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

A

AboutMenuAction - Class in es.imim.DisGeNET.internal

Creates a new menu item under Apps menu section.

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

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.CreateVisualStyleAction

DOCUMENT ME!

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.NetAction

This method is called when the user clicks create network.

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

addColumn(String) - Method in class es.imim.DisGeNET.database.Query

addCondition(String) - Method in class es.imim.DisGeNET.database.Query

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

addTable(String) - Method in class es.imim.DisGeNET.database.Query

AnimatedLabel - Class in es.imim.DisGeNET.search

AnimatedLabel(String, int) - Constructor for class es.imim.DisGeNET.search.AnimatedLabel

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

B

build() - Method in class es.imim.DisGeNET.database.Query

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

Generic function to creat 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(ArrayList<String>, ArrayList<String>, String, GuiParameters) - Method in class es.imim.DisGeNET.network.NetworkBuilder

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

C

cancel() - Method in class es.imim.DisGeNET.tool.DownloadDBTask

changeDBFolder() - Method in interface es.imim.DisGeNET.database.DatabaseManager

changeDBFolder()

changeDBFolder() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

changeDBFolder() - Method in interface es.imim.DisGeNET.DatabaseManager

changeDBFolder()

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

checkDBFile() - Method in interface es.imim.DisGeNET.database.DatabaseManager

checkDBFile()

checkDBFile() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

checkDBFile() - Method in interface es.imim.DisGeNET.DatabaseManager

checkDBFile()

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

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

close() - Method in interface es.imim.DisGeNET.database.DatabaseManager

close()

close() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

close()

close() - Method in class es.imim.DisGeNET.database.QueryExecutor

close() - Method in interface es.imim.DisGeNET.DatabaseManager

close()

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

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

construct() - Method in class es.imim.DisGeNET.tool.SwingWorker

Compute the value to be returned by the get method.

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

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

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.ApplyCustomLayoutTaskFactory

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

CreateVisualStyleAction - Class in es.imim.DisGeNET.internal

CreateVisualStyleAction(CyApplicationManager, VisualMappingManager, VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory) - Constructor for class es.imim.DisGeNET.internal.CreateVisualStyleAction

CustomLayout - Class in es.imim.DisGeNET.internal

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

Creates a new MyLayout object.

CustomLayoutContext - Class in es.imim.DisGeNET.internal

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

Class implements all queries to create networks

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

DatabaseManager - Interface in es.imim.DisGeNET.database

This interface handles the database connection for all database functions

DatabaseManager() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

DatabaseManager - Interface in es.imim.DisGeNET

This interface handles the database connection for all database functions

DatabaseManagerImpl - Class in es.imim.DisGeNET.database

Implementation of the DatabaseManager to handle db connection If SQLite DB file cannot be found in chosen folder be it will automatically downloaded from our server

deleteDirectory(File) - Static method in class es.imim.DisGeNET.tool.DownloadDBTask

deleteFile(String) - Static method in class es.imim.DisGeNET.tool.DownloadDBTask

deleteFile(String) - Static method in class es.imim.DisGeNET.tool.FileDownloadTools

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

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

DiseaseColourMapping - Class in es.imim.DisGeNET

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

DiseaseColourMapping() - Constructor for class es.imim.DisGeNET.DiseaseColourMapping

DisGeNetCyTablesTask - Class in es.imim.DisGeNET.internal

DisGeNetCyTablesTask() - Constructor for class es.imim.DisGeNET.internal.DisGeNetCyTablesTask

DisGeNETCytoPanel - Class in es.imim.DisGeNET.internal

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

DisGeNETVisualStyle - Class in es.imim.DisGeNET.network

A visual style for the DisGeNET Plugin set the visual style of different node size and color.

DisGeNETVisualStyle(String) - Constructor for class es.imim.DisGeNET.network.DisGeNETVisualStyle

Constructor for the visual style

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

DownloadDBTask - Class in es.imim.DisGeNET.tool

helper class to download extract the database file

DownloadDBTask(String, String, String) - Constructor for class es.imim.DisGeNET.tool.DownloadDBTask

E

es.imim.DisGeNET - package es.imim.DisGeNET

es.imim.DisGeNET.database - package es.imim.DisGeNET.database

es.imim.DisGeNET.gui - package es.imim.DisGeNET.gui

es.imim.DisGeNET.internal - package es.imim.DisGeNET.internal

es.imim.DisGeNET.network - package es.imim.DisGeNET.network

es.imim.DisGeNET.search - package es.imim.DisGeNET.search

es.imim.DisGeNET.tool - package es.imim.DisGeNET.tool

executeQuery(Statement, String) - Method in class es.imim.DisGeNET.database.QueryExecutor

Executes an SQL query.

