Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
XTandemXMLFile Class Reference

Used to load XTandemXML files. More...

#include <OpenMS/FORMAT/XTandemXMLFile.h>

Inheritance diagram for XTandemXMLFile:
XMLHandler XMLFile

Public Member Functions

 XTandemXMLFile ()
 Default constructor. More...
 
virtual ~XTandemXMLFile ()
 Destructor. More...
 
void load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data)
 loads data from a XTandemXML file More...
 
void setModificationDefinitionsSet (const ModificationDefinitionsSet &rhs)
 sets the valid modifications 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)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 

Protected Member Functions

void startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags. More...
 
void endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname)
 Parsing method for closing tags. More...
 
void characters (const XMLCh *const chars, const XMLSize_t)
 Parsing method for character data. More...
 
 XTandemXMLFile (const XTandemXMLFile &rhs)
 
XTandemXMLFileoperator= (const XTandemXMLFile &rhs)
 
- Protected Member Functions inherited from XMLHandler
bool equal_ (const XMLCh *a, const XMLCh *b) const
 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...
 
double attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a double. 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_ (double &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the double 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...
 
double attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a double. 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_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the double 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 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)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 

Private Attributes

ProteinIdentificationprotein_identification_
 
bool protein_open_
 
bool is_description_
 
Map< UInt, std::vector
< PeptideHit > > 
peptide_hits_
 
Map< String, ProteinHitprotein_hits_
 
String actual_protein_id_
 
Int actual_charge_
 
Int actual_id_
 
String tag_
 
UInt actual_start_
 
UInt actual_stop_
 
ModificationDefinitionsSet mod_def_set_
 

Additional Inherited Members

- Protected Types inherited from XMLHandler
enum  ActionMode { LOAD, STORE }
 Action to set the current mode (for error messages) More...
 
- Static Protected Member Functions inherited from XMLHandler
static String writeXMLEscape (const String &to_escape)
 Escapes a string and returns the escaped string. 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< Stringopen_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 dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...
 

Detailed Description

Used to load XTandemXML files.

This class is used to load documents that implement the schema of XTandemXML files.

Constructor & Destructor Documentation

Default constructor.

virtual ~XTandemXMLFile ( )
virtual

Destructor.

XTandemXMLFile ( const XTandemXMLFile rhs)
protected

Member Function Documentation

void characters ( const XMLCh *const  chars,
const XMLSize_t  length 
)
protectedvirtual

Parsing method for character data.

Reimplemented from XMLHandler.

void endElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const  qname 
)
protectedvirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

XTandemXMLFile& operator= ( const XTandemXMLFile rhs)
protected
void setModificationDefinitionsSet ( const ModificationDefinitionsSet rhs)

sets the valid modifications

void startElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const  qname,
const xercesc::Attributes &  attrs 
)
protectedvirtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

Member Data Documentation

Int actual_charge_
private
Int actual_id_
private
String actual_protein_id_
private
UInt actual_start_
private
UInt actual_stop_
private
bool is_description_
private
ModificationDefinitionsSet mod_def_set_
private
Map<UInt, std::vector<PeptideHit> > peptide_hits_
private
Map<String, ProteinHit> protein_hits_
private
ProteinIdentification* protein_identification_
private
bool protein_open_
private
String tag_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:47 using doxygen 1.8.5