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MascotXMLHandler Class Reference

Handler that is used for parsing MascotXML data. More...

#include <OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h>

Inheritance diagram for MascotXMLHandler:
XMLHandler

Public Types

typedef Map< Size, floatRTMapping
 
- Public Types inherited from XMLHandler
enum  ActionMode { LOAD, STORE }
 Action to set the current mode (for error messages) More...
 

Public Member Functions

 MascotXMLHandler (ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &identifications, const String &filename, std::map< String, std::vector< AASequence > > &peptides, const RTMapping &rt_mapping=RTMapping(), const String &scan_regex="")
 Constructor. More...
 
virtual ~MascotXMLHandler ()
 Destructor. More...
 
virtual void endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname)
 Parsing method for closing tags. More...
 
virtual void startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags. More...
 
virtual void characters (const XMLCh *const chars, const XMLSize_t)
 Parsing method for character data. More...
 
- Public Member Functions inherited from XMLHandler
 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)
 

Static Public Attributes

static const String primary_scan_regex
 

Private Attributes

ProteinIdentificationprotein_identification_
 the protein identifications More...
 
std::vector< PeptideIdentification > & id_data_
 the identifications (storing the peptide hits) More...
 
ProteinHit actual_protein_hit_
 
PeptideHit actual_peptide_hit_
 
PeptideEvidence actual_peptide_evidence_
 
UInt peptide_identification_index_
 
String tag_
 
DateTime date_
 
String date_time_string_
 
UInt actual_query_
 
ProteinIdentification::SearchParameters search_parameters_
 
String identifier_
 
String actual_title_
 
std::map< String, std::vector< AASequence > > & modified_peptides_
 
StringList tags_open_
 tracking the current XML tree More...
 
String character_buffer_
 filled by MascotXMLHandler::characters More...
 
String major_version_
 
String minor_version_
 
const RTMappingrt_mapping_
 
std::vector< boost::regex > scan_regex_
 List of possible Perl-style regular expressions used to extract the scan number (named group "SCAN") or retention time (named group "RT"), and possibly precursor m/z (named group "MZ") from the "pep_scan_title" element. More...
 
bool no_rt_error_
 Error for missing RT information already reported? More...
 

Additional Inherited Members

- Static Public Member Functions inherited from XMLHandler
static String writeXMLEscape (const String &to_escape)
 Escapes a string and returns the escaped string. More...
 
- 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)
 
- 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...
 

Detailed Description

Handler that is used for parsing MascotXML data.

Member Typedef Documentation

typedef Map<Size, float> RTMapping

Constructor & Destructor Documentation

MascotXMLHandler ( ProteinIdentification protein_identification,
std::vector< PeptideIdentification > &  identifications,
const String filename,
std::map< String, std::vector< AASequence > > &  peptides,
const RTMapping rt_mapping = RTMapping(),
const String scan_regex = "" 
)

Constructor.

virtual ~MascotXMLHandler ( )
virtual

Destructor.

Member Function Documentation

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

Parsing method for character data.

Reimplemented from XMLHandler.

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

Parsing method for closing tags.

Reimplemented from XMLHandler.

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

Parsing method for opening tags.

Reimplemented from XMLHandler.

Member Data Documentation

PeptideEvidence actual_peptide_evidence_
private
PeptideHit actual_peptide_hit_
private
ProteinHit actual_protein_hit_
private
UInt actual_query_
private
String actual_title_
private
String character_buffer_
private
DateTime date_
private
String date_time_string_
private
std::vector<PeptideIdentification>& id_data_
private

the identifications (storing the peptide hits)

String identifier_
private
String major_version_
private
String minor_version_
private
std::map<String, std::vector<AASequence> >& modified_peptides_
private
bool no_rt_error_
private

Error for missing RT information already reported?

UInt peptide_identification_index_
private
const String primary_scan_regex
static
ProteinIdentification& protein_identification_
private

the protein identifications

const RTMapping& rt_mapping_
private

optional mapping of scan indices to RTs if scan numbers are given; without this mapping, other sources of RT information are used (if available); if all fails, there will be no RT information for peptide hits

std::vector<boost::regex> scan_regex_
private

List of possible Perl-style regular expressions used to extract the scan number (named group "SCAN") or retention time (named group "RT"), and possibly precursor m/z (named group "MZ") from the "pep_scan_title" element.

ProteinIdentification::SearchParameters search_parameters_
private
String tag_
private
StringList tags_open_
private

tracking the current XML tree


OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:14:12 using doxygen 1.8.9.1