org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler Class Reference

Class to handle XML parse events from weak arg xml. More...

Collaboration diagram for org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler:


Public Member Functions
void	characters (char[] ch, int start, int length) throws SAXException
void	endDocument () throws SAXException
void	endElement (String uri, String localName, String qName) throws SAXException
void	endPrefixMapping (String prefix) throws SAXException
void	ignorableWhitespace (char[] ch, int start, int length) throws SAXException
void	normalize (int[][] data)
void	processingInstruction (String target, String data) throws SAXException
void	setDocumentLocator (Locator locator)
void	skippedEntity (String name) throws SAXException
void	startDocument () throws SAXException
void	startElement (String uri, String localName, String qName, Attributes atts) throws SAXException
void	startPrefixMapping (String prefix, String uri) throws SAXException
void	summarize ()
Package Functions
	WeakArgXmlHandler (WeakArgDataModel model, XmfaViewerModel xmfa)
Package Attributes
double	aFrom
double	aTo
int	curblock = -1
String	curBlocks
String	curElement
String	curNameMap
int	eFrom
int	end
int	eTo
boolean[]	gap
int[][]	inEdgeTally
int	iterations
WeakArgDataModel	model
int[][]	outEdgeTally
byte[][]	regionalColors
long[]	seq_coords
int	start
XmfaViewerModel	xmfa
Private Member Functions
void	recordRecEdge (int[][] tally, int genome)

Detailed Description

Class to handle XML parse events from weak arg xml.

Author:: koadman

Definition at line 111 of file WeakArgModelBuilder.java.

Constructor & Destructor Documentation

org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::WeakArgXmlHandler ( WeakArgDataModel model,

XmfaViewerModel xmfa

) [inline, package]

Definition at line 134 of file WeakArgModelBuilder.java.
References gap, org::gel::mauve::BaseViewerModel::getGenomes(), org::gel::mauve::BaseViewerModel::getSequenceCount(), inEdgeTally, outEdgeTally, and seq_coords.

Member Function Documentation

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::characters ( char[] ch,

int start,

int length

) throws SAXException [inline]

Definition at line 149 of file WeakArgModelBuilder.java.
References aFrom, aTo, curBlocks, curElement, curNameMap, eFrom, eTo, and org::gel::mauve::recombination::WeakArgDataModel::treeString.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::endDocument ( ) throws SAXException [inline]

Definition at line 223 of file WeakArgModelBuilder.java.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::endElement ( String uri,

String localName,

String qName

) throws SAXException [inline]

Definition at line 190 of file WeakArgModelBuilder.java.
References eFrom, eTo, org::gel::mauve::BaseViewerModel::getSequenceCount(), inEdgeTally, outEdgeTally, and recordRecEdge().

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::endPrefixMapping ( String prefix ) throws SAXException [inline]

Definition at line 224 of file WeakArgModelBuilder.java.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::ignorableWhitespace ( char[] ch,

int start,

int length

) throws SAXException [inline]

Definition at line 225 of file WeakArgModelBuilder.java.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::normalize ( int data[][] ) [inline]

Definition at line 245 of file WeakArgModelBuilder.java.
References curblock.
Referenced by summarize().

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::processingInstruction ( String target,

String data

) throws SAXException [inline]

Definition at line 226 of file WeakArgModelBuilder.java.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::recordRecEdge ( int tally[][],

int genome

) [inline, private]

Definition at line 205 of file WeakArgModelBuilder.java.
References curblock, gap, org::gel::mauve::XmfaViewerModel::getColumnCoordinates(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::Genome::getLength(), and seq_coords.
Referenced by endElement().

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::setDocumentLocator ( Locator locator ) [inline]

Definition at line 227 of file WeakArgModelBuilder.java.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::skippedEntity ( String name ) throws SAXException [inline]

Definition at line 228 of file WeakArgModelBuilder.java.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::startDocument ( ) throws SAXException [inline]

Definition at line 229 of file WeakArgModelBuilder.java.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::startElement ( String uri,

String localName,

String qName,

Attributes atts

) throws SAXException [inline]

Definition at line 232 of file WeakArgModelBuilder.java.
References curblock, and curElement.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::startPrefixMapping ( String prefix,

String uri

) throws SAXException [inline]

Definition at line 230 of file WeakArgModelBuilder.java.