A C D E F G I L M N O P R S T U V W

A

actionPerformed(ActionEvent) - Method in class cyTransFinder.AddCytoPanelAction

actionPerformed(ActionEvent) - Method in class cyTransFinder.MyCytoPanel

AddCytoPanelAction - Class in cyTransFinder

AddCytoPanelAction(CySwingApplication, MyCytoPanel) - Constructor for class cyTransFinder.AddCytoPanelAction

addEdge(CyNode, CyNode, String, String, String) - Method in class cyTransFinder.Network

Used for enhancing with protein, since in this case we use CyNode instead od String NodeID.

addEdgePrepare(String, String, String, String, String, String) - Method in class cyTransFinder.Network

addGene(String, String, String) - Method in class cyTransFinder.Network

addGeneID(String, String) - Method in class cyTransFinder.Network

addIntronicMirna(String, String, String, String, String) - Method in class cyTransFinder.Network

addNode(String, String, String, String, String, String, String, String, String, String, String) - Method in class cyTransFinder.Network

addNodeProtein(String, String, String, String) - Method in class cyTransFinder.Network

addSourceMirna(String) - Method in class cyTransFinder.Network

AllDownStreamList - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

allFinished(FinishStatus) - Method in class cyTransFinder.myTaskObserver

AllTFHash - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

AllTFList - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

AllTFTargetList - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

AllUpstreamList - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

analyzeFirstElement() - Method in class cyTransFinder.WebserviceTask_motifProcessing

analyzeLastElement() - Method in class cyTransFinder.WebserviceTask_motifProcessing

C

close() - Method in class cyTransFinder.UncloseableInputStream

copyAttributes(CyRow, CyRow) - Static method in class cyTransFinder.NetworkReactome

Copy the contents of one CyRow into another CyRow.

copyToCyNetwork(CyNetwork, CyNetwork, Collection<CyNode>, Collection<CyEdge>) - Static method in class cyTransFinder.NetworkReactome

Copies nodes and edges from one CyNetwork to another without sharing.

count - Variable in class cyTransFinder.WebserviceTask_NCBI

createTaskIterator(CyNetworkView) - Method in class cyTransFinder.MyLayoutTask

CY_ACTIVATOR - Variable in class cyTransFinder.Network

CyActivator - Class in cyTransFinder

CyActivator() - Constructor for class cyTransFinder.CyActivator

cyTransFinder - package cyTransFinder

D

document - Variable in class cyTransFinder.Network

document - Variable in class cyTransFinder.WebserviceTask_mirIAD

document - Variable in class cyTransFinder.WebserviceTask_mirIAD_InterGenic

document - Variable in class cyTransFinder.WebserviceTask_NCBI

document - Variable in class cyTransFinder.WebserviceTask_TFe

document - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

document - Variable in class cyTransFinder.WebserviceTask_UCSC

document - Variable in class cyTransFinder.WebserviceTask_Uniprot

downloadZip() - Method in class cyTransFinder.WebserviceTask_mirIAD

downloadZip() - Method in class cyTransFinder.WebserviceTask_mirIAD_InterGenic

E

enhanceGeneInfo(String) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceIntergenicMirna(String, String, int) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceIntronicMirna(String, String, int) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceMirnaTargets(String, String, String, Map<String, String>, String) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceProtein(String, String) - Method in class cyTransFinder.MyCytoPanel

enhanceTF(String) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceTFDownStream(String) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceTFRetrieveAll(int) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceTFtarget(String) - Method in class cyTransFinder.WebserviceTask_motifProcessing

enhanceTFUpstream(String) - Method in class cyTransFinder.WebserviceTask_motifProcessing

F

finalization() - Method in class cyTransFinder.NetworkReactome

fullSimple - Variable in class cyTransFinder.WebserviceTask_motifTypeParser

G

geneID - Variable in class cyTransFinder.WebserviceTask_mirIAD

geneID - Variable in class cyTransFinder.WebserviceTask_mirIAD_InterGenic

geneID - Variable in class cyTransFinder.WebserviceTask_NCBI

geneID - Variable in class cyTransFinder.WebserviceTask_TFe

geneID - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

geneID - Variable in class cyTransFinder.WebserviceTask_UCSC

geneID - Variable in class cyTransFinder.WebserviceTask_Uniprot

genePrecededByMirna(Integer) - Method in class cyTransFinder.WebserviceTask_motifProcessing

genePrecededByTF(int) - Method in class cyTransFinder.WebserviceTask_motifProcessing

geneSYM - Variable in class cyTransFinder.WebserviceTask_NCBI

getAccessions() - Method in class cyTransFinder.WebserviceTask_Uniprot

getAllTF() - Method in class cyTransFinder.WebserviceTask_TFTargetmine

getComponent() - Method in class cyTransFinder.MyCytoPanel

getCyNetworkFactoryServiceRef() - Method in class cyTransFinder.CyActivator

getCyNetworkManagerServiceRef() - Method in class cyTransFinder.CyActivator

getCyNetworkNamingServiceRef() - Method in class cyTransFinder.CyActivator

getCyNetworkViewFactoryServiceRef() - Method in class cyTransFinder.CyActivator

getCyNetworkViewManagerServiceRef() - Method in class cyTransFinder.CyActivator

getCytoPanelName() - Method in class cyTransFinder.MyCytoPanel

getDialog() - Method in class cyTransFinder.WebserviceTask_motifProcessing

getFullName() - Method in class cyTransFinder.WebserviceTask_Uniprot

getGeneId(String, Object) - Method in class cyTransFinder.Network

getGeneSymbol(String, Object) - Method in class cyTransFinder.Network

getHumanReadable() - Method in class cyTransFinder.UtilOrganism

getIcon() - Method in class cyTransFinder.MyCytoPanel

getIntronicMirnaList() - Method in class cyTransFinder.WebserviceTask_mirIAD

getIntronicMirnaList() - Method in class cyTransFinder.WebserviceTask_mirIAD_InterGenic

getIsoforms() - Method in class cyTransFinder.WebserviceTask_Uniprot

getKeggID() - Method in class cyTransFinder.UtilOrganism

getMotifCUSTOM() - Method in class cyTransFinder.WebserviceTask_motifTypeParser

getMotifmiRNAT1() - Method in class cyTransFinder.WebserviceTask_motifTypeParser

getMotifmiRNAT2() - Method in class cyTransFinder.WebserviceTask_motifTypeParser

getMotifT0() - Method in class cyTransFinder.WebserviceTask_motifTypeParser

getMotifT1() - Method in class cyTransFinder.WebserviceTask_motifTypeParser

getMotifT2() - Method in class cyTransFinder.WebserviceTask_motifTypeParser

getMyCyNet() - Method in class cyTransFinder.CyActivator

getMyNetwork() - Method in class cyTransFinder.CyActivator

getMyOrganismsList() - Method in class cyTransFinder.UtilOrganism

getMyView() - Method in class cyTransFinder.CyActivator

getNcbiID() - Method in class cyTransFinder.UtilOrganism

getNetList() - Method in class cyTransFinder.NetworkReactomeTask

getNodesWithTwoValue(String, Object, String, Object) - Method in class cyTransFinder.Network

getNodesWithValue(String, String) - Method in class cyTransFinder.MyCytoPanel

getNodesWithValue(String, Object) - Method in class cyTransFinder.Network

getNodeWithID(String, Object) - Method in class cyTransFinder.Network

getPhilogeneticID() - Method in class cyTransFinder.UtilOrganism

getRawDocFromUrl(String) - Method in class cyTransFinder.WebserviceTask_NCBI

getReactomeID() - Method in class cyTransFinder.UtilOrganism

getResults(Class<? extends R>) - Method in class cyTransFinder.WebserviceTask_motifProcessing

