Index
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
All Classes|All Packages|Constant Field Values|Serialized Form