A B C D E F G H I J L M N O P R S T U V W X Y

A

AboutMenuAction - Class in es.imim.DISGENET.internal

Creates a new menu item under Apps menu section.

AboutMenuAction(CyApplicationManager, String, CySwingApplication) - Constructor for class es.imim.DISGENET.internal.AboutMenuAction

AbstractEnrichmentTask - Class in es.imim.DISGENET.internal.enrichment

AbstractEnrichmentTask(CyNetworkView) - Constructor for class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.internal.AboutMenuAction

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.internal.ChangeDBMenuAction

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.internal.ExternalNetworksMenu

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.internal.MenuAction

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.internal.StartDisGeNETMenuAction

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.internal.WebMenuAction

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.network.colorMapping.ColorAction

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.network.colorMapping.RemoveColorAction

actionPerformed(ActionEvent) - Method in class es.imim.DISGENET.network.NetAction

This method is called when the user clicks create network.

Activator - Class in es.imim.DISGENET.internal

Activator() - Constructor for class es.imim.DISGENET.internal.Activator

add(String) - Method in class es.imim.DISGENET.search.MemComboBox

addCustomGraphicsFactory(CyCustomGraphics2Factory<?>, Map<Object, Object>) - Method in class es.imim.DISGENET.internal.CustomChartListener

Adds a custom graphics factory if its ID matches the specified factory ID.

addEdgeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

addEdgeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

addEdgeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

addEdgeColumns(CyTable) - Method in interface es.imim.DISGENET.internal.tables.DisGeNETCyTableNodeInterface

addEdgeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableVariant

addNetCreationListener(NetCreationListener) - Method in class es.imim.DISGENET.network.NetworkBuilder

addNodeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

addNodeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

Adds all the colums related to the diseases to the cytoscape table.

addNodeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

Adds all the colums related to the diseases to the cytoscape table.

addNodeColumns(CyTable) - Method in interface es.imim.DISGENET.internal.tables.DisGeNETCyTableNodeInterface

addNodeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableVariant

Adds all the colums related to the diseases to the cytoscape table.

addToDictionary(String) - Method in class es.imim.DISGENET.search.AutoSuggestor

addWordToSuggestions(String) - Method in class es.imim.DISGENET.search.AutoSuggestor

allFinished(FinishStatus) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTaskObserver

allFinished(FinishStatus) - Method in class es.imim.DISGENET.network.NetTaskObserver

AnnotateDiseasesGenesTaskFactory - Class in es.imim.DISGENET.internal.annotation

AnnotateDiseasesGenesTaskFactory() - Constructor for class es.imim.DISGENET.internal.annotation.AnnotateDiseasesGenesTaskFactory

AnnotateDiseasesTask - Class in es.imim.DISGENET.internal.annotation

AnnotateDiseasesTask(CyNetworkView, int) - Constructor for class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

AnnotateDiseasesVariantsTaskFactory - Class in es.imim.DISGENET.internal.annotation

AnnotateDiseasesVariantsTaskFactory() - Constructor for class es.imim.DISGENET.internal.annotation.AnnotateDiseasesVariantsTaskFactory

AnnotateGenesTask - Class in es.imim.DISGENET.internal.annotation

AnnotateGenesTask(CyNetworkView) - Constructor for class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

AnnotateGenesTaskFactory - Class in es.imim.DISGENET.internal.annotation

AnnotateGenesTaskFactory() - Constructor for class es.imim.DISGENET.internal.annotation.AnnotateGenesTaskFactory

AnnotateVariantsTask - Class in es.imim.DISGENET.internal.annotation

AnnotateVariantsTask(CyNetworkView, String) - Constructor for class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

AnnotateVariantsTaskFactory - Class in es.imim.DISGENET.internal.annotation

AnnotateVariantsTaskFactory() - Constructor for class es.imim.DISGENET.internal.annotation.AnnotateVariantsTaskFactory

AnnotationService - Class in es.imim.DISGENET.internal.annotation

AnnotationService(CyServiceRegistrar) - Constructor for class es.imim.DISGENET.internal.annotation.AnnotationService

ApiClient - Class in es.imim.DISGENET.database

ApiClient() - Constructor for class es.imim.DISGENET.database.ApiClient

ApiKeyDialog - Class in es.imim.DISGENET.database

ApiKeyDialog() - Constructor for class es.imim.DISGENET.database.ApiKeyDialog

ApplyCustomLayoutTaskFactory - Class in es.imim.DISGENET.internal

Applies CustomLayout to the given CyNetworkView with specific Tunable parameters.

ApplyCustomLayoutTaskFactory(CyLayoutAlgorithmManager, TunableSetter) - Constructor for class es.imim.DISGENET.internal.ApplyCustomLayoutTaskFactory

ASSOCIATION_TYPE_OPTIONS - Static variable in class es.imim.DISGENET.gui.GuiProps

assocTypeOptions - Static variable in class es.imim.DISGENET.validation.ParametersValidation

assocTypes - Variable in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

assocTypes - Variable in class es.imim.DISGENET.network.ExpandCurrentNetworkTask

assocTypes - Variable in class es.imim.DISGENET.network.ExpandNewNetworkTask

AutomationGeneEnrichmentTask - Class in es.imim.DISGENET.internal.enrichment

AutomationGeneEnrichmentTask(CyNetworkView, Long, String, String, String, boolean, double, Integer) - Constructor for class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

AutomationParams - Interface in es.imim.DISGENET.internal.automation.parameters

AutomationVariantEnrichmentTask - Class in es.imim.DISGENET.internal.enrichment

AutomationVariantEnrichmentTask(CyNetworkView, Long, String, String, String, boolean, double, Integer) - Constructor for class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

AutoSuggestor - Class in es.imim.DISGENET.search

AutoSuggestor(JTextField, Window, ArrayList<String>, Color, Color, Color, float) - Constructor for class es.imim.DISGENET.search.AutoSuggestor

B

buildDiseaseNet(GuiParameters) - Method in class es.imim.DISGENET.network.NetworkBuilder

Generic function to create disease network

buildGeneDiseaseNet(GuiParameters) - Method in class es.imim.DISGENET.network.NetworkBuilder

Get the gene/disease net information from the database and call generic function to build net

buildGeneNet(GuiParameters) - Method in class es.imim.DISGENET.network.NetworkBuilder

Generic function to create gene network

buildNet(List<String>, List<String>, List<String>, String, GuiParameters) - Method in class es.imim.DISGENET.network.NetworkBuilder

Builds a new disease-disease or gene-gene network.

buildNetWithEdgeAttributes(ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>, GuiParameters) - Method in class es.imim.DISGENET.network.NetworkBuilder

buildSearchField() - Method in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

buildSearchField() - Method in class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

buildSearchField() - Method in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

buildVariantDiseaseNet(GuiParameters) - Method in class es.imim.DISGENET.network.NetworkBuilder

Get the variant/disease net information from the database and call generic function to build net

byLineLengthAsc() - Constructor for class es.imim.DISGENET.tool.HelperFunctions.byLineLengthAsc

byLineLengthDesc() - Constructor for class es.imim.DISGENET.tool.HelperFunctions.byLineLengthDesc

C

cancel() - Method in class es.imim.DISGENET.network.NetTask

ChangeDBMenuAction - Class in es.imim.DISGENET.internal

Creates a new menu item under Apps menu section.

ChangeDBMenuAction(CyApplicationManager, String) - Constructor for class es.imim.DISGENET.internal.ChangeDBMenuAction

checkApiKey() - Method in class es.imim.DISGENET.database.DatabaseManagerImpl

CheckColorTable(CyNetwork) - Method in class es.imim.DISGENET.network.colorMapping.ColorAction

checkStringIsNotEmpty(String) - Static method in class es.imim.DISGENET.tool.HelperFunctions

checkUserTypeAndSuggestUpgrade() - Static method in class es.imim.DISGENET.database.UserTypeUtil

clear() - Method in class es.imim.DISGENET.search.MemComboBox

clearList() - Method in class es.imim.DISGENET.search.MemComboBox

colGenesBG - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

colGenesRatio - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

colGenesSUID - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

colID - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

colListGenes - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

colName - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

COLOR_NODES_BUTTON_TEXT - Static variable in class es.imim.DISGENET.gui.GuiProps

COLOR_NODES_BUTTON_TOOLTIP - Static variable in class es.imim.DISGENET.gui.GuiProps

ColorAction - Class in es.imim.DISGENET.network.colorMapping

listener for the disease color button which calls the function to color nodes according to their disease classes and puts a legend into the results panel if it is not already there

ColorAction() - Constructor for class es.imim.DISGENET.network.colorMapping.ColorAction

ColorTable - Class in es.imim.DISGENET.network.colorMapping

This class provides utility methods for creating and managing color tables in Cytoscape networks.