getSourceGenes() - Method in class cyTransFinder.NetworkFromSources

getTargetGenes() - Method in class cyTransFinder.NetworkFromSources

getTfList() - Method in class cyTransFinder.NetworkFromSources

getTitle() - Method in class cyTransFinder.MyCytoPanel

getUniprotID() - Method in class cyTransFinder.WebserviceTask_Uniprot

getVisualStyleFactoryServiceRef() - Method in class cyTransFinder.CyActivator

getVmfFactoryC() - Method in class cyTransFinder.CyActivator

getVmfFactoryD() - Method in class cyTransFinder.CyActivator

getVmfFactoryP() - Method in class cyTransFinder.CyActivator

getVmmServiceRef() - Method in class cyTransFinder.CyActivator

getVs() - Method in class cyTransFinder.VisualInterfaceKEGG

I

imirnaPrecededByWhatever(Integer) - Method in class cyTransFinder.WebserviceTask_motifProcessing

init() - Method in class cyTransFinder.VisualInterfaceKEGG

IntronicMirnaList - Variable in class cyTransFinder.CyActivator

IntronicMirnaList - Variable in class cyTransFinder.WebserviceTask_mirIAD

IntronicMirnaList - Variable in class cyTransFinder.WebserviceTask_mirIAD_InterGenic

isReady(CyNetworkView) - Method in class cyTransFinder.MyLayoutTask

L

labelSelectedDataInput - Variable in class cyTransFinder.MyCytoPanel

labelSelectedDataOutput - Variable in class cyTransFinder.MyCytoPanel

listAllTF() - Method in class cyTransFinder.WebserviceTask_TFTargetmine

listAndAddTFTargets(String, CyNode) - Method in class cyTransFinder.WebserviceTask_TFTargetmine

listDownstreamTF(String) - Method in class cyTransFinder.WebserviceTask_TFTargetmine

listTFTargets(String) - Method in class cyTransFinder.WebserviceTask_TFTargetmine

listUpstreamTF(String) - Method in class cyTransFinder.WebserviceTask_TFTargetmine

loadNetwork(File, String, String, MyCytoPanel) - Method in class cyTransFinder.Network

loadURIMethod(File, String, String) - Method in class cyTransFinder.MyCytoPanel

M

mergeDuplicatesNodes(String, String, String) - Method in class cyTransFinder.Network

mirnaList - Variable in class cyTransFinder.WebserviceTask_UCSC

motif - Variable in class cyTransFinder.WebserviceTask_motifTypeParser

myActivator - Variable in class cyTransFinder.NetworkReactomeTask

myActivator - Variable in class cyTransFinder.WebserviceTask_NCBI

myBis - Variable in class cyTransFinder.NetworkReactomeTask

MyCytoPanel - Class in cyTransFinder

MyCytoPanel(CyActivator) - Constructor for class cyTransFinder.MyCytoPanel

myCytoPanel - Variable in class cyTransFinder.WebserviceTask_motifProcessing

myCytoPanel - Variable in class cyTransFinder.WebserviceTask_motifTypeParser

myCytoPanel - Variable in class cyTransFinder.WebserviceTask_TargetHub

myCytoPanel - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

myCytoPanel - Variable in class cyTransFinder.WebserviceTask_UCSC

myCytoPanel - Variable in class cyTransFinder.WebserviceTask_Uniprot

myfile - Variable in class cyTransFinder.WebserviceTask_motifTypeParser

myFunction - Variable in class cyTransFinder.WebserviceTask_motifProcessing

myFunction - Variable in class cyTransFinder.WebserviceTask_motifTypeParser

myFunction - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

myIter - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

MyLayoutTask - Class in cyTransFinder

Applies MyLayout to the given CyNetworkView with specific Tunable parameters.

MyLayoutTask(CyLayoutAlgorithmManager) - Constructor for class cyTransFinder.MyLayoutTask

myMotif - Variable in class cyTransFinder.WebserviceTask_motifProcessing

myNet - Variable in class cyTransFinder.Network

myNodes - Variable in class cyTransFinder.WebserviceTask_NCBI

myTaskObserver - Class in cyTransFinder

myTaskObserver() - Constructor for class cyTransFinder.myTaskObserver

N

ncbiDocument - Variable in class cyTransFinder.WebserviceTask_NCBI

ncbiInfo - Variable in class cyTransFinder.WebserviceTask_NCBI

Network - Class in cyTransFinder

Network(CyNetwork, CyActivator) - Constructor for class cyTransFinder.Network

NetworkFromSources - Class in cyTransFinder

NetworkFromSources(File, String, String, CyActivator) - Constructor for class cyTransFinder.NetworkFromSources

networkFromSources - Variable in class cyTransFinder.WebserviceTask_NCBI

NetworkReactome - Class in cyTransFinder

NetworkReactome(String, CyActivator, CyNetwork) - Constructor for class cyTransFinder.NetworkReactome

NetworkReactomeTask - Class in cyTransFinder

NetworkReactomeTask(BufferedInputStream, CyActivator) - Constructor for class cyTransFinder.NetworkReactomeTask

O

Organism - Variable in class cyTransFinder.Network

organismListPrepare() - Method in class cyTransFinder.UtilOrganism

P

parseCSV(BufferedReader) - Method in class cyTransFinder.NetworkFromSources

parseTF(BufferedReader) - Method in class cyTransFinder.NetworkFromSources

prepareTables() - Method in class cyTransFinder.Network

printDocument(Document, OutputStream) - Method in class cyTransFinder.WebserviceTask_NCBI

R

read() - Method in class cyTransFinder.UncloseableInputStream

removeDuppedEdges() - Method in class cyTransFinder.Network

removeSomeNodes(String, String) - Method in class cyTransFinder.MyCytoPanel

removeTypeNodes(String, String) - Method in class cyTransFinder.Network

renameSomeNodes(String, String, String) - Method in class cyTransFinder.MyCytoPanel

retrieveAllIntronicMirna(String) - Method in class cyTransFinder.WebserviceTask_UCSC

retrieveEutils_GeneID(String, String) - Method in class cyTransFinder.WebserviceTask_NCBI

retrieveNCBI_GeneticINFOZ(String, String, String) - Method in class cyTransFinder.WebserviceTask_NCBI

run(TaskMonitor) - Method in class cyTransFinder.NetworkReactomeTask

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_mirIAD

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_mirIAD_InterGenic

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_motifProcessing

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_motifTypeParser

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_NCBI

Run the task for the basic gene information (Faster)

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_TargetHub

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_TFe

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_TFTargetmine

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_UCSC

run(TaskMonitor) - Method in class cyTransFinder.WebserviceTask_Uniprot

S

SERVICETYPE - Variable in class cyTransFinder.Network

setEdgeArrow() - Method in class cyTransFinder.VisualInterface

setEdgeArrow() - Method in class cyTransFinder.VisualInterfaceKEGG

setEdgeColor() - Method in class cyTransFinder.VisualInterface

setEdgeColor() - Method in class cyTransFinder.VisualInterfaceKEGG

setEdgeLabel() - Method in class cyTransFinder.VisualInterface

setEdgeLabel() - Method in class cyTransFinder.VisualInterfaceKEGG

setEdgeLineType() - Method in class cyTransFinder.VisualInterface

setEdgeLineType() - Method in class cyTransFinder.VisualInterfaceKEGG

setEdgeWidth() - Method in class cyTransFinder.VisualInterfaceKEGG

setNetworkProperties(String) - Method in class cyTransFinder.Network

setNodeColor() - Method in class cyTransFinder.VisualInterface

setNodeColor() - Method in class cyTransFinder.VisualInterfaceKEGG

setNodeLabel() - Method in class cyTransFinder.VisualInterface

setNodeLabel() - Method in class cyTransFinder.VisualInterfaceKEGG

setNodeShape() - Method in class cyTransFinder.VisualInterface

setNodeShape() - Method in class cyTransFinder.VisualInterfaceKEGG

start(BundleContext) - Method in class cyTransFinder.CyActivator

T

taskFinished(ObservableTask) - Method in class cyTransFinder.myTaskObserver

tfPrecedeByMirna(Integer) - Method in class cyTransFinder.WebserviceTask_motifProcessing

tfPrecedeByTF(Integer) - Method in class cyTransFinder.WebserviceTask_motifProcessing

TFTargetList - Variable in class cyTransFinder.WebserviceTask_TFe

TFTargetList - Variable in class cyTransFinder.WebserviceTask_TFTargetmine

tmpList - Variable in class cyTransFinder.NetworkFromSources

U

UncloseableInputStream - Class in cyTransFinder

UncloseableInputStream(InputStream) - Constructor for class cyTransFinder.UncloseableInputStream

unZipIt(InputStream) - Method in class cyTransFinder.WebserviceTask_mirIAD

unZipIt(InputStream) - Method in class cyTransFinder.WebserviceTask_mirIAD_InterGenic

updateView() - Method in class cyTransFinder.MyCytoPanel

UtilOrganism - Class in cyTransFinder

UtilOrganism(String) - Constructor for class cyTransFinder.UtilOrganism

V

VisualInterface - Class in cyTransFinder

VisualInterface(VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, CyNetworkView, VisualMappingManager) - Constructor for class cyTransFinder.VisualInterface

VisualInterfaceKEGG - Class in cyTransFinder

VisualInterfaceKEGG(CyNetwork, CyNetworkViewFactory, CyNetworkViewManager, VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, CyNetworkView, VisualMappingManager) - Constructor for class cyTransFinder.VisualInterfaceKEGG

W

WebserviceTask_mirIAD - Class in cyTransFinder

WebserviceTask_mirIAD(CyActivator, Set<CyNode>, MyCytoPanel, String, int) - Constructor for class cyTransFinder.WebserviceTask_mirIAD

WebserviceTask_mirIAD_InterGenic - Class in cyTransFinder

WebserviceTask_mirIAD_InterGenic(CyActivator, Set<CyNode>, MyCytoPanel, String, int) - Constructor for class cyTransFinder.WebserviceTask_mirIAD_InterGenic

WebserviceTask_motifProcessing - Class in cyTransFinder

WebserviceTask_motifProcessing(CyActivator, CyNetworkView, MyCytoPanel, String[], String) - Constructor for class cyTransFinder.WebserviceTask_motifProcessing

WebserviceTask_motifTypeParser - Class in cyTransFinder

WebserviceTask_motifTypeParser(File, CyActivator, CyNetworkView, MyCytoPanel, String) - Constructor for class cyTransFinder.WebserviceTask_motifTypeParser

WebserviceTask_NCBI - Class in cyTransFinder

WebserviceTask_NCBI(Set<CyNode>, String[], String, CyActivator, NetworkFromSources) - Constructor for class cyTransFinder.WebserviceTask_NCBI

WebserviceTask_TargetHub - Class in cyTransFinder

Documentation: http://app1.bioinformatics.mdanderson.org/tarhub/_design/basic/api.html

WebserviceTask_TargetHub(Set<CyNode>, Set<CyNode>, CyActivator, CyNetworkView, boolean, boolean, boolean, int, boolean, boolean, boolean, boolean, MyCytoPanel, String, Map<String, String>, String) - Constructor for class cyTransFinder.WebserviceTask_TargetHub

WebserviceTask_TFe - Class in cyTransFinder

WebserviceTask_TFe(String, Set<CyNode>, CyActivator, CyNetworkView) - Constructor for class cyTransFinder.WebserviceTask_TFe

WebserviceTask_TFTargetmine - Class in cyTransFinder

WebserviceTask_TFTargetmine(String, Set<CyNode>, CyActivator, CyNetworkView, MyCytoPanel, String, int) - Constructor for class cyTransFinder.WebserviceTask_TFTargetmine

WebserviceTask_UCSC - Class in cyTransFinder

WebserviceTask_UCSC(String, Set<CyNode>, CyActivator, CyNetworkView, MyCytoPanel) - Constructor for class cyTransFinder.WebserviceTask_UCSC

WebserviceTask_Uniprot - Class in cyTransFinder

WebserviceTask_Uniprot(String, Set<CyNode>, CyActivator, CyNetworkView, MyCytoPanel) - Constructor for class cyTransFinder.WebserviceTask_Uniprot

A C D E F G I L M N O P R S T U V W