A B C D E F G H I K L M N O P Q R S T V W

A

AboutActionHGPEC - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

AboutActionHGPEC() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.AboutActionHGPEC

AboutDialog - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

AboutDialog(Frame, boolean) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.AboutDialog

Creates new form AboutDialog

AboutDialogHGPEC - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

AboutDialogHGPEC(Frame, boolean) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.AboutDialogHGPEC

AboutDialogHGPEC() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.AboutDialogHGPEC

actionPerformed(ActionEvent) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.AboutActionHGPEC

actionPerformed(ActionEvent) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.HelpAction

actionPerformed(ActionEvent) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.MyNodeViewContextMenuFactory

allFinished(FinishStatus) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

AllFPFs - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

AllPrecisions - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

AllTPFs - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

applyNetworkVisualStyle(CyNetwork, CyNetworkView, String, VisualMappingManager, VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

AssociatedNodeArray - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Disease

AssociatedNodeSet - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Disease

AUC - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

autoRWRMTN - Interface in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

autoRWRMTNImp - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

autoRWRMTNImp(MyUtils) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTNImp

B

backProb - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankParameters

backProb - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

BuildNetworkTask - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

BuildNetworkTask(SynchronousTaskManager, TaskManager, CyNetwork, CyNetworkManager, CyNetworkReaderManager, CyNetworkFactory, CyNetworkNaming) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

BuildNetworkTaskFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

BuildNetworkTaskFactory(TaskManager, CyNetworkManager, CyNetworkReaderManager, CyNetworkFactory, CyNetworkNaming, SynchronousTaskManager) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTaskFactory

C

calcAUC() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

calculateIncomingNeighbors(ArrayList<Interaction>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

calculateOutgoingNeighbors(ArrayList<Interaction>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

calculateOverallAUCROC(String, int, ArrayList<ArrayList<Double>>, ArrayList<ArrayList<Double>>, ArrayList<ArrayList<Double>>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

calTPFs_FPFs() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

cancel() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

cancel() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTask

cancel() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadmiRNANetworkTask

cancel() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadPhenotypeNetworkTask

cancel() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTask

candidateOption - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

Common - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.model

Common() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

createMenuItem(CyNetworkView, View<CyNode>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.MyNodeViewContextMenuFactory

createNetworkVisualStyle(CyNetwork, String, VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

createTaskIterator(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTaskFactory

createTaskIterator(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTaskFactory

createTaskIterator() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadmiRNANetworkTaskFactory

createTaskIterator() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadPhenotypeNetworkTaskFactory

createTaskIterator(View<CyNode>, CyNetworkView) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.PMInfoContextmenuTaskFactory

createTaskIterator(CyNetworkView) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.PMInfoContextmenuTaskFactory

createTaskIterator(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTaskFactory

createTaskIterator(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTaskFactory

curNet - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadmiRNANetworkTask

curNet - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadPhenotypeNetworkTask

CyActivator - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal

CyActivator() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.CyActivator

CyNetworkUtils - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.model

CyNetworkUtils() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

D

Disease - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.Base

Disease() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Disease

Disease2miRNA2WeightMapMap - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

DISEASE_LIST - Static variable in interface vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTN

DiseaseFileName - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

DiseaseID - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Disease

diseaseID - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.rDisease

DiseaseInteractionArray - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

DiseasekNodeSet - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

diseaseName - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.rDisease

diseaseName - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

DiseaseNodeArray - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

diseaseOMIMID - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankParameters

DiseaseTerm - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

E

ErrorMessage - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

ErrorMessage(String) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.ErrorMessage

ErrorMessage() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.ErrorMessage

Eval - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

evaluateByRWRMDA(Set<String>, Map<String, ArrayList<NodeInteraction>>, double) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

evaluateByRWRMTN(Map<String, Double>, Set<String>, Map<String, Map<String, Double>>, Map<String, ArrayList<NodeInteraction>>, double, double, ArrayList<String>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

evaluatePerformance(int, ArrayList<Integer>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

Evaluation - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.model

Evaluation() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

EvidenceResult - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

EvidenceResult() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

EvidenceResult(String, Set<String>) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

ExamineRankedGenesandDiseasesTask - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

ExamineRankedGenesandDiseasesTask(CyNetworkFactory, CyNetworkManager, CyNetwork, TaskManager, SynchronousTaskManager) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTask

ExamineRankedGenesandDiseasesTaskFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

ExamineRankedGenesandDiseasesTaskFactory(CyNetworkFactory, CyNetworkManager) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTaskFactory

executeCommand(String, String, Map<String, Object>, TaskObserver) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

F

fillPhenotypeTable(String, CyNetworkFactory, CyNetworkManager) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

FPFs - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

G

Gene2MimNetwork - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

getAllConnectingEdges(CyNetwork, Collection<CyNode>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

Checks the specified network has values for the given node attributes.

getAuthors() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

getComponent() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

getCytoPanelName() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

getDiseaseId(String) - Method in interface vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTN

getDiseaseId(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTNImp

getDiseaseList() - Method in interface vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTN

getDiseaseList() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTNImp

getIcon() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

getIdentifier() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

getInfo() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

getJson(ArrayList<EvidenceResult>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTask

getJson(ArrayList<RankedResult>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

getKeyByValue(Map<T, E>, E) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

getKeysByValue(Map<T, E>, E) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

getName() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

getNeighborMap(CyNetwork, CyNode) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

Gets all the neighbors of the given node and their frequencies.

getNeighborMap(CyNetwork, CyNode, List<CyEdge>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

Gets all the neighbors of the given node and their frequencies.

getNeighbors(CyNetwork, CyNode) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

Gets all the neighbors of the given node.

getNeighbors(CyNetwork, CyNode, List<CyEdge>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

Gets all the neighbors of the given node.

getNetworkByName(CyNetworkManager, String) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

getNodeScore() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

getPages() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

getPairConnCount(CyNetwork, Collection<CyNode>, boolean) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

Gets the number of pair connections between the given set of nodes.

getPMIDinfo(String) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

getPubdate() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

getPubMedIDFromPubMedSearch(String, Map<String, PMInfo>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

getPubMedIds() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

getRank() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

getRankedGenes(int) - Method in interface vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTN

getRankedGenes(int) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTNImp

getRankExample() - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.CyActivator

getRankNode() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

getResultClasses() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

getResultClasses() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTask

getResultClasses() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

getResultClasses() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTask

getResults(Class<? extends R>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

getResults(Class<? extends R>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTask

getResults(Class<? extends R>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

getResults(Class<? extends R>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTask

getRnaName() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

getScore() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

getService(Class<S>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

getTitle() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

getTitle() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

getTitle() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

getTitle() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTask

getTitle() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

getType() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

getVisualStyleByName(String, VisualMappingManager) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

H

handleEvent(RowsSetEvent) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

HelpAction - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

HelpAction() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.HelpAction

HoldoutRanks - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

I

ID2NameMap - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

IncomingNodeTable - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

Index - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Interaction

InfoPanel - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.ui

InfoPanel(CyApplicationManager, CySwingApplication) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

Interaction - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.Base

Interaction() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Interaction

isKnown() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

isReady(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTaskFactory

isReady(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTaskFactory

isReady(CyNetworkView) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.PMInfoContextmenuTaskFactory

isReady(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTaskFactory

isReady(CyNetwork) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTaskFactory

isWeighted - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

K

known - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankOutput

L

lbl - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

listOfmiRNAs - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankParameters

loadAllLowerNodeInfo(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Resource

loadDisease2Nodes() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Resource

loadEntity2Elements(String) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

LoadmiRNANetworkTask - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

LoadmiRNANetworkTask(CyNetworkFactory, CyNetworkNaming, CyNetworkManager) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadmiRNANetworkTask

LoadmiRNANetworkTaskFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

LoadmiRNANetworkTaskFactory(CyNetworkFactory, CyNetworkNaming, CyNetworkManager) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadmiRNANetworkTaskFactory

loadNetwork() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Resource

LoadPhenotypeNetworkTask - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

LoadPhenotypeNetworkTask(CyNetworkFactory, CyNetworkNaming, CyNetworkManager) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadPhenotypeNetworkTask

LoadPhenotypeNetworkTaskFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

LoadPhenotypeNetworkTaskFactory(CyNetworkFactory, CyNetworkNaming, CyNetworkManager) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadPhenotypeNetworkTaskFactory

M

main(String[]) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.AboutDialog

MaxRank - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

message - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.ErrorMessage

Messages - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.model

Messages(String) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Messages

Mim2GeneNetwork - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

miR2DiseaseDB - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankParameters

miR2DiseaseDB - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

miRNA2Gene2WeightMapMap - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

miRNAFile - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

miRNAList - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

miRTargetDB - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankParameters

miRTargetDB - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

MutInteger - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.model

MutInteger() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MutInteger

Initializes a new instance of MutInteger and sets the value to 0.

MutInteger(int) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MutInteger

Initializes a new instance of MutInteger.

MYAPP_COMMAND_NAMESPACE - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.CyActivator

MyNodeViewContextMenuFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.ui

MyNodeViewContextMenuFactory(CySwingApplication, CyApplicationManager, CyServiceRegistrar) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.MyNodeViewContextMenuFactory

MyUtils - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.model

MyUtils(CyServiceRegistrar) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

N

Name - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Disease

Name - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Node

NetworkFileName - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

NetworkInteractionArray - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

NetworkMIMSet - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

NetworkNodeArray - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

NetworkNodeSet - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

Node - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.Base

Node() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Node

Node - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.NodeInteraction

NodeDst - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Interaction

NodeID - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Node

NodeInteraction - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.Base

NodeInteraction() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.NodeInteraction

NodeInteraction(String, double) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.NodeInteraction

NodeSrc - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Interaction

normL2(Map<String, Double>, Map<String, Double>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

numOfEvidence - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

O

OriginalNetwork - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

OriginalNetworkNode - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

OriginalPhenotypeNetwork - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

OriginalPhenotypeNetworkNode - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

P

PMID_info - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

PMInfo - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

PMInfo() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

PMInfo(String, ArrayList<String>, String, String) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

PMInfoContextmenuTaskFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

PMInfoContextmenuTaskFactory() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.PMInfoContextmenuTaskFactory

Precisions - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

preprocessInteractionList(ArrayList<Interaction>, String) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

Q

quickSortInteraction(ArrayList<Interaction>, int, int) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

quickSortNodeInDescScore(ArrayList<Node>, int, int) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

R

Rank - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Node

rankByRWR(Map<String, ArrayList<NodeInteraction>>, double, Map<String, Double>, Map<String, Double>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

rankDisease(String, float, float, ArrayList<String>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

RankedResult - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

RankedResult() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

RankedResult(String, double, int, String, boolean) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

RankMethod - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

RankOutput - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

RankOutput() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankOutput

RankParameters - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

RankParameters() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankParameters

rDisease - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

rDisease() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.rDisease

readJsonStream(InputStream) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

readStream(InputStream) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

readUserRNANetwork(CyNetworkManager) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Resource

removeSelfLoops(CyNetwork) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

Removes all self-loops in a network and returns the number of removed self-loops.

Resource - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.Base

Resource() - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Resource

result - Static variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTask

result - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

rnaName - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankOutput

rnaRank - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankOutput

rnaScore - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankOutput

run(TaskMonitor) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.BuildNetworkTask

run(TaskMonitor) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.ExamineRankedGenesandDiseasesTask

run(TaskMonitor) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadmiRNANetworkTask

run(TaskMonitor) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.LoadPhenotypeNetworkTask

run(TaskMonitor) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

run(TaskMonitor) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTask

S

Score - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Node

searchUsingBinaryInteraction(String, ArrayList<Interaction>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

searchUsingBinaryInteractionDetail(String, ArrayList<Interaction>, int, int) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

SelectDiseaseTask - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

SelectDiseaseTask(CyNetworkFactory, CyNetworkManager, CyNetwork, MyUtils) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

SelectDiseaseTaskFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

SelectDiseaseTaskFactory(CyNetworkFactory, CyNetworkManager, MyUtils) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTaskFactory

selectRankDisease(RankParameters) - Method in interface vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTN

selectRankDisease(RankParameters) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.autoRWRMTNImp

setAuthors(ArrayList<String>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

setInfo(Map<String, PMInfo>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

setKnown(boolean) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

setLbl(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.ui.InfoPanel

setName(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

setPages(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

setPubdate(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

setPubMedIds(Set<String>) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

setRank(int) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

setRnaName(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.EvidenceResult

setScore(double) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

setTitle(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

setType(String) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankedResult

sortQuickInteractionListInAsc(ArrayList<Interaction>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

sortQuickNodeListInDescScore(ArrayList<Node>) - Static method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

start(BundleContext) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.CyActivator

subnetWeight - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankParameters

subnetWeight - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.SelectDiseaseTask

T

taskFinished(ObservableTask) - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MyUtils

toString() - Method in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.PMInfo

TPFs - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Evaluation

Type - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Interaction

type - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel.RankOutput

V

value - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.model.MutInteger

Value of this mutable integer.

visualizeOptions - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTask

VisualizeSubNetworkTask - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

VisualizeSubNetworkTask(CyNetworkFactory, CyNetworkNaming, CyNetworkManager, CyLayoutAlgorithmManager, TaskManager, CyNetworkViewFactory, CyNetworkViewManager, VisualMappingManager, VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTask

VisualizeSubNetworkTaskFactory - Class in vn.edu.tlu.hatrang.autoRWRMTN.internal.task

VisualizeSubNetworkTaskFactory(CyNetworkFactory, CyNetworkNaming, CyNetworkManager, CyLayoutAlgorithmManager, TaskManager, CyNetworkViewFactory, CyNetworkViewManager, VisualMappingManager, VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory) - Constructor for class vn.edu.tlu.hatrang.autoRWRMTN.internal.task.VisualizeSubNetworkTaskFactory

vn.edu.tlu.hatrang.autoRWRMTN.internal - package vn.edu.tlu.hatrang.autoRWRMTN.internal

vn.edu.tlu.hatrang.autoRWRMTN.internal.Base - package vn.edu.tlu.hatrang.autoRWRMTN.internal.Base

vn.edu.tlu.hatrang.autoRWRMTN.internal.model - package vn.edu.tlu.hatrang.autoRWRMTN.internal.model

vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel - package vn.edu.tlu.hatrang.autoRWRMTN.internal.RESTmodel

vn.edu.tlu.hatrang.autoRWRMTN.internal.task - package vn.edu.tlu.hatrang.autoRWRMTN.internal.task

vn.edu.tlu.hatrang.autoRWRMTN.internal.ui - package vn.edu.tlu.hatrang.autoRWRMTN.internal.ui

W

Weight - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Interaction

Weight - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.NodeInteraction

WeightOriginal - Variable in class vn.edu.tlu.hatrang.autoRWRMTN.internal.Base.Interaction

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