ColorTable() - Constructor for class es.imim.DISGENET.network.colorMapping.ColorTable

Default constructor for ColorTable.

colPvalue - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

colSource - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

columnName - Variable in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

columnName - Variable in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

columnNames - Variable in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

columnNames - Variable in class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

columnNames - Variable in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

columnNames - Variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

columnNames - Variable in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

compare(Object, Object) - Method in class es.imim.DISGENET.tool.HelperFunctions.byLineLengthAsc

compare(Object, Object) - Method in class es.imim.DISGENET.tool.HelperFunctions.byLineLengthDesc

CREATE_NET_BUTTON_TEXT - Static variable in class es.imim.DISGENET.gui.GuiProps

CREATE_NET_BUTTON_TOOLTIP - Static variable in class es.imim.DISGENET.gui.GuiProps

CreateColorTable(CyNetwork) - Static method in class es.imim.DISGENET.network.colorMapping.ColorTable

Creates a color table for the given Cytoscape network.

createCyEdgeAttributeColumns(CyNetwork) - Method in class es.imim.DISGENET.network.NetworkBuilder

createCyNetwork(String) - Method in class es.imim.DISGENET.network.NetworkBuilder

createGdaEdgeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

createGeneDiseaseNetwork(GeneDiseaseParams) - Method in interface es.imim.DISGENET.internal.automation.NetworkAutomation

createGeneDiseaseNetwork(GeneDiseaseParams) - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

createGeneEnrichment(GeneEnrichmentParams) - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

createLayoutContext() - Method in class es.imim.DISGENET.internal.CustomLayout

createNetwork() - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

createNodeAttributeColumns(CyNetwork) - Method in class es.imim.DISGENET.network.NetworkBuilder

createPopup() - Method in class es.imim.DISGENET.search.MemComboBox.MyComboBoxUI

createPopup() - Method in class es.imim.DISGENET.search.MemComboBox.myComboUI

createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesGenesTaskFactory

createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesVariantsTaskFactory

createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateGenesTaskFactory

createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTaskFactory

createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.ApplyCustomLayoutTaskFactory

createTaskIterator(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in class es.imim.DISGENET.internal.CustomLayout

createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTaskFactory

createTaskIterator() - Method in class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTaskFactory

createTaskIterator(boolean, boolean) - Method in class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTaskFactory

createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTaskFactory

createTaskIterator(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.ExpandCurrentNetActionTaskFactory

createTaskIterator(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.ExpandNewNetActionTaskFactory

createTaskIterator(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutDiseaseTaskFactory

createTaskIterator(View<CyEdge>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutEdgeTaskFactory

createTaskIterator(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutGeneTaskFactory

createTaskIterator(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutVariantTaskFactory

createVariantDiseaseNetwork(VariantDiseaseParams) - Method in interface es.imim.DISGENET.internal.automation.NetworkAutomation

createVariantDiseaseNetwork(VariantDiseaseParams) - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

createVariantEnrichment(VariantEnrichmentParams) - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

createVdaEdgeColumns(CyTable) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

CustomChartListener - Class in es.imim.DISGENET.internal

This class manages the addition and removal of custom chart factories in Cytoscape.

CustomChartListener() - Constructor for class es.imim.DISGENET.internal.CustomChartListener

CustomLayout - Class in es.imim.DISGENET.internal

CustomLayout(UndoSupport) - Constructor for class es.imim.DISGENET.internal.CustomLayout

CustomLayoutContext - Class in es.imim.DISGENET.internal

CustomLayoutContext() - Constructor for class es.imim.DISGENET.internal.CustomLayoutContext

Default constructor for CustomLayoutContext.

CyActivator - Class in es.imim.DISGENET.internal

CyActivator() - Constructor for class es.imim.DISGENET.internal.CyActivator

D

Database - Interface in es.imim.DISGENET.database

DatabaseImpl - Class in es.imim.DISGENET.database

DatabaseImpl() - Constructor for class es.imim.DISGENET.database.DatabaseImpl

DatabaseManager - Interface in es.imim.DISGENET.database

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

DatabaseManagerImpl - Class in es.imim.DISGENET.database

DatabaseProps - Class in es.imim.DISGENET.database

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

DatabaseProps() - Constructor for class es.imim.DISGENET.database.DatabaseProps

DIS_PROJ_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

DIS_PROJ_SEARCH_FIELD - Static variable in class es.imim.DISGENET.gui.GuiProps

DIS_PROJ_SEARCH_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

DIS_PROJ_SOURCE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

DIS_PROJ_TAB_TITLE - Static variable in class es.imim.DISGENET.gui.GuiProps

disClassOptions - Static variable in class es.imim.DISGENET.validation.ParametersValidation

DisColorLegendPanel - Class in es.imim.DISGENET.gui

DisColorLegendPanel(BorderLayout) - Constructor for class es.imim.DISGENET.gui.DisColorLegendPanel

DISEASE_CLASS_OPTIONS - Static variable in class es.imim.DISGENET.gui.GuiProps

DISEASE_CODE_REGEX - Static variable in class es.imim.DISGENET.database.DatabaseProps

DISEASE_CUI_REGEX - Static variable in class es.imim.DISGENET.validation.NodeValidation

DISEASE_LAYER - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

DISEASE_LAYERS - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

DISEASE_LINKOUT_URL - Static variable in class es.imim.DISGENET.internal.linkout.LinkoutProperties

DISEASE_SEARCH_REGEX - Static variable in class es.imim.DISGENET.database.DatabaseProps

diseaseClasses - Variable in class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

diseaseClasses - Variable in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

diseaseClasses - Variable in class es.imim.DISGENET.network.ExpandCurrentNetworkTask

diseaseClasses - Variable in class es.imim.DISGENET.network.ExpandNewNetworkTask

diseaseClassSplitter(List<String>) - Static method in class es.imim.DISGENET.tool.HelperFunctions

Iterates from a list of combinations of diseases classes and returns de disease classes found in non-repeated values array.

DiseaseColourMapping - Class in es.imim.DISGENET.network.colorMapping

simple function to map the color codes to the corresponding colours and names

DiseaseColourMapping() - Constructor for class es.imim.DISGENET.network.colorMapping.DiseaseColourMapping

diseaseProjParameters(DiseaseProjParams) - Static method in class es.imim.DISGENET.validation.ParametersValidation

DiseaseProjParams - Class in es.imim.DISGENET.internal.automation.parameters

DiseaseProjParams() - Constructor for class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

DiseaseProjParams(String, String, String) - Constructor for class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

DisGeNetCyTableBase - Class in es.imim.DISGENET.internal.tables

Class that loads all the data for the table networks.

DisGeNetCyTableBase() - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

DisGeNetCyTableBase(GuiParameters) - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

DisGeNetCyTableDisease - Class in es.imim.DISGENET.internal.tables

Class to manage all the parameters relative to the diseases attributes of the cytoscape table.

DisGeNetCyTableDisease(GuiParameters) - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

DisGeNetCyTableDisease() - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

DisGeNetCyTableGene - Class in es.imim.DISGENET.internal.tables

Class to manage all the parameters relative to the gene attributes of the cytoscape table.

DisGeNetCyTableGene(GuiParameters) - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

DisGeNetCyTableGene() - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

DisGeNETCyTableNodeInterface - Interface in es.imim.DISGENET.internal.tables

DisGeNetCyTableVariant - Class in es.imim.DISGENET.internal.tables

Class to manage all the parameters relative to the gene attributes of the cytoscape table.

DisGeNetCyTableVariant(GuiParameters) - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableVariant

DisGeNETCytoPanel - Class in es.imim.DISGENET.internal

DisGeNETCytoPanel() - Constructor for class es.imim.DISGENET.internal.DisGeNETCytoPanel

DisGeNetException - Exception in es.imim.DISGENET.exceptions

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

DisGeNetException() - Constructor for exception es.imim.DISGENET.exceptions.DisGeNetException

DisGeNetException(String) - Constructor for exception es.imim.DISGENET.exceptions.DisGeNetException

DisGeNetException(Throwable) - Constructor for exception es.imim.DISGENET.exceptions.DisGeNetException

DisGeNetException(String, Throwable) - Constructor for exception es.imim.DISGENET.exceptions.DisGeNetException

DisGeNetException(String, Throwable, boolean, boolean) - Constructor for exception es.imim.DISGENET.exceptions.DisGeNetException

DisGenetStyleManager - Class in es.imim.DISGENET.styles

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

disProj_DisClassComboBoxActionPerformed(ActionEvent) - Method in class es.imim.DISGENET.gui.MainPanel

E

EI_HIGH_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

EI_LOW_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

EL_OPTIONS - Static variable in class es.imim.DISGENET.gui.GuiProps

EM_COLORS - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

EM_ICON_LAYER_1 - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

EM_ICON_LAYER_2 - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

EM_ICON_LAYER_3 - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

ENRICH_LAYER - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

ENRICH_LAYERS - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

EnrichmentCytoPanel - Class in es.imim.DISGENET.internal.enrichment

EnrichmentCytoPanel() - Constructor for class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

EnrichmentNetworkListener - Class in es.imim.DISGENET.internal.enrichment

EnrichmentNetworkListener() - Constructor for class es.imim.DISGENET.internal.enrichment.EnrichmentNetworkListener

EnrichmentService - Class in es.imim.DISGENET.internal.enrichment

EnrichmentService(CyServiceRegistrar) - Constructor for class es.imim.DISGENET.internal.enrichment.EnrichmentService

EnrichmentTable - Class in es.imim.DISGENET.internal.tables

EnrichmentTable(CyTable, String[]) - Constructor for class es.imim.DISGENET.internal.tables.EnrichmentTable

EnrichmentTableModel - Class in es.imim.DISGENET.internal.enrichment

EnrichmentTableModel(CyTable, String[]) - Constructor for class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

EnrichmentTaskObserver - Class in es.imim.DISGENET.internal.enrichment

EnrichmentTaskObserver() - Constructor for class es.imim.DISGENET.internal.enrichment.EnrichmentTaskObserver

enrichmentTypeIds - Static variable in class es.imim.DISGENET.validation.ParametersValidation

enrichmentUniverse - Static variable in class es.imim.DISGENET.validation.ParametersValidation

enrichmentURL - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

ENSEMBL_SEARCH_REGEX - Static variable in class es.imim.DISGENET.database.DatabaseProps

es.imim.DISGENET - package es.imim.DISGENET

es.imim.DISGENET.database - package es.imim.DISGENET.database

es.imim.DISGENET.exceptions - package es.imim.DISGENET.exceptions

es.imim.DISGENET.gui - package es.imim.DISGENET.gui

es.imim.DISGENET.internal - package es.imim.DISGENET.internal

es.imim.DISGENET.internal.annotation - package es.imim.DISGENET.internal.annotation

es.imim.DISGENET.internal.automation - package es.imim.DISGENET.internal.automation

es.imim.DISGENET.internal.automation.parameters - package es.imim.DISGENET.internal.automation.parameters

es.imim.DISGENET.internal.enrichment - package es.imim.DISGENET.internal.enrichment

es.imim.DISGENET.internal.linkout - package es.imim.DISGENET.internal.linkout

es.imim.DISGENET.internal.tables - package es.imim.DISGENET.internal.tables

es.imim.DISGENET.internal.utils - package es.imim.DISGENET.internal.utils

es.imim.DISGENET.network - package es.imim.DISGENET.network

es.imim.DISGENET.network.colorMapping - package es.imim.DISGENET.network.colorMapping

es.imim.DISGENET.search - package es.imim.DISGENET.search

es.imim.DISGENET.styles - package es.imim.DISGENET.styles

es.imim.DISGENET.tool - package es.imim.DISGENET.tool

es.imim.DISGENET.validation - package es.imim.DISGENET.validation

EXIT_BUTTON_TEXT - Static variable in class es.imim.DISGENET.gui.GuiProps

ExpandCurrentNetActionTaskFactory - Class in es.imim.DISGENET.internal

ExpandCurrentNetActionTaskFactory() - Constructor for class es.imim.DISGENET.internal.ExpandCurrentNetActionTaskFactory

ExpandCurrentNetworkTask - Class in es.imim.DISGENET.network

ExpandCurrentNetworkTask(CyNetworkView, View<CyNode>) - Constructor for class es.imim.DISGENET.network.ExpandCurrentNetworkTask

expandGeneDiseaseNet(GuiParameters, Map<String, Long>) - Method in class es.imim.DISGENET.network.NetworkBuilder

Expands the selected gene disease network using the selected nodes as reference.

ExpandNewNetActionTaskFactory - Class in es.imim.DISGENET.internal

ExpandNewNetActionTaskFactory() - Constructor for class es.imim.DISGENET.internal.ExpandNewNetActionTaskFactory

ExpandNewNetworkTask - Class in es.imim.DISGENET.network

Task class to create a new network with the selected nodes from a previous task.

ExpandNewNetworkTask(CyNetworkView, View<CyNode>) - Constructor for class es.imim.DISGENET.network.ExpandNewNetworkTask

expandVariantDiseaseNet(GuiParameters, Map<String, Long>) - Method in class es.imim.DISGENET.network.NetworkBuilder

Expands the selected variant disease network using the selected nodes as reference.

ExternalNetworksMenu - Class in es.imim.DISGENET.internal

ExternalNetworksMenu(CyApplicationManager, String) - Constructor for class es.imim.DISGENET.internal.ExternalNetworksMenu

F

fillColorTable(CyNetwork) - Method in class es.imim.DISGENET.network.colorMapping.ColorAction

fillEdgeColumns(CyNetwork, Map<CyEdge, Map<String, Object>>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

fillEdgeColumns(CyNetwork, Map<CyEdge, Map<String, Object>>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

fillEdgeColumns(CyNetwork, Map<CyEdge, Map<String, Object>>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

fillEdgeColumns(CyNetwork, Map<CyEdge, Map<String, Object>>) - Method in interface es.imim.DISGENET.internal.tables.DisGeNETCyTableNodeInterface

fillEdgeColumns(CyNetwork, Map<CyEdge, Map<String, Object>>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableVariant

fillNodeColumns(CyTable, Map<String, Long>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableBase

fillNodeColumns(CyTable, Map<String, Long>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

Fills the disease related columns with the data retrived from the current search parameters.

fillNodeColumns(CyTable, Map<String, Long>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

Fills the gene related columns with the data retrived from the current search parameters.

fillNodeColumns(CyTable, Map<String, Long>) - Method in interface es.imim.DISGENET.internal.tables.DisGeNETCyTableNodeInterface

fillNodeColumns(CyTable, Map<String, Long>) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableVariant

Fills the variant related columns with the data retrived from the current search parameters.

FilterEnrichmentTask - Class in es.imim.DISGENET.internal.enrichment

FilterEnrichmentTask(EnrichmentCytoPanel, CyNetwork, Integer, Integer, int[]) - Constructor for class es.imim.DISGENET.internal.enrichment.FilterEnrichmentTask

filterNodeType(String) - Static method in class es.imim.DISGENET.validation.NodeValidation

Filters the given string and checks for one of the following matches, gene symbol, disease cui or variant snp.

G

GENE_DIS_ASSO_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_CLASS_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_LOW_SCORE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_SEARCH_DIS_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_SEARCH_GENE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_SEARCH_TEXT - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_SOURCE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_TAB_TITLE - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_DIS_UP_SCORE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_LINKOUT_URL - Static variable in class es.imim.DISGENET.internal.linkout.LinkoutProperties

GENE_PROJ_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_PROJ_SEARCH_FIELD - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_PROJ_SEARCH_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_PROJ_SOURCE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_PROJ_TAB_TITLE - Static variable in class es.imim.DISGENET.gui.GuiProps

GENE_SEARCH_REGEX - Static variable in class es.imim.DISGENET.database.DatabaseProps

geneDis_AssoComboBoxPopupMenuWillBecomeVisible(PopupMenuEvent) - Method in class es.imim.DISGENET.gui.MainPanel

geneDis_disClassComboBoxActionPerformed(ActionEvent) - Method in class es.imim.DISGENET.gui.MainPanel

geneDis_ElComboBoxActionPerformed(ActionEvent) - Method in class es.imim.DISGENET.gui.MainPanel

geneDiseaseParameters(GeneDiseaseParams) - Static method in class es.imim.DISGENET.validation.ParametersValidation

GeneDiseaseParams - Class in es.imim.DISGENET.internal.automation.parameters

GeneDiseaseParams() - Constructor for class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

GeneDiseaseParams(String, String, String, String, String, String, String) - Constructor for class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

GeneEnrichment - Class in es.imim.DISGENET.internal.enrichment

GeneEnrichment() - Constructor for class es.imim.DISGENET.internal.enrichment.GeneEnrichment

GeneEnrichment(String, String, String, String, String, Double, List<Integer>, List<Long>) - Constructor for class es.imim.DISGENET.internal.enrichment.GeneEnrichment

geneEnrichmentParameters(GeneEnrichmentParams) - Static method in class es.imim.DISGENET.validation.ParametersValidation

GeneEnrichmentParams - Class in es.imim.DISGENET.internal.automation.parameters

GeneEnrichmentParams() - Constructor for class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

GeneEnrichmentTask - Class in es.imim.DISGENET.internal.enrichment

GeneEnrichmentTask(CyNetworkView) - Constructor for class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

GeneEnrichmentTaskFactory - Class in es.imim.DISGENET.internal.enrichment

GeneEnrichmentTaskFactory() - Constructor for class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTaskFactory

geneProj_DisClassComboBoxActionPerformed(ActionEvent) - Method in class es.imim.DISGENET.gui.MainPanel

geneProjParameters(GeneProjParams) - Static method in class es.imim.DISGENET.validation.ParametersValidation

GeneProjParams - Class in es.imim.DISGENET.internal.automation.parameters

GeneProjParams() - Constructor for class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

GeneProjParams(String, String, String) - Constructor for class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

GeneSearchField - Class in es.imim.DISGENET.search

GeneSearchField() - Constructor for class es.imim.DISGENET.search.GeneSearchField

genNamesToId(List<String>) - Method in class es.imim.DISGENET.database.DatabaseImpl

Converts a list of gene symbols to their corresponding gene IDs.

genWildCard(String) - Method in class es.imim.DISGENET.database.DatabaseImpl

Retrieves all the gene IDs associated to one or more given gene string name/s

getActiveTab() - Method in class es.imim.DISGENET.gui.GuiParameters

getActiveTab() - Method in class es.imim.DISGENET.gui.MainPanel

getAddedSuggestionLabels() - Method in class es.imim.DISGENET.search.AutoSuggestor

getAllRowCount() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getApiKey() - Method in interface es.imim.DISGENET.database.DatabaseManager

Gets the API key.

getApiKey() - Method in class es.imim.DISGENET.database.DatabaseManagerImpl

getAppInfo() - Method in interface es.imim.DISGENET.internal.automation.NetworkAutomation

getAppInfo() - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

getApplicationManagerService() - Method in class es.imim.DISGENET.internal.CyActivator

getAssociatedGenesToVariants(List<String>) - Method in interface es.imim.DISGENET.database.Database

getAssociatedGenesToVariants(List<String>) - Method in class es.imim.DISGENET.database.DatabaseImpl

Returns a map with the gene ID for each gene symbol of the provided list

getAssociationType() - Method in class es.imim.DISGENET.gui.GuiParameters

getAutoSuggestionPopUpWindow() - Method in class es.imim.DISGENET.search.AutoSuggestor

getBgRatio() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getCallResult() - Method in class es.imim.DISGENET.tool.OperationResult

getColumnClass(int) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getColumnCount() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getColumnIdentifierFactory() - Method in class es.imim.DISGENET.internal.CyActivator

getColumnName() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

getColumnName() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

getColumnName(int) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getComponent() - Method in class es.imim.DISGENET.gui.DisColorLegendPanel

getComponent() - Method in class es.imim.DISGENET.internal.DisGeNETCytoPanel

getComponent() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

getConn() - Method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

getContainer() - Method in class es.imim.DISGENET.search.AutoSuggestor

getContext() - Method in class es.imim.DISGENET.internal.CyActivator

getCurParams() - Method in class es.imim.DISGENET.network.NetTask

getCurrentlyTypedWord() - Method in class es.imim.DISGENET.search.AutoSuggestor

getCurrNetwork() - Method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

getCustomGraphics() - Method in class es.imim.DISGENET.internal.CyActivator

getCyApplicationManager() - Method in class es.imim.DISGENET.internal.CyActivator

getCyTableFactory() - Method in class es.imim.DISGENET.internal.CyActivator

getCyTableManager() - Method in class es.imim.DISGENET.internal.CyActivator

getCytoPanelName() - Method in class es.imim.DISGENET.gui.DisColorLegendPanel

getCytoPanelName() - Method in class es.imim.DISGENET.internal.DisGeNETCytoPanel

getCytoPanelName() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

getDB() - Method in class es.imim.DISGENET.network.NetworkBuilder

getDesktopService() - Method in class es.imim.DISGENET.internal.CyActivator

getDialogTaskManagerService() - Method in class es.imim.DISGENET.internal.CyActivator

getDiseaseAttributes(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getDiseaseAttributes(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getDiseaseClass() - Method in class es.imim.DISGENET.gui.GuiParameters

getDiseaseClass() - Method in class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

getDiseaseClass() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

getDiseaseClass() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

getDiseaseClass() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

getDiseaseColourMapping() - Static method in class es.imim.DISGENET.network.colorMapping.DiseaseColourMapping

getDiseaseColourNameMapping() - Static method in class es.imim.DISGENET.network.colorMapping.DiseaseColourMapping

getDiseaseColourNumericMapping() - Static method in class es.imim.DISGENET.network.colorMapping.DiseaseColourMapping

getDiseaseList(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getDiseaseList(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

Case in gene-dis panel

getDiseaseListVariant(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getDiseaseListVariant(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

Case in var-dis panel

getDiseaseNames(String) - Method in class es.imim.DISGENET.database.DatabaseImpl

getDiseaseProjectionBySrc(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getDiseaseProjectionBySrc(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getDiseasesAssociatedToGenes(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getDiseasesAssociatedToGenes(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getDiseaseSearch() - Method in class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

getDiseaseSearch() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

getDiseaseSearch() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

getDisgenetNodeAttributesTable() - Method in class es.imim.DISGENET.internal.CyActivator

getDisSearchText() - Method in class es.imim.DISGENET.gui.GuiParameters

getEl() - Method in class es.imim.DISGENET.gui.GuiParameters

getEnrichList() - Method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

getEnrichmentTables() - Method in class es.imim.DISGENET.internal.CyActivator

getFactory() - Method in class es.imim.DISGENET.internal.CustomChartListener

Retrieves the currently stored custom graphics factory.

getFinalScoreValue() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

getFinalScoreValue() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

getGeneAttributes(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getGeneAttributes(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getGeneDiseaseNetworkBySrc(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getGeneDiseaseNetworkBySrc(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getGeneId(String) - Method in interface es.imim.DISGENET.database.Database

getGeneId(String) - Method in class es.imim.DISGENET.database.DatabaseImpl

Converts a symbol of gene to their corresponding gene ID.

getGeneIdList(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getGeneIdList(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

Case in gen-dis panel

getGeneIds() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getGeneList(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getGeneList(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

Case in gene-dis panel

getGeneListVariant(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getGeneListVariant(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

Case in var-dis panel

getGeneNames(String) - Method in class es.imim.DISGENET.database.DatabaseImpl

getGeneNodes() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getGeneProjectionBySrc(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getGeneProjectionBySrc(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getGeneProteinClass() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

getGeneRatio() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getGeneSearch() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

getGeneSearch() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

getGeneSearch() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

getGenSearchText() - Method in class es.imim.DISGENET.gui.GuiParameters

getGlobalTaskIterator() - Method in class es.imim.DISGENET.internal.CyActivator

getHighEi() - Method in class es.imim.DISGENET.gui.GuiParameters

getHighScore() - Method in class es.imim.DISGENET.gui.GuiParameters

getIcon() - Method in class es.imim.DISGENET.gui.DisColorLegendPanel

getIcon() - Method in class es.imim.DISGENET.internal.DisGeNETCytoPanel

getIcon() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

getIconFont(float) - Static method in class es.imim.DISGENET.internal.utils.IconUtils

getIconHeight() - Method in class es.imim.DISGENET.internal.utils.TextIcon

getIconWidth() - Method in class es.imim.DISGENET.internal.utils.TextIcon

getIdentifier() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

getInitialScoreValue() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

getInitialScoreValue() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

getInstance() - Static method in class es.imim.DISGENET.database.DatabaseImpl

getInstance() - Static method in class es.imim.DISGENET.database.DatabaseManagerImpl

Singleton implementation of the database class.

getInstance() - Static method in class es.imim.DISGENET.internal.CyActivator

getInstance(LoadVizmapFileTaskFactory, VisualMappingManager, VisualStyleFactory) - Static method in class es.imim.DISGENET.styles.DisGenetStyleManager

getLowEi() - Method in class es.imim.DISGENET.gui.GuiParameters

getLowScore() - Method in class es.imim.DISGENET.gui.GuiParameters

getMainPanel() - Method in class es.imim.DISGENET.internal.CyActivator

getMessage() - Method in class es.imim.DISGENET.tool.OperationResult

getMinNumberOfGenes() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

getMinNumberOfVariants() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

getName() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getNetName() - Method in class es.imim.DISGENET.network.ExpandNewNetworkTask

getNetTableMgr() - Method in class es.imim.DISGENET.internal.CyActivator

getNetType() - Method in class es.imim.DISGENET.network.ExpandNewNetworkTask

getNetworkFactoryService() - Method in class es.imim.DISGENET.internal.CyActivator

getNetworkId() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

getNetworkId() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

getNetworkManagerService() - Method in class es.imim.DISGENET.internal.CyActivator

getNetworkName() - Method in class es.imim.DISGENET.gui.GuiParameters

getNetworkViewFactoryService() - Method in class es.imim.DISGENET.internal.CyActivator

getNetworkViewManagerService() - Method in class es.imim.DISGENET.internal.CyActivator

getNodeNamesFromNet() - Method in class es.imim.DISGENET.network.NetworkBuilder

Function to retrieve all node names from currently selected network to be able to search for them.

getNumberGenes() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getOpenBrowser() - Method in class es.imim.DISGENET.internal.linkout.LinkoutNodeTask

getParams() - Method in class es.imim.DISGENET.gui.MainPanel

getParams() - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

getParams() - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

getParams() - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableVariant

getProteinClass() - Method in class es.imim.DISGENET.gui.GuiParameters

getpValue() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getPValueThreshold() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

getPvalueThreshold() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

getResult() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTaskObserver

getResult() - Method in class es.imim.DISGENET.network.NetTaskObserver

getResultClasses() - Method in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

getResultClasses() - Method in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

getResults(Class<? extends R>) - Method in class es.imim.DISGENET.internal.automation.NetTaskAutomation

getResults(Class<? extends R>) - Method in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

getResults(Class<? extends R>) - Method in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

getRowCount() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getRowNames() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getSearchBox() - Method in class es.imim.DISGENET.search.GeneSearchField

getSearchBox() - Method in class es.imim.DISGENET.search.SearchField

getSearchBox() - Method in class es.imim.DISGENET.search.VariantSearchField

getServiceRegistrar() - Method in class es.imim.DISGENET.internal.CyActivator

getShowEnrichmentFactory() - Method in class es.imim.DISGENET.internal.CyActivator

getSource() - Method in class es.imim.DISGENET.gui.GuiParameters

getSource() - Method in class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

getSource() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

getSource() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

getSource() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

getSource() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

getSource() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

getSource() - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

getStatusMessage() - Method in enum es.imim.DISGENET.Status

getSynchTaskManagerService() - Method in class es.imim.DISGENET.internal.CyActivator

getTableFactoryService() - Method in class es.imim.DISGENET.internal.CyActivator

getTaskManagerService() - Method in class es.imim.DISGENET.internal.CyActivator

getTextField() - Method in class es.imim.DISGENET.search.AutoSuggestor

getTitle() - Method in class es.imim.DISGENET.gui.DisColorLegendPanel

getTitle() - Method in class es.imim.DISGENET.internal.DisGeNETCytoPanel

getTitle() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

getTypeId() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

getTypeId() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

getValidationState(Appendable) - Method in class es.imim.DISGENET.internal.CustomLayoutContext

getValueAt(int, int) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getValueAt(int, String) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

getVariantAttributes(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getVariantDiseaseNetworkBySrc(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getVariantDiseaseNetworkBySrc(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

getVariantList(GuiParameters) - Method in interface es.imim.DISGENET.database.Database

getVariantList(GuiParameters) - Method in class es.imim.DISGENET.database.DatabaseImpl

Case in var-dis panel

getVariantNames(String) - Method in class es.imim.DISGENET.database.DatabaseImpl

getVariantSearch() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

getVarSearchText() - Method in class es.imim.DISGENET.gui.GuiParameters

getVisualMappingMgr() - Method in class es.imim.DISGENET.internal.CyActivator

getVisualStyleByName(VisualMappingManager, String) - Static method in class es.imim.DISGENET.styles.DisGenetStyleManager

Get the visual style by name.

getVisualStyleFactor() - Method in class es.imim.DISGENET.internal.CyActivator

getWidestItemWidth() - Method in class es.imim.DISGENET.search.MemComboBox.MyComboBoxUI

GuiParameters<PostTranslational_Modification,Altered_Expression> - Class in es.imim.DISGENET.gui

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

GuiParameters() - Constructor for class es.imim.DISGENET.gui.GuiParameters

GuiProps - Class in es.imim.DISGENET.gui

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

GuiProps() - Constructor for class es.imim.DISGENET.gui.GuiProps

H

handleEvent(RowsSetEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

handleEvent(SetCurrentNetworkEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

handleEvent(SetCurrentNetworkEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentNetworkListener

handleEvent(SessionLoadedEvent) - Method in class es.imim.DISGENET.styles.DisGenetStyleManager

HelperFunctions - Class in es.imim.DISGENET.tool

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

HelperFunctions() - Constructor for class es.imim.DISGENET.tool.HelperFunctions

HelperFunctions.byLineLengthAsc - Class in es.imim.DISGENET.tool

HelperFunctions.byLineLengthDesc - Class in es.imim.DISGENET.tool

functions to sort string lists by line length

HGNC_SEARCH_REGEX - Static variable in class es.imim.DISGENET.database.DatabaseProps

I

IconUtils - Class in es.imim.DISGENET.internal.utils

implodeInteger(String, Collection<Integer>) - Static method in class es.imim.DISGENET.tool.HelperFunctions

implodeString(String, Collection<String>) - Static method in class es.imim.DISGENET.tool.HelperFunctions

initAdditionalStyleAttributes(GuiParameters<?, ?>) - Method in class es.imim.DISGENET.network.NetworkBuilder

Fills the attribute columns for the different type of networks.

initPanel() - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

initPanel(CyNetwork) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

isCellEditable(int, int) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

isEmptyNet() - Method in class es.imim.DISGENET.gui.GuiParameters

isExpandedWithGenes(CyNetwork) - Static method in class es.imim.DISGENET.validation.NetworkValidation

Checks if the variant network is already expanded.

isForeignNet(CyNetwork) - Static method in class es.imim.DISGENET.validation.NetworkValidation

Checks if the current network is original DISGENET network or not.

isInterrupted() - Method in class es.imim.DISGENET.network.NetTask

isNetBuildInterrupted() - Method in class es.imim.DISGENET.gui.GuiParameters

isNewNetwork() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

isNewNetwork() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

isPanelRegistered() - Static method in class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTask

isProjectionNet(CyNetwork, String) - Static method in class es.imim.DISGENET.validation.NetworkValidation

isReady(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesGenesTaskFactory

isReady(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesVariantsTaskFactory

isReady(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateGenesTaskFactory

isReady(CyNetworkView) - Method in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTaskFactory

isReady(CyNetworkView) - Method in class es.imim.DISGENET.internal.ApplyCustomLayoutTaskFactory

isReady(CyNetworkView) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTaskFactory

isReady() - Method in class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTaskFactory

isReady(CyNetworkView) - Method in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTaskFactory

isReady(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.ExpandCurrentNetActionTaskFactory

isReady(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.ExpandNewNetActionTaskFactory

isReady(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutDiseaseTaskFactory

isReady(View<CyEdge>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutEdgeTaskFactory

isReady(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutGeneTaskFactory

isReady(View<CyNode>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutVariantTaskFactory

isRunning() - Method in class es.imim.DISGENET.internal.StartDisGeNETMenuAction

isShowGenes() - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

isVarGeneDisNetwork() - Method in class es.imim.DISGENET.gui.GuiParameters

isVariantNet(CyNetwork) - Static method in class es.imim.DISGENET.validation.NetworkValidation

Checks if the current network is a variant-disease network.

J

JsonParser - Class in es.imim.DISGENET.database

JsonParser() - Constructor for class es.imim.DISGENET.database.JsonParser

L

LAYERED_EM_ICON - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

LAYERED_STRING_ICON - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

layoutAlgoManager - Static variable in class es.imim.DISGENET.internal.CyActivator

LinkoutDiseaseTask - Class in es.imim.DISGENET.internal.linkout

LinkoutDiseaseTask(CyNetwork, CyNode) - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutDiseaseTask

LinkoutDiseaseTaskFactory - Class in es.imim.DISGENET.internal.linkout

LinkoutDiseaseTaskFactory() - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutDiseaseTaskFactory

LinkoutEdgeTask - Class in es.imim.DISGENET.internal.linkout

LinkoutEdgeTask(CyNetwork, CyEdge) - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutEdgeTask

LinkoutEdgeTaskFactory - Class in es.imim.DISGENET.internal.linkout

LinkoutEdgeTaskFactory() - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutEdgeTaskFactory

LinkoutGeneTask - Class in es.imim.DISGENET.internal.linkout

LinkoutGeneTask(CyNetwork, CyNode) - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutGeneTask

LinkoutGeneTaskFactory - Class in es.imim.DISGENET.internal.linkout

LinkoutGeneTaskFactory() - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutGeneTaskFactory

LinkoutNodeTask - Class in es.imim.DISGENET.internal.linkout

LinkoutNodeTask() - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutNodeTask

LinkoutProperties - Class in es.imim.DISGENET.internal.linkout

LinkoutProperties() - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutProperties

LinkoutService - Class in es.imim.DISGENET.internal.linkout

LinkoutService(CyServiceRegistrar) - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutService

LinkoutVariantTask - Class in es.imim.DISGENET.internal.linkout

LinkoutVariantTask(CyNetwork, CyNode) - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutVariantTask

LinkoutVariantTaskFactory - Class in es.imim.DISGENET.internal.linkout

LinkoutVariantTaskFactory() - Constructor for class es.imim.DISGENET.internal.linkout.LinkoutVariantTaskFactory

listNodeColumnsNames() - Method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

loadStyles() - Method in class es.imim.DISGENET.styles.DisGenetStyleManager

Load the visual styles of the app.

M

m_locator - Variable in class es.imim.DISGENET.search.GeneSearchField

m_locator - Variable in class es.imim.DISGENET.search.SearchField

m_locator - Variable in class es.imim.DISGENET.search.VariantSearchField

main(String[]) - Static method in class es.imim.DISGENET.database.DatabaseImpl

main(String[]) - Static method in class es.imim.DISGENET.database.JsonParser

main(String[]) - Static method in class es.imim.DISGENET.database.UserTypeUtil

main(String[]) - Static method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

main(String[]) - Static method in class es.imim.DISGENET.search.GeneSearchField

main(String[]) - Static method in class es.imim.DISGENET.search.SearchField

main(String[]) - Static method in class es.imim.DISGENET.search.Test

main(String[]) - Static method in class es.imim.DISGENET.search.VariantSearchField

MainPanel - Class in es.imim.DISGENET.gui

This class generates the main gui panel with the options and buttons that call the functions to create networks, colour nodes,...

MainPanel(StartDisGeNETMenuAction) - Constructor for class es.imim.DISGENET.gui.MainPanel

Creates new MainPanel

makeApiRequest(Map<String, String>, String) - Method in class es.imim.DISGENET.database.ApiClient

MAX_MEM_LEN - Static variable in class es.imim.DISGENET.search.MemComboBox

maxScoreRange - Variable in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

maxScoreRange - Variable in class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

maxScoreRange - Variable in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

maxScoreRange - Variable in class es.imim.DISGENET.network.ExpandCurrentNetworkTask

maxScoreRange - Variable in class es.imim.DISGENET.network.ExpandNewNetworkTask

MemComboBox - Class in es.imim.DISGENET.search

MemComboBox() - Constructor for class es.imim.DISGENET.search.MemComboBox

MemComboBox.MyComboBoxUI - Class in es.imim.DISGENET.search

MemComboBox.myComboUI - Class in es.imim.DISGENET.search

MemComboBox.ReshowPopup - Class in es.imim.DISGENET.search

MenuAction - Class in es.imim.DISGENET.internal

Creates a new menu item under Apps menu section.

MenuAction(CyApplicationManager, String) - Constructor for class es.imim.DISGENET.internal.MenuAction

minNumGenes - Variable in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

minNumGenes - Variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

minNumVariants - Variable in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

minNumVariants - Variable in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

minScoreRange - Variable in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

minScoreRange - Variable in class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

minScoreRange - Variable in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

minScoreRange - Variable in class es.imim.DISGENET.network.ExpandCurrentNetworkTask

minScoreRange - Variable in class es.imim.DISGENET.network.ExpandNewNetworkTask

MyComboBoxUI() - Constructor for class es.imim.DISGENET.search.MemComboBox.MyComboBoxUI

myComboUI() - Constructor for class es.imim.DISGENET.search.MemComboBox.myComboUI

N

NetAction - Class in es.imim.DISGENET.network

Class to handle the clicking of the create network Button

NetAction() - Constructor for class es.imim.DISGENET.network.NetAction

NetAction(GuiParameters) - Constructor for class es.imim.DISGENET.network.NetAction

NetAction(GuiParameters, JTabbedPane) - Constructor for class es.imim.DISGENET.network.NetAction

NetCompletionChangeEvent - Class in es.imim.DISGENET.network

part of event handler class to allow updating the progress bar from different task

NetCompletionChangeEvent(TaskMonitor) - Constructor for class es.imim.DISGENET.network.NetCompletionChangeEvent

NetCreationEvent - Class in es.imim.DISGENET.network

part of event handler class to allow updating the progress bar from different task

NetCreationEvent(Object, Double) - Constructor for class es.imim.DISGENET.network.NetCreationEvent

NetCreationEventReceived(NetCreationEvent) - Method in class es.imim.DISGENET.network.NetCompletionChangeEvent

NetCreationEventReceived(NetCreationEvent) - Method in interface es.imim.DISGENET.network.NetCreationListener

NetCreationListener - Interface in es.imim.DISGENET.network

part of event handler class to allow updating the progress bar from different task

NetTask - Class in es.imim.DISGENET.network

NetTask(GuiParameters) - Constructor for class es.imim.DISGENET.network.NetTask

NetTaskAutomation - Class in es.imim.DISGENET.internal.automation

NetTaskAutomation(GuiParameters) - Constructor for class es.imim.DISGENET.internal.automation.NetTaskAutomation

NetTaskObserver - Class in es.imim.DISGENET.network

NetTaskObserver() - Constructor for class es.imim.DISGENET.network.NetTaskObserver

NetworkAutomation - Interface in es.imim.DISGENET.internal.automation

NetworkAutomationImpl - Class in es.imim.DISGENET.internal.automation

NetworkAutomationImpl() - Constructor for class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

NetworkBuilder - Class in es.imim.DISGENET.network

NetworkBuilder() - Constructor for class es.imim.DISGENET.network.NetworkBuilder

NetworkBuilder(GuiParameters) - Constructor for class es.imim.DISGENET.network.NetworkBuilder

NetworkValidation - Class in es.imim.DISGENET.validation

NetworkValidation() - Constructor for class es.imim.DISGENET.validation.NetworkValidation

newNetwork - Variable in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

newNetwork - Variable in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

newNetwork - Variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

newNetwork - Variable in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

NodeValidation - Class in es.imim.DISGENET.validation

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

NodeValidation() - Constructor for class es.imim.DISGENET.validation.NodeValidation

numGeneMaximum - Variable in class es.imim.DISGENET.internal.enrichment.FilterEnrichmentTask

numGeneMinimum - Variable in class es.imim.DISGENET.internal.enrichment.FilterEnrichmentTask

O

ogPvalue - Variable in class es.imim.DISGENET.internal.enrichment.FilterEnrichmentTask

openConnection(URL) - Method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

OperationResult - Class in es.imim.DISGENET.tool

OperationResult() - Constructor for class es.imim.DISGENET.tool.OperationResult

OperationResult(String, Map, Map) - Constructor for class es.imim.DISGENET.tool.OperationResult

P

paintIcon(Component, Graphics, int, int) - Method in class es.imim.DISGENET.internal.utils.TextIcon

paintNodes(CyNetwork) - Method in class es.imim.DISGENET.network.colorMapping.ColorAction

ParametersValidation - Class in es.imim.DISGENET.validation

ParametersValidation() - Constructor for class es.imim.DISGENET.validation.ParametersValidation

parseJSON(List<String>, Map<String, String>, String) - Method in class es.imim.DISGENET.database.JsonParser

parseJSON(List<String>, Map<String, String>, String, String, String) - Method in class es.imim.DISGENET.database.JsonParser

parseJSONDict(Map<String, String>, String) - Method in class es.imim.DISGENET.database.JsonParser

parseJSONDictList(Map<String, String>, String) - Method in class es.imim.DISGENET.database.JsonParser

parseJSONDictList(Map<String, String>, String, String, String) - Method in class es.imim.DISGENET.database.JsonParser

pct() - Method in class es.imim.DISGENET.network.NetCreationEvent

performGeneDiseaseEnrichment(GeneEnrichmentParams) - Method in interface es.imim.DISGENET.internal.automation.NetworkAutomation

performGeneDiseaseEnrichment(GeneEnrichmentParams) - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

performVariantDiseaseEnrichment(VariantEnrichmentParams) - Method in interface es.imim.DISGENET.internal.automation.NetworkAutomation

performVariantDiseaseEnrichment(VariantEnrichmentParams) - Method in class es.imim.DISGENET.internal.automation.NetworkAutomationImpl

propertyChange(PropertyChangeEvent) - Method in class es.imim.DISGENET.gui.MainPanel

PUBMED_LAYER - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

PUBMED_LAYERS - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

PUBMED_LINKOUT_URL - Static variable in class es.imim.DISGENET.internal.linkout.LinkoutProperties

pvalueThreshold - Variable in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

pvalueThreshold - Variable in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

pvalueThreshold - Variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

pvalueThreshold - Variable in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

R

REMOVE_COLOR_BUTTON_TEXT - Static variable in class es.imim.DISGENET.gui.GuiProps

REMOVE_COLOR_BUTTON_TOOLTIP - Static variable in class es.imim.DISGENET.gui.GuiProps

RemoveColorAction - Class in es.imim.DISGENET.network.colorMapping

RemoveColorAction() - Constructor for class es.imim.DISGENET.network.colorMapping.RemoveColorAction

removeColorClass(CyNetwork) - Method in class es.imim.DISGENET.network.colorMapping.RemoveColorAction

removeCustomGraphicsFactory(CyCustomGraphics2Factory<?>, Map<Object, Object>) - Method in class es.imim.DISGENET.internal.CustomChartListener

Removes the currently stored custom graphics factory.

removeGenesFromVariantNet() - Method in class es.imim.DISGENET.network.NetworkBuilder

Removes the gene nodes from the variant disease network and updates the view.

removeMoodListener(NetCreationListener) - Method in class es.imim.DISGENET.network.NetworkBuilder

reregister() - Method in class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTaskFactory

ReshowPopup() - Constructor for class es.imim.DISGENET.search.MemComboBox.ReshowPopup

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.automation.NetTaskAutomation

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.enrichment.FilterEnrichmentTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.linkout.LinkoutDiseaseTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.linkout.LinkoutEdgeTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.linkout.LinkoutGeneTask

run(TaskMonitor) - Method in class es.imim.DISGENET.internal.linkout.LinkoutVariantTask

run(TaskMonitor) - Method in class es.imim.DISGENET.network.ExpandCurrentNetworkTask

run(TaskMonitor) - Method in class es.imim.DISGENET.network.ExpandNewNetworkTask

run(TaskMonitor) - Method in class es.imim.DISGENET.network.NetTask

run(TaskMonitor) - Method in class es.imim.DISGENET.network.ShowGenesVariantTask

run() - Method in class es.imim.DISGENET.search.MemComboBox.ReshowPopup

S

SearchDictionaries - Class in es.imim.DISGENET.search

The DISGENET Cytoscape App is designed to visualize, query, and analyze a network representation of DISGENET data.

SearchDictionaries() - Constructor for class es.imim.DISGENET.search.SearchDictionaries

SearchField - Class in es.imim.DISGENET.search

SearchField() - Constructor for class es.imim.DISGENET.search.SearchField

set_activator(CyActivator) - Method in class es.imim.DISGENET.internal.StartDisGeNETMenuAction

setActiveTab(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setApiKey(String) - Method in interface es.imim.DISGENET.database.DatabaseManager

Sets the API key.

setApiKey(String) - Method in class es.imim.DISGENET.database.DatabaseManagerImpl

setAssociationType(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setBgRatio(String) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

setCallResult(Map) - Method in class es.imim.DISGENET.tool.OperationResult

setColumnIdentifierFactory(CyColumnIdentifierFactory) - Method in class es.imim.DISGENET.internal.CyActivator

setColumnName(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

setColumnName(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

setContext(BundleContext) - Method in class es.imim.DISGENET.internal.CyActivator

setCurParams(GuiParameters) - Method in class es.imim.DISGENET.network.NetTask

setCustomGraphics(CustomChartListener) - Method in class es.imim.DISGENET.internal.CyActivator

setCyApplicationManager(CyApplicationManager) - Method in class es.imim.DISGENET.internal.CyActivator

setCyTableFactory(CyTableFactory) - Method in class es.imim.DISGENET.internal.CyActivator

setCyTableManager(CyTableManager) - Method in class es.imim.DISGENET.internal.CyActivator

setDictionary(ArrayList<String>) - Method in class es.imim.DISGENET.search.AutoSuggestor

setDiseaseClass(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setDiseaseClass(String) - Method in class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

setDiseaseClass(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

setDiseaseClass(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

setDiseaseClass(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setDiseaseSearch(String) - Method in class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

setDiseaseSearch(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

setDiseaseSearch(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setDisgenetNodeAttributesTable(CyTable) - Method in class es.imim.DISGENET.internal.CyActivator

setDisSearchText(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setEl(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setEmptyNet(boolean) - Method in class es.imim.DISGENET.gui.GuiParameters

setFinalScoreValue(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

setFinalScoreValue(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setGeneIds(List<Integer>) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

setGeneNodes(List<Long>) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

setGeneProteinClass(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

setGeneRatio(String) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

setGeneSearch(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

setGeneSearch(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

setGeneSearch(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setGenSearchText(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setHighEi(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setHighScore(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setInitialScoreValue(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setLowEi(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setLowScore(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setLowScore(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

setMessage(String) - Method in class es.imim.DISGENET.tool.OperationResult

setMinNumberOfGenes(Integer) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

setMinNumberOfVariants(Integer) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

setName(String) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

setNetBuildInterrupted(boolean) - Method in class es.imim.DISGENET.gui.GuiParameters

setNetName(String) - Method in class es.imim.DISGENET.network.ExpandNewNetworkTask

setNetTableMgr(CyNetworkTableManager) - Method in class es.imim.DISGENET.internal.CyActivator

setNetType(String) - Method in class es.imim.DISGENET.network.ExpandNewNetworkTask

setNetworkId(Long) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

setNetworkId(Long) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

setNetworkName(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setNewNetwork(boolean) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

setNewNetwork(boolean) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

setOpenBrowser(OpenBrowser) - Method in class es.imim.DISGENET.internal.linkout.LinkoutNodeTask

setParams(GuiParameters<Object, Object>) - Method in class es.imim.DISGENET.gui.MainPanel

setParams(GuiParameters) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease

setParams(GuiParameters) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene

setParams(GuiParameters) - Method in class es.imim.DISGENET.internal.tables.DisGeNetCyTableVariant

setProteinClass(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setpValue(Double) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

setPValueThreshold(double) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

setPvalueThreshold(double) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

setRunning(boolean) - Method in class es.imim.DISGENET.internal.StartDisGeNETMenuAction

setServiceRegistrar(CyServiceRegistrar) - Method in class es.imim.DISGENET.internal.CyActivator

setShowGenes(boolean) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setSource(String) - Method in class es.imim.DISGENET.gui.GuiParameters

setSource(String) - Method in class es.imim.DISGENET.internal.automation.parameters.DiseaseProjParams

setSource(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneDiseaseParams

setSource(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

setSource(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneProjParams

setSource(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setSource(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

setSource(String) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

setTaskMonitor(TaskMonitor) - Method in class es.imim.DISGENET.network.NetTask

setTypeId(String) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams

setTypeId(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

setUrlParams(String) - Method in class es.imim.DISGENET.internal.enrichment.AbstractEnrichmentTask

setValueAt(Object, int, int) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTableModel

setVarGeneDisNetwork(boolean) - Method in class es.imim.DISGENET.gui.GuiParameters

setVariantSearch(String) - Method in class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

setVarSearchText(String) - Method in class es.imim.DISGENET.gui.GuiParameters

showApiKeyDialog() - Static method in class es.imim.DISGENET.database.ApiKeyDialog

ShowEnrichmentPanelTask - Class in es.imim.DISGENET.internal.enrichment

ShowEnrichmentPanelTask(ShowEnrichmentPanelTaskFactory, boolean, boolean) - Constructor for class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTask

ShowEnrichmentPanelTaskFactory - Class in es.imim.DISGENET.internal.enrichment

ShowEnrichmentPanelTaskFactory() - Constructor for class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTaskFactory

ShowGenesVariantTask - Class in es.imim.DISGENET.network

Class that handles the display of gene nodes in networks containing variants.

ShowGenesVariantTask(boolean, CyNetwork) - Constructor for class es.imim.DISGENET.network.ShowGenesVariantTask

showVariantNetWithGenes() - Method in class es.imim.DISGENET.network.NetworkBuilder

Calls the method to expand a variant disease network and updates the view.

source - Variable in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

source - Variable in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

SOURCE_OPTIONS - Static variable in class es.imim.DISGENET.gui.GuiProps

sourceOptions - Static variable in class es.imim.DISGENET.validation.ParametersValidation

sources - Variable in class es.imim.DISGENET.internal.annotation.AnnotateDiseasesTask

sources - Variable in class es.imim.DISGENET.internal.annotation.AnnotateGenesTask

sources - Variable in class es.imim.DISGENET.internal.annotation.AnnotateVariantsTask

sources - Variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

sources - Variable in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

sources - Variable in class es.imim.DISGENET.network.ExpandCurrentNetworkTask

sources - Variable in class es.imim.DISGENET.network.ExpandNewNetworkTask

start(BundleContext) - Method in class es.imim.DISGENET.internal.Activator

start(BundleContext) - Method in class es.imim.DISGENET.internal.CyActivator

StartDisGeNETMenuAction - Class in es.imim.DISGENET.internal

Creates a new menu item under Apps menu section.

StartDisGeNETMenuAction(CyApplicationManager, CyServiceRegistrar, String) - Constructor for class es.imim.DISGENET.internal.StartDisGeNETMenuAction

Status - Enum in es.imim.DISGENET

STITCH_LAYER - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STITCH_LAYERS - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

stop(BundleContext) - Method in class es.imim.DISGENET.internal.Activator

STRING_COLORS - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STRING_ICON - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STRING_ICON_LAYER_1 - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STRING_ICON_LAYER_2 - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STRING_ICON_LAYER_3 - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STRING_ICON_LAYER_4 - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STRING_LAYER - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

STRING_LAYERS - Static variable in class es.imim.DISGENET.internal.utils.IconUtils

swingColumnsEnrichment - Static variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichment

T

tableChanged(TableModelEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

taskFinished(ObservableTask) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentTaskObserver

taskFinished(ObservableTask) - Method in class es.imim.DISGENET.network.NetTaskObserver

Test - Class in es.imim.DISGENET.search

Test() - Constructor for class es.imim.DISGENET.search.Test

TextIcon - Class in es.imim.DISGENET.internal.utils

TextIcon(String, Font, Color, int, int) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

TextIcon(String, Font, int, int) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

The icon color is the target component's foreground.

TextIcon(String[], Font, Color[], int, int) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

TextIcon(String[], Font, int, int) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

The icon color is the target component's foreground.

TextIcon(String[], Font, Color[], int, int, Integer...) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

TextIcon(String[], Font[], Color[], int, int) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

TextIcon(String[], Font[], int, int) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

The icon color is the target component's foreground.

TextIcon(String[], Font[], Color[], int, int, Integer...) - Constructor for class es.imim.DISGENET.internal.utils.TextIcon

typeId - Variable in class es.imim.DISGENET.internal.enrichment.AutomationGeneEnrichmentTask

typeId - Variable in class es.imim.DISGENET.internal.enrichment.AutomationVariantEnrichmentTask

typeId - Variable in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTask

typeId - Variable in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

U

unregister() - Method in class es.imim.DISGENET.internal.StartDisGeNETMenuAction

unregister_disgenet_panel(DisGeNETCytoPanel) - Method in class es.imim.DISGENET.internal.CyActivator

update(String) - Method in class es.imim.DISGENET.search.MemComboBox

updateParams() - Method in class es.imim.DISGENET.gui.MainPanel

UserTypeUtil - Class in es.imim.DISGENET.database

UserTypeUtil() - Constructor for class es.imim.DISGENET.database.UserTypeUtil

V

valueChanged(ListSelectionEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel

valueOf(String) - Static method in enum es.imim.DISGENET.Status

Returns the enum constant of this type with the specified name.

values() - Static method in enum es.imim.DISGENET.Status

Returns an array containing the constants of this enum type, in the order they are declared.

VARIANT_ASSOCIATION_TYPE_OPTIONS - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_CODE_REGEX - Static variable in class es.imim.DISGENET.database.DatabaseProps

VARIANT_DIS_CLASS_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_LOW_SCORE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_SEARCH_DIS_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_SEARCH_GEN_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_SEARCH_TEXT - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_SEARCH_VAR_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_SOURCE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_TAB_TITLE - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_DIS_UP_SCORE_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_LINKOUT_URL - Static variable in class es.imim.DISGENET.internal.linkout.LinkoutProperties

VARIANT_SNP_REGEX - Static variable in class es.imim.DISGENET.validation.NodeValidation

VARIANT_SOURCE_OPTIONS - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_STRING_SEARCH - Static variable in class es.imim.DISGENET.database.DatabaseProps

VARIANT_VAR_GEN_CHECKBOX_LABEL - Static variable in class es.imim.DISGENET.gui.GuiProps

VARIANT_VAR_GEN_CHECKBOX_TOOLTIP - Static variable in class es.imim.DISGENET.gui.GuiProps

variantDis_AssoComboBoxPopupMenuWillBecomeVisible(PopupMenuEvent) - Method in class es.imim.DISGENET.gui.MainPanel

variantDis_disClassComboBoxActionPerformed(ActionEvent) - Method in class es.imim.DISGENET.gui.MainPanel

variantDis_ElComboBoxActionPerformed(ActionEvent) - Method in class es.imim.DISGENET.gui.MainPanel

variantDiseaseParameters(VariantDiseaseParams) - Static method in class es.imim.DISGENET.validation.ParametersValidation

VariantDiseaseParams - Class in es.imim.DISGENET.internal.automation.parameters

VariantDiseaseParams() - Constructor for class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

VariantDiseaseParams(String, String, String, String, String, String, String, boolean) - Constructor for class es.imim.DISGENET.internal.automation.parameters.VariantDiseaseParams

variantEnrichmentParameters(VariantEnrichmentParams) - Static method in class es.imim.DISGENET.validation.ParametersValidation

VariantEnrichmentParams - Class in es.imim.DISGENET.internal.automation.parameters

VariantEnrichmentParams() - Constructor for class es.imim.DISGENET.internal.automation.parameters.VariantEnrichmentParams

VariantEnrichmentService - Class in es.imim.DISGENET.internal.enrichment

VariantEnrichmentService(CyServiceRegistrar) - Constructor for class es.imim.DISGENET.internal.enrichment.VariantEnrichmentService

VariantEnrichmentTask - Class in es.imim.DISGENET.internal.enrichment

VariantEnrichmentTask(CyNetworkView) - Constructor for class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTask

VariantEnrichmentTaskFactory - Class in es.imim.DISGENET.internal.enrichment

VariantEnrichmentTaskFactory() - Constructor for class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTaskFactory

VARIANTS_DICT - Static variable in class es.imim.DISGENET.search.SearchDictionaries

VariantSearchField - Class in es.imim.DISGENET.search

VariantSearchField() - Constructor for class es.imim.DISGENET.search.VariantSearchField

W

WebMenuAction - Class in es.imim.DISGENET.internal

Creates a new menu item under Apps menu section.

WebMenuAction(CyApplicationManager, String, OpenBrowser) - Constructor for class es.imim.DISGENET.internal.WebMenuAction

X

XRange - Variable in class es.imim.DISGENET.internal.CustomLayoutContext

Y

YRange - Variable in class es.imim.DISGENET.internal.CustomLayoutContext

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