nct.service.interactions
Class DIPInteractionNetwork

java.lang.Object
  org.xml.sax.helpers.DefaultHandler
      nct.service.interactions.DIPInteractionNetwork

All Implemented Interfaces:

InteractionNetwork<java.lang.String,java.lang.Double>, org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler

public class DIPInteractionNetwork
extends org.xml.sax.helpers.DefaultHandler
implements InteractionNetwork<java.lang.String,java.lang.Double>

Implements the InteractionNetwork interface by reading a DIP XIN (xml) file. Read about DIP here: http://dip.doe-mbi.ucla.edu/

Field Summary

protected boolean	getOrganism
protected boolean	getValue
protected Graph<java.lang.String,java.lang.Double>	graph
protected java.util.Map<java.lang.String,java.lang.String>	idNameMap
protected java.util.Map<java.lang.String,java.lang.String>	idUidMap
protected java.lang.String	nodeId
protected java.util.Map<java.lang.String,java.lang.String>	nodeOrganismMap
protected java.lang.String	organism
static java.lang.String	organismID
protected java.lang.String	targetOrganism
protected java.lang.StringBuffer	value

Constructor Summary

DIPInteractionNetwork(java.lang.String targetOrganism)
A SAX event handler that extracts graph information (nodes and edges) for a specific organism from a specified DIP XIN database file http://dip.doe-mbi.ucla.edu.

Method Summary

void	characters(char[] ch, int start, int length) Basic SAX event handler.
void	endDocument() Basic SAX event handler.
void	endElement(java.lang.String uri, java.lang.String name, java.lang.String qName) Basic SAX event handler.
void	startDocument() Basic SAX event handler.
void	startElement(java.lang.String uri, java.lang.String name, java.lang.String qName, org.xml.sax.Attributes atts) Basic SAX event handler.
void	updateGraph(Graph<java.lang.String,java.lang.Double> graph) Updates the specified graph with the relevant nodes and edges contained in the XIN file and for the organism specified in the constructor.

Methods inherited from class org.xml.sax.helpers.DefaultHandler

endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

organismID

public static java.lang.String organismID

nodeId

protected java.lang.String nodeId

organism

protected java.lang.String organism

value

protected java.lang.StringBuffer value

getOrganism

protected boolean getOrganism

getValue

protected boolean getValue

nodeOrganismMap

protected java.util.Map<java.lang.String,java.lang.String> nodeOrganismMap

idUidMap

protected java.util.Map<java.lang.String,java.lang.String> idUidMap

idNameMap

protected java.util.Map<java.lang.String,java.lang.String> idNameMap

graph

protected Graph<java.lang.String,java.lang.Double> graph

targetOrganism

protected java.lang.String targetOrganism

Constructor Detail

DIPInteractionNetwork

public DIPInteractionNetwork(java.lang.String targetOrganism)

A SAX event handler that extracts graph information (nodes and edges) for a specific organism from a specified DIP XIN database file http://dip.doe-mbi.ucla.edu.

Parameters:

targetOrganism - The target organism the graph is being constructed for. The name must match the organism names used in the DIP file.

Method Detail

startDocument

public void startDocument()

Basic SAX event handler.

Specified by:

startDocument in interface org.xml.sax.ContentHandler

Overrides:

startDocument in class org.xml.sax.helpers.DefaultHandler

endDocument

public void endDocument()

Basic SAX event handler.

Specified by:

endDocument in interface org.xml.sax.ContentHandler

Overrides:

endDocument in class org.xml.sax.helpers.DefaultHandler

startElement

public void startElement(java.lang.String uri,
                         java.lang.String name,
                         java.lang.String qName,
                         org.xml.sax.Attributes atts)

Basic SAX event handler.

Specified by:

startElement in interface org.xml.sax.ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

endElement

public void endElement(java.lang.String uri,
                       java.lang.String name,
                       java.lang.String qName)

Basic SAX event handler.

Specified by:

endElement in interface org.xml.sax.ContentHandler

Overrides:

endElement in class org.xml.sax.helpers.DefaultHandler

characters

public void characters(char[] ch,
                       int start,
                       int length)

Basic SAX event handler.

Specified by:

characters in interface org.xml.sax.ContentHandler

Overrides:

characters in class org.xml.sax.helpers.DefaultHandler

updateGraph

public void updateGraph(Graph<java.lang.String,java.lang.Double> graph)

Updates the specified graph with the relevant nodes and edges contained in the XIN file and for the organism specified in the constructor.

Specified by:

updateGraph in interface InteractionNetwork<java.lang.String,java.lang.Double>

Parameters:

graph - The graph to be updated by adding nodes and edges.