# Index

A B C D E F G H I J L M N O P R S T U V W X Y
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

## 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
CONNECTION_ERROR - Enum constant in enum class es.imim.DISGENET.Status
CONNECTION_WRONG_ADDRESS_ERROR - Enum constant in enum class es.imim.DISGENET.Status
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() - 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.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) - Method in class es.imim.DISGENET.internal.enrichment.GeneEnrichmentTaskFactory
createTaskIterator(CyNetworkView) - Method in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTaskFactory
createTaskIterator(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in class es.imim.DISGENET.internal.CustomLayout
createTaskIterator(View<CyEdge>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutEdgeTaskFactory
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<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
DB_CLOSE_CON_ERROR - Enum constant in enum class es.imim.DISGENET.Status
DB_CONNECTION_ERROR - Enum constant in enum class es.imim.DISGENET.Status
DB_DRIVER_ERROR - Enum constant in enum class es.imim.DISGENET.Status
DB_ENTRY_ALREADY_IN_DB - Enum constant in enum class es.imim.DISGENET.Status
DB_ERROR - Enum constant in enum class es.imim.DISGENET.Status
DB_FILE_NOT_SET - Enum constant in enum class es.imim.DISGENET.Status
DB_NO_SPECIFIED_DATABASE - Enum constant in enum class es.imim.DISGENET.Status
DB_WRITE_ERROR - Enum constant in enum class es.imim.DISGENET.Status
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
DISCONNECTION_ERROR - Enum constant in enum class es.imim.DISGENET.Status
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() - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableDisease
DisGeNetCyTableDisease(GuiParameters) - 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() - Constructor for class es.imim.DISGENET.internal.tables.DisGeNetCyTableGene
DisGeNetCyTableGene(GuiParameters) - 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(String, Throwable) - Constructor for exception es.imim.DISGENET.exceptions.DisGeNetException
DisGeNetException(String, Throwable, boolean, boolean) - Constructor for exception es.imim.DISGENET.exceptions.DisGeNetException
DisGeNetException(Throwable) - 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

FAIL - Enum constant in enum class es.imim.DISGENET.Status
FILE_ERROR - Enum constant in enum class es.imim.DISGENET.Status
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.VariantEnrichmentParams
getPValueThreshold() - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams
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 class 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(SetCurrentNetworkEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel
handleEvent(SetCurrentNetworkEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentNetworkListener
handleEvent(RowsSetEvent) - Method in class es.imim.DISGENET.internal.enrichment.EnrichmentCytoPanel
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() - Method in class es.imim.DISGENET.internal.enrichment.ShowEnrichmentPanelTaskFactory
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(CyNetworkView) - Method in class es.imim.DISGENET.internal.enrichment.VariantEnrichmentTaskFactory
isReady(View<CyEdge>, CyNetworkView) - Method in class es.imim.DISGENET.internal.linkout.LinkoutEdgeTaskFactory
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<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
NETWORK_ERROR - Enum constant in enum class es.imim.DISGENET.Status
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() - Method in 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

## 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) - 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
setParams(GuiParameters<Object, Object>) - Method in class es.imim.DISGENET.gui.MainPanel
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.VariantEnrichmentParams
setPValueThreshold(double) - Method in class es.imim.DISGENET.internal.automation.parameters.GeneEnrichmentParams
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
SQL_ERROR - Enum constant in enum class es.imim.DISGENET.Status
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 Class 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
SUCCESS - Enum constant in enum class es.imim.DISGENET.Status
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[], 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[], Color[], int, int, Integer...) - 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, Color[], int, int, Integer...) - 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
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 class es.imim.DISGENET.Status
  Returns the enum constant of this class with the specified name.
values() - Static method in enum class es.imim.DISGENET.Status
  Returns an array containing the constants of this enum class, 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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