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ConsensusXMLHandler Class Template Reference

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

Inheritance diagram for ConsensusXMLHandler:

XMLHandler xercesc::DefaultHandler

List of all members.


Detailed Description

template<typename AlignmentT>
class OpenMS::Internal::ConsensusXMLHandler< AlignmentT >

XML Handler for a consensusXML.

Public Types

typedef
AlignmentT::ElementContainerType 
ElementContainerType
typedef AlignmentT::ElementType ElementType
typedef
AlignmentT::ConsensusElementType 
ConsensusElementType
typedef DPosition< 2 > PositionType

Public Member Functions

 ConsensusXMLHandler (ConsensusMap< ConsensusElementType > &consensus_map, const String &filename, const String &version, bool load_elements_maps=true)
 Constructor.
 ConsensusXMLHandler (const StarAlignment< ConsensusElementType > &alignment, const String &filename, const String &version)
 Copy constructor.
virtual ~ConsensusXMLHandler ()
 Destructor.
virtual void endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname)
 Parsing method for closing tags.
virtual void startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags.
virtual void characters (const XMLCh *const chars, unsigned int length)
 Parsing method for character data.
void writeTo (std::ostream &os)
 Writes the contents to a stream.
template<>
void loadFile_ (const String &file_name, UInt id, const ConsensusFeature< FeatureMap< > > &) throw(Exception::FileNotFound, Exception::ParseError)
template<>
void loadFile_ (const String &file_name, UInt id, const ConsensusPeak< DPeakArray< Peak2D > > &) throw(Exception::FileNotFound, Exception::ParseError)
template<>
void loadFile_ (const String &file_name, UInt id, const ConsensusFeature< ConsensusMap< ConsensusFeature< FeatureMap< > > > > &) throw(Exception::FileNotFound, Exception::ParseError)

Protected Member Functions

template<typename ConsensusElementT>
void loadFile_ (const String &, UInt, const ConsensusElementT &) throw (Exception::FileNotFound, Exception::ParseError)
 This function fills the members of a picked peak of type OutputPeakType.
void writeCellList_ (std::ostream &os, const Grid &grid)

Protected Attributes

ConsensusMap
< ConsensusElementType > * 
consensus_map_
ConsensusElementType act_cons_element_
const StarAlignment
< ConsensusElementType > * 
calignment_
bool consensus_element_range_
bool feature_map_flag_
bool consensus_map_flag_
bool load_elements_maps_
ConsensusElementType::PositionType pos_
ConsensusElementType::IntensityType it_
ConsensusElementType::PositionBoundingBoxType pos_range_
ConsensusElementType::IntensityBoundingBoxType it_range_

Member Typedef Documentation

typedef AlignmentT::ElementContainerType ElementContainerType

typedef AlignmentT::ElementType ElementType

typedef AlignmentT::ConsensusElementType ConsensusElementType

typedef DPosition<2> PositionType


Constructor & Destructor Documentation

ConsensusXMLHandler ( ConsensusMap< ConsensusElementType > &  consensus_map,
const String filename,
const String version,
bool  load_elements_maps = true 
) [inline]

Constructor.

ConsensusXMLHandler ( const StarAlignment< ConsensusElementType > &  alignment,
const String filename,
const String version 
) [inline]

Copy constructor.

virtual ~ConsensusXMLHandler (  )  [inline, virtual]

Destructor.


Member Function Documentation

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

Parsing method for closing tags.

Reimplemented from XMLHandler.

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

Parsing method for opening tags.

Reimplemented from XMLHandler.

void characters ( const XMLCh *const   chars,
unsigned int  length 
) [inline, virtual]

Parsing method for character data.

Reimplemented from XMLHandler.

void writeTo ( std::ostream &  os  )  [inline, virtual]

Writes the contents to a stream.

Reimplemented from XMLHandler.

void loadFile_ ( const String ,
UInt  ,
const ConsensusElementT &   
) throw (Exception::FileNotFound, Exception::ParseError) [inline, protected]

This function fills the members of a picked peak of type OutputPeakType.

void writeCellList_ ( std::ostream &  os,
const Grid grid 
) [inline, protected]

void loadFile_< ConsensusFeature< FeatureMap< > > > ( const String file_name,
UInt  id,
const ConsensusFeature< FeatureMap< > > &   
) throw(Exception::FileNotFound, Exception::ParseError) [inline]

void loadFile_< ConsensusPeak< DPeakArray< Peak2D > > > ( const String file_name,
UInt  id,
const ConsensusPeak< DPeakArray< Peak2D > > &   
) throw(Exception::FileNotFound, Exception::ParseError) [inline]

void loadFile_< ConsensusFeature< ConsensusMap< ConsensusFeature< FeatureMap< > > > > > ( const String file_name,
UInt  id,
const ConsensusFeature< ConsensusMap< ConsensusFeature< FeatureMap< > > > > &   
) throw(Exception::FileNotFound, Exception::ParseError) [inline]


Member Data Documentation

ConsensusMap<ConsensusElementType>* consensus_map_ [protected]

ConsensusElementType act_cons_element_ [protected]

const StarAlignment< ConsensusElementType >* calignment_ [protected]

bool consensus_element_range_ [protected]

bool feature_map_flag_ [protected]

bool consensus_map_flag_ [protected]

bool load_elements_maps_ [protected]

ConsensusElementType::PositionType pos_ [protected]

ConsensusElementType::IntensityType it_ [protected]

ConsensusElementType::PositionBoundingBoxType pos_range_ [protected]

ConsensusElementType::IntensityBoundingBoxType it_range_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:49 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1