parsing method for closing tags.
Reimplemented in ConsensusXMLHandler, FeaturePairsHandler, FeatureXMLHandler, GridHandler, MascotXMLHandler, MzDataExpSettHandler, MzDataHandler, MzXMLHandler, OMSSAXMLHandler, ParamXMLHandler, PTMXMLHandler, and IdXMLFile.
virtual void writeTo | ( | std::ostream & | ) | [inline, virtual] |
Writes the contents to a stream.
Reimplemented in ConsensusXMLHandler, FeaturePairsHandler, FeatureXMLHandler, GridHandler, MzDataExpSettHandler, MzDataHandler, MzXMLHandler, and PTMXMLHandler.
String errorString | ( | ) |
Returns the last error description.
bool equal_ | ( | const XMLCh * | a, | |
const XMLCh * | b | |||
) | [inline, protected] |
Returns if two xerces strings are equal.
void writeCVS_ | ( | std::ostream & | os, | |
DoubleReal | value, | |||
const String & | acc, | |||
const String & | name, | |||
int | indent = 4 | |||
) | const [inline, protected] |
write cvParam containing strings to stream
value
string value acc
accession number defined by ontology name
term defined by ontology indent
number of tabs used in front of tag
Example: <cvParam cvLabel="psi" accession="PSI:acc"
name="name"
value="value"/>
void writeCVS_ | ( | std::ostream & | os, | |
const String & | value, | |||
const String & | acc, | |||
const String & | name, | |||
int | indent = 4 | |||
) | const [inline, protected] |
write cvParam containing strings to stream
value
string value acc
accession number defined by ontology name
term defined by ontology indent
number of tabs used in front of tag
Example: <cvParam cvLabel="psi" accession="PSI:acc"
name="name"
value="value"/>
void writeCVS_ | ( | std::ostream & | os, | |
int | value, | |||
int | map, | |||
const String & | acc, | |||
const String & | name, | |||
int | indent = 4 | |||
) | [protected] |
write cvParam element to stream
os
Output stream value
enumeration value map
index if the terms in cv_terms_ acc
accession number defined by ontology name
term defined by ontology indent
number of tabs used in front of tag
Example: <cvParam cvLabel="psi" accession="PSI:acc"
name="name"
value=""/>
void writeUserParam_ | ( | std::ostream & | os, | |
const MetaInfoInterface & | meta, | |||
int | indent = 4 | |||
) | [inline, protected] |
Writing the MetaInfo as UserParam to the file.
void writeUserParam_ | ( | const String & | tag_name, | |
std::ostream & | os, | |||
const MetaInfoInterface & | meta, | |||
UInt | indent | |||
) | const [protected] |
Writes the content of MetaInfoInterface to the file.
UInt cvStringToEnum_ | ( | UInt | section, | |
const String & | term, | |||
const char * | message | |||
) | [inline, protected] |
Converts term
to the index of the term in the cv_terms_ entry section
.
Int asInt_ | ( | const XMLCh * | in | ) | [inline, protected] |
Conversion of a Xerces string to an integer value.
Conversion of a String to an unsigned integer value.
double asDouble_ | ( | const String & | in | ) | [inline, protected] |
Conversion of a String to a double value.
Conversion of a String to a DataTime value.
char* attributeAsString_ | ( | const xercesc::Attributes & | a, | |
const char * | name | |||
) | const [inline, protected] |
Converts an attribute to a String.
Int attributeAsInt_ | ( | const xercesc::Attributes & | a, | |
const char * | name | |||
) | const [inline, protected] |
Converts an attribute to a Int.
DoubleReal attributeAsDouble_ | ( | const xercesc::Attributes & | a, | |
const char * | name | |||
) | const [inline, protected] |
Converts an attribute to a DoubleReal.
void optionalAttributeAsString_ | ( | String & | value, | |
const xercesc::Attributes & | a, | |||
const char * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the String value if the attribute is present.
void optionalAttributeAsInt_ | ( | Int & | value, | |
const xercesc::Attributes & | a, | |||
const char * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the Int value if the attribute is present.
void optionalAttributeAsUInt_ | ( | UInt & | value, | |
const xercesc::Attributes & | a, | |||
const char * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the UInt value if the attribute is present.
void optionalAttributeAsDouble_ | ( | DoubleReal & | value, | |
const xercesc::Attributes & | a, | |||
const char * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the DoubleReal value if the attribute is present.
char* attributeAsString_ | ( | const xercesc::Attributes & | a, | |
const XMLCh * | name | |||
) | const [inline, protected] |
Converts an attribute to a String.
Int attributeAsInt_ | ( | const xercesc::Attributes & | a, | |
const XMLCh * | name | |||
) | const [inline, protected] |
Converts an attribute to a Int.
DoubleReal attributeAsDouble_ | ( | const xercesc::Attributes & | a, | |
const XMLCh * | name | |||
) | const [inline, protected] |
Converts an attribute to a DoubleReal.
void optionalAttributeAsString_ | ( | String & | value, | |
const xercesc::Attributes & | a, | |||
const XMLCh * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the String value if the attribute is present.
void optionalAttributeAsInt_ | ( | Int & | value, | |
const xercesc::Attributes & | a, | |||
const XMLCh * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the Int value if the attribute is present.
void optionalAttributeAsUInt_ | ( | UInt & | value, | |
const xercesc::Attributes & | a, | |||
const XMLCh * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the UInt value if the attribute is present.
void optionalAttributeAsDouble_ | ( | DoubleReal & | value, | |
const xercesc::Attributes & | a, | |||
const XMLCh * | name | |||
) | const [inline, protected] |
Assigns the attribute content to the DoubleReal value if the attribute is present.
String error_message_ [mutable, protected] |
Error message of the last error.
StringManager sm_ [protected] |
Helper class for string conversion.
std::vector<String> open_tags_ [protected] |
Stack of open XML tags.
This member is used only in those XML parsers that need this information.
Array of CV term lists (one sublist denotes one term and it's children).
Generated Tue Apr 1 15:36:49 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |