cyTransFinder

Class WebserviceTask_NCBI

java.lang.Object

org.cytoscape.work.AbstractTask

cyTransFinder.WebserviceTask_NCBI

All Implemented Interfaces:

org.cytoscape.work.Task

public class WebserviceTask_NCBI
extends org.cytoscape.work.AbstractTask

Field Summary

Fields

Modifier and Type	Field and Description
protected String	count
protected Document	document
protected String	geneID
protected String	geneSYM
protected CyActivator	myActivator
protected Set<org.cytoscape.model.CyNode>	myNodes
protected Document	ncbiDocument
protected Map<String,String>	ncbiInfo
protected NetworkFromSources	networkFromSources

Fields inherited from class org.cytoscape.work.AbstractTask

cancelled

Constructor Summary

Constructors

Constructor and Description
WebserviceTask_NCBI(Set<org.cytoscape.model.CyNode> GENE_NODES, String[] values, String TYPE, CyActivator myActivator, NetworkFromSources networkFromSources)

Method Summary

Modifier and Type	Method and Description
protected Document	getRawDocFromUrl(String url)
protected void	printDocument(Document doc, OutputStream out)
String	retrieveEutils_GeneID(String geneValue, String mode)
Map<String,String>	retrieveNCBI_GeneticINFOZ(String geneID, String geneSymbol, String organism)
void	run(org.cytoscape.work.TaskMonitor taskMonitor) Run the task for the basic gene information (Faster)

Methods inherited from class org.cytoscape.work.AbstractTask

cancel, insertTasksAfterCurrentTask, insertTasksAfterCurrentTask, setTaskIterator

Methods inherited from class java.lang.Object

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

Field Detail

document

protected Document document

geneID

protected String geneID

geneSYM

protected String geneSYM

count

protected String count

ncbiDocument

protected Document ncbiDocument

ncbiInfo

protected Map<String,String> ncbiInfo

networkFromSources

protected NetworkFromSources networkFromSources

myActivator

protected CyActivator myActivator

myNodes

protected Set<org.cytoscape.model.CyNode> myNodes

Constructor Detail

WebserviceTask_NCBI

public WebserviceTask_NCBI(Set<org.cytoscape.model.CyNode> GENE_NODES,
                           String[] values,
                           String TYPE,
                           CyActivator myActivator,
                           NetworkFromSources networkFromSources)

Method Detail

retrieveNCBI_GeneticINFOZ

public Map<String,String> retrieveNCBI_GeneticINFOZ(String geneID,
                                                    String geneSymbol,
                                                    String organism)
                                             throws IOException

Throws:

IOException

printDocument

protected void printDocument(Document doc,
                             OutputStream out)
                      throws IOException,
                             TransformerException

Throws:

IOException

TransformerException

retrieveEutils_GeneID

public String retrieveEutils_GeneID(String geneValue,
                                    String mode)
                             throws IOException

Throws:

IOException

getRawDocFromUrl

protected Document getRawDocFromUrl(String url)
                             throws IOException,
                                    SAXException

Throws:

IOException

SAXException

run

public void run(org.cytoscape.work.TaskMonitor taskMonitor)
         throws Exception

Run the task for the basic gene information (Faster)

Specified by:

run in interface org.cytoscape.work.Task

Specified by:

run in class org.cytoscape.work.AbstractTask

Throws:

Exception