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java.lang.Objectorg.xml.sax.helpers.DefaultHandler
nct.service.interactions.DIPInteractionNetwork
public class DIPInteractionNetwork
Implements the InteractionNetwork interface by reading a DIP XIN (xml) file. Read about DIP here: http://dip.doe-mbi.ucla.edu/
Field Summary | |
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protected boolean |
getOrganism
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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 | |
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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 | |
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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 |
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endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startPrefixMapping, unparsedEntityDecl, warning |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static java.lang.String organismID
protected java.lang.String nodeId
protected java.lang.String organism
protected java.lang.StringBuffer value
protected boolean getOrganism
protected boolean getValue
protected java.util.Map<java.lang.String,java.lang.String> nodeOrganismMap
protected java.util.Map<java.lang.String,java.lang.String> idUidMap
protected java.util.Map<java.lang.String,java.lang.String> idNameMap
protected Graph<java.lang.String,java.lang.Double> graph
protected java.lang.String targetOrganism
Constructor Detail |
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public DIPInteractionNetwork(java.lang.String targetOrganism)
targetOrganism
- The target organism the graph is being constructed for.
The name must match the organism names used in the DIP file.Method Detail |
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public void startDocument()
startDocument
in interface org.xml.sax.ContentHandler
startDocument
in class org.xml.sax.helpers.DefaultHandler
public void endDocument()
endDocument
in interface org.xml.sax.ContentHandler
endDocument
in class org.xml.sax.helpers.DefaultHandler
public void startElement(java.lang.String uri, java.lang.String name, java.lang.String qName, org.xml.sax.Attributes atts)
startElement
in interface org.xml.sax.ContentHandler
startElement
in class org.xml.sax.helpers.DefaultHandler
public void endElement(java.lang.String uri, java.lang.String name, java.lang.String qName)
endElement
in interface org.xml.sax.ContentHandler
endElement
in class org.xml.sax.helpers.DefaultHandler
public void characters(char[] ch, int start, int length)
characters
in interface org.xml.sax.ContentHandler
characters
in class org.xml.sax.helpers.DefaultHandler
public void updateGraph(Graph<java.lang.String,java.lang.Double> graph)
updateGraph
in interface InteractionNetwork<java.lang.String,java.lang.Double>
graph
- The graph to be updated by adding nodes and edges.
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