Used to load and store TransformationXML files. More...
#include <OpenMS/FORMAT/TransformationXMLFile.h>
Public Member Functions | |
| TransformationXMLFile () | |
| Constructor. More... | |
| void | load (const String &filename, TransformationDescription &transformation) |
| Loads the transformation from an TransformationXML file. More... | |
| void | store (String filename, const TransformationDescription &transformation) |
| Stores the data in an TransformationXML file. More... | |
Public Member Functions inherited from XMLFile | |
| XMLFile () | |
| Default constructor. More... | |
| XMLFile (const String &schema_location, const String &version) | |
| Constructor that sets the schema location. More... | |
| virtual | ~XMLFile () |
| Destructor. More... | |
| bool | isValid (const String &filename, std::ostream &os=std::cerr) |
| Checks if a file validates against the XML schema. More... | |
| const String & | getVersion () const |
| return the version of the schema More... | |
Protected Member Functions | |
| virtual void | startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) |
| Parsing method for opening tags. More... | |
Protected Member Functions inherited from XMLHandler | |
| bool | equal_ (const XMLCh *a, const XMLCh *b) |
| Returns if two xerces strings are equal. More... | |
| void | writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const |
| Writes the content of MetaInfoInterface to the file. More... | |
| 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... | |
| 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... | |
| SignedSize | cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0) |
| 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 | 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... | |
| void | fatalError (const xercesc::SAXParseException &exception) |
| void | error (const xercesc::SAXParseException &exception) |
| void | warning (const xercesc::SAXParseException &exception) |
Protected Member Functions inherited from XMLFile | |
| void | parse_ (const String &filename, XMLHandler *handler) |
Parses the XML file given by filename using the handler given by handler. More... | |
| void | save_ (const String &filename, XMLHandler *handler) const |
Stores the contents of the XML handler given by handler in the file given by filename. More... | |
| void | enforceEncoding_ (const String &encoding) |
| XMLFile () | |
| Default constructor. More... | |
| XMLFile (const String &schema_location, const String &version) | |
| Constructor that sets the schema location. More... | |
| virtual | ~XMLFile () |
| Destructor. More... | |
| bool | isValid (const String &filename, std::ostream &os=std::cerr) |
| Checks if a file validates against the XML schema. More... | |
| const String & | getVersion () const |
| return the version of the schema More... | |
Protected Attributes | |
Members for use during loading data | |
| Param | params_ |
| Param to fill in during parse. More... | |
| TransformationDescription::DataPoints | data_ |
| Data vector. More... | |
| String | model_type_ |
| Model type. More... | |
Protected Attributes inherited from XMLHandler | |
| 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... | |
| std::vector< std::vector < String > > | cv_terms_ |
| Array of CV term lists (one sublist denotes one term and it's children) More... | |
Protected Attributes inherited from XMLFile | |
| String | schema_location_ |
| XML schema file location. More... | |
| String | schema_version_ |
| Version string. More... | |
| String | enforced_encoding_ |
| Encoding string that replaces the encoding (system dependend or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More... | |
Additional Inherited Members | |
Protected Types inherited from XMLHandler | |
| enum | ActionMode { LOAD, STORE } |
| Action to set the current mode (for error messages) More... | |
Used to load and store TransformationXML files.
This class is used to load and store documents that implement the schema of TransformationXML files.
A documented schema for this format can be found at http://open-ms.sourceforge.net/schemas/.
Constructor.
| void load | ( | const String & | filename, |
| TransformationDescription & | transformation | ||
| ) |
Loads the transformation from an TransformationXML file.
The information is read in and the information is stored in the corresponding variables
| Exception::FileNotFound | is thrown if the file could not be opened |
| Exception::ParseError | is thrown if an error occurs during parsing |
|
protectedvirtual |
Parsing method for opening tags.
Reimplemented from XMLHandler.
| void store | ( | String | filename, |
| const TransformationDescription & | transformation | ||
| ) |
Stores the data in an TransformationXML file.
The data is read in and stored in the file named 'filename'.
| Exception::UnableToCreateFile | is thrown if the file could not be created |
| Exception::IllegalArgument | is thrown if unsupported parameter types have been set |
Referenced by InternalCalibration::calibrateMapGlobally().
|
protected |
Data vector.
|
protected |
Model type.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |