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|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
 
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.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.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
 
AutomationParams - Interface in es.imim.DISGENET.internal.automation.parameters
 
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
 
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.
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
 
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
 
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(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
 
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
 
EnrichmentTable - Class in es.imim.DISGENET.internal.tables
 
EnrichmentTable(CyTable, String[]) - Constructor for class es.imim.DISGENET.internal.tables.EnrichmentTable
 
enrichmentTypeIds - Static variable in class es.imim.DISGENET.validation.ParametersValidation
 
enrichmentUniverse - Static variable in class es.imim.DISGENET.validation.ParametersValidation
 
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.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.
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
 
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
 
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.
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
 
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
 
getCallResult() - Method in class es.imim.DISGENET.tool.OperationResult
 
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
 
getComponent() - Method in class es.imim.DISGENET.gui.DisColorLegendPanel
 
getComponent() - Method in class es.imim.DISGENET.internal.DisGeNETCytoPanel
 
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
 
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
 
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
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
 
getDisGeNETdb() - Method in class es.imim.DISGENET.internal.CyActivator
 
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
 
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
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
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
 
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
 
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
 
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
 
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
 
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.
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
 
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.network.NetTaskObserver
 
getResults(Class<? extends R>) - Method in class es.imim.DISGENET.internal.automation.NetTaskAutomation
 
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
 
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
 
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
 
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
 
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
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(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

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.
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
 
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(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
 
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.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
 
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
 
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
 

O

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
 
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
 

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
 
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.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

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

T

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
 

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

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
 
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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