cyTransFinder

Class WebserviceTask_motifProcessing

java.lang.Object

org.cytoscape.work.AbstractTask

cyTransFinder.WebserviceTask_motifProcessing

All Implemented Interfaces:

org.cytoscape.work.ObservableTask, org.cytoscape.work.Task

public class WebserviceTask_motifProcessing
extends org.cytoscape.work.AbstractTask
implements org.cytoscape.work.ObservableTask

Field Summary

Fields

Modifier and Type	Field and Description
protected MyCytoPanel	myCytoPanel
protected String	myFunction
protected String[]	myMotif

Fields inherited from class org.cytoscape.work.AbstractTask

cancelled

Constructor Summary

Constructors

Constructor and Description
WebserviceTask_motifProcessing(CyActivator CY_ACTIVATOR, org.cytoscape.view.model.CyNetworkView MYVIEW, MyCytoPanel myCytoPanel, String[] MYMOTIF, String IntraInterMirna)

Method Summary

Modifier and Type	Method and Description
protected void	analyzeFirstElement()
protected void	analyzeLastElement()
protected void	enhanceGeneInfo(String TYPE)
protected void	enhanceIntergenicMirna(String TF_TARGET_TYPE, String TF_TARGET_TYPE2, int ITER)
protected void	enhanceIntronicMirna(String TF_TARGET_TYPE, String TF_TARGET_TYPE2, int ITER)
protected void	enhanceMirnaTargets(String targetType, String mirnaType, String Modality, Map<String,String> listAllTF, String temporaryTFType)
protected void	enhanceTF(String TF_TARGET_TYPE)
protected void	enhanceTFDownStream(String SOURCE_TYPE)
protected Map<String,String>	enhanceTFRetrieveAll(int Iter)
protected void	enhanceTFtarget(String TF_TYPE)
protected void	enhanceTFUpstream(String TARGET_TYPE)
protected void	genePrecededByMirna(Integer ACTUAL)
protected void	genePrecededByTF(int ACTUAL)
protected JDialog	getDialog()
<R> R	getResults(Class<? extends R> arg0)
protected void	imirnaPrecededByWhatever(Integer ACTUAL)
void	run(org.cytoscape.work.TaskMonitor taskMonitor)
protected void	tfPrecedeByMirna(Integer ACTUAL)
protected void	tfPrecedeByTF(Integer ACTUAL)

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

Methods inherited from interface org.cytoscape.work.Task

cancel

Field Detail

myCytoPanel

protected MyCytoPanel myCytoPanel

myFunction

protected String myFunction

myMotif

protected String[] myMotif

Constructor Detail

WebserviceTask_motifProcessing

public WebserviceTask_motifProcessing(CyActivator CY_ACTIVATOR,
                                      org.cytoscape.view.model.CyNetworkView MYVIEW,
                                      MyCytoPanel myCytoPanel,
                                      String[] MYMOTIF,
                                      String IntraInterMirna)

Method Detail

analyzeFirstElement

protected void analyzeFirstElement()

analyzeLastElement

protected void analyzeLastElement()

enhanceGeneInfo

protected void enhanceGeneInfo(String TYPE)

enhanceTF

protected void enhanceTF(String TF_TARGET_TYPE)

enhanceTFtarget

protected void enhanceTFtarget(String TF_TYPE)

enhanceTFDownStream

protected void enhanceTFDownStream(String SOURCE_TYPE)

enhanceTFUpstream

protected void enhanceTFUpstream(String TARGET_TYPE)

enhanceTFRetrieveAll

protected Map<String,String> enhanceTFRetrieveAll(int Iter)

enhanceMirnaTargets

protected void enhanceMirnaTargets(String targetType,
                                   String mirnaType,
                                   String Modality,
                                   Map<String,String> listAllTF,
                                   String temporaryTFType)

enhanceIntergenicMirna

protected void enhanceIntergenicMirna(String TF_TARGET_TYPE,
                                      String TF_TARGET_TYPE2,
                                      int ITER)

enhanceIntronicMirna

protected void enhanceIntronicMirna(String TF_TARGET_TYPE,
                                    String TF_TARGET_TYPE2,
                                    int ITER)

genePrecededByTF

protected void genePrecededByTF(int ACTUAL)

genePrecededByMirna

protected void genePrecededByMirna(Integer ACTUAL)

imirnaPrecededByWhatever

protected void imirnaPrecededByWhatever(Integer ACTUAL)

tfPrecedeByMirna

protected void tfPrecedeByMirna(Integer ACTUAL)

tfPrecedeByTF

protected void tfPrecedeByTF(Integer ACTUAL)

getDialog

protected JDialog getDialog()

run

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

Specified by:

run in interface org.cytoscape.work.Task

Specified by:

run in class org.cytoscape.work.AbstractTask

Throws:

Exception

getResults

public <R> R getResults(Class<? extends R> arg0)

Specified by:

getResults in interface org.cytoscape.work.ObservableTask