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

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

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List of all members.

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.

void org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::summarize  )  [inline]
 

Definition at line 262 of file WeakArgModelBuilder.java.

References inEdgeTally, normalize(), and outEdgeTally.

Referenced by org::gel::mauve::recombination::WeakArgModelBuilder::readWargXmlBzip2().


Member Data Documentation

double org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::aFrom [package]
 

Definition at line 120 of file WeakArgModelBuilder.java.

Referenced by characters().

double org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::aTo [package]
 

Definition at line 120 of file WeakArgModelBuilder.java.

Referenced by characters().

int org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::curblock = -1 [package]
 

Definition at line 121 of file WeakArgModelBuilder.java.

Referenced by normalize(), recordRecEdge(), and startElement().

String org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::curBlocks [package]
 

Definition at line 117 of file WeakArgModelBuilder.java.

Referenced by characters().

String org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::curElement [package]
 

Definition at line 115 of file WeakArgModelBuilder.java.

Referenced by characters(), and startElement().

String org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::curNameMap [package]
 

Definition at line 116 of file WeakArgModelBuilder.java.

Referenced by characters().

int org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::eFrom [package]
 

Definition at line 119 of file WeakArgModelBuilder.java.

Referenced by characters(), and endElement().

int org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::end [package]
 

Definition at line 119 of file WeakArgModelBuilder.java.

int org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::eTo [package]
 

Definition at line 119 of file WeakArgModelBuilder.java.

Referenced by characters(), and endElement().

boolean [] org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::gap [package]
 

Definition at line 128 of file WeakArgModelBuilder.java.

Referenced by recordRecEdge(), and WeakArgXmlHandler().

int [][] org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::inEdgeTally [package]
 

Definition at line 124 of file WeakArgModelBuilder.java.

Referenced by endElement(), org::gel::mauve::recombination::WeakArgModelBuilder::readWargXmlBzip2(), summarize(), and WeakArgXmlHandler().

int org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::iterations [package]
 

Definition at line 130 of file WeakArgModelBuilder.java.

WeakArgDataModel org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::model [package]
 

Definition at line 113 of file WeakArgModelBuilder.java.

int [][] org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::outEdgeTally [package]
 

Definition at line 125 of file WeakArgModelBuilder.java.

Referenced by endElement(), org::gel::mauve::recombination::WeakArgModelBuilder::readWargXmlBzip2(), summarize(), and WeakArgXmlHandler().

byte [][] org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::regionalColors [package]
 

Definition at line 126 of file WeakArgModelBuilder.java.

long [] org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::seq_coords [package]
 

Definition at line 127 of file WeakArgModelBuilder.java.

Referenced by recordRecEdge(), and WeakArgXmlHandler().

int org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::start [package]
 

Definition at line 119 of file WeakArgModelBuilder.java.

XmfaViewerModel org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler::xmfa [package]
 

Definition at line 114 of file WeakArgModelBuilder.java.


The documentation for this class was generated from the following file:
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