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

expandGeneDiseaseNet(GuiParameters, ArrayList<String>, boolean, boolean) - Method in class es.imim.DisGeNET.network.NetworkBuilder

F

FileDownloadTools - Class in es.imim.DisGeNET.tool

general helper class to download files and extract them; used to download database file

FileDownloadTools() - Constructor for class es.imim.DisGeNET.tool.FileDownloadTools

fillSearchBox(ArrayList<String>) - Method in class es.imim.DisGeNET.search.MemComboBox

finished() - Method in class es.imim.DisGeNET.tool.SwingWorker

Called on the event dispatching thread (not on the worker thread) after the construct method has returned.

Fusion_Gene - Static variable in class es.imim.DisGeNET.gui.GuiParameters

G

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

GENE_DIS_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_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

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

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

geneDisCheckBoxChanged(PropertyChangeEvent) - Method in class es.imim.DisGeNET.gui.MainPanel

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

get() - Method in class es.imim.DisGeNET.tool.SwingWorker

Return the value created by the construct method.

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

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

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

getAssociatedDiseases(String, String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getAssociatedDiseases(String, String, String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getAssociatedDiseases(String, String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getAssociatedDiseases(String, String, String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getAssociatedGeneNames(String, String, String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getAssociatedGeneNames(String, String, String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

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

getCon() - Method in interface es.imim.DisGeNET.database.DatabaseManager

getCon()

getCon() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

getCon()

getCon() - Method in interface es.imim.DisGeNET.DatabaseManager

getCon()

getCurrentSelectedDisClass() - Method in class es.imim.DisGeNET.gui.GuiParameters

getCurrentSelectedSource() - Method in class es.imim.DisGeNET.gui.GuiParameters

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

getDatabaseHost() - Method in interface es.imim.DisGeNET.database.DatabaseManager

getDatabaseHost() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

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() - Method in interface es.imim.DisGeNET.database.Database

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

getDiseaseClassForAllDiseases(GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getDiseaseClassForAllDiseases(GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getDiseaseClassForAllGenes(String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getDiseaseClassForAllGenes(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getDiseaseClassId(String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getDiseaseClassId(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getDiseaseColourMapping() - Method in class es.imim.DisGeNET.DiseaseColourMapping

getDiseaseColourNameMapping() - Method in class es.imim.DisGeNET.DiseaseColourMapping

getDiseaseId(String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getDiseaseId(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getDiseaseIdWildCard(String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getDiseaseIdWildCard(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

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

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

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

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

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

getDisGeNETvisualStyle() - Method in class es.imim.DisGeNET.gui.GuiParameters

getDisProjDisClass() - Method in class es.imim.DisGeNET.gui.GuiParameters

getDisProjSource() - Method in class es.imim.DisGeNET.gui.GuiParameters

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

getEdgeAttributes(String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getEdgeAttributes(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getExpandedGeneDiseaseNetwork(GuiParameters, ArrayList<String>) - Method in interface es.imim.DisGeNET.database.Database

getExpandedGeneDiseaseNetwork(GuiParameters, ArrayList<String>) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getFile(String, String, TaskMonitor) - Static method in class es.imim.DisGeNET.tool.DownloadDBTask

getFile(String, String) - Static method in class es.imim.DisGeNET.tool.FileDownloadTools

getGenDis_DisClass() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGenDisAssociationType() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGenDisDisSearchText() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGenDisGenSearchText() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGenDisLowScore() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGenDisSource() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGenDisUpScore() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGeneAttributes(String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

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

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

getGeneAttributes(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

getGeneDiseaseList(GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getGeneDiseaseList(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, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getGeneId(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

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

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

getGeneIdWildCard(String, GuiParameters) - Method in interface es.imim.DisGeNET.database.Database

getGeneIdWildCard(String, GuiParameters) - Method in class es.imim.DisGeNET.database.DatabaseImpl

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

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

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

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

getGenProjDisClass() - Method in class es.imim.DisGeNET.gui.GuiParameters

getGenProjSource() - Method in class es.imim.DisGeNET.gui.GuiParameters

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

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

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

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

getInstance()

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

getManager() - Method in class es.imim.DisGeNET.database.DatabaseImpl

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

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.

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

getRemoteFileSize(String) - Static method in class es.imim.DisGeNET.tool.DownloadDBTask

getRemoteFileSize(String) - Static method in class es.imim.DisGeNET.tool.FileDownloadTools

getRunning() - Method in class es.imim.DisGeNET.search.AnimatedLabel

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

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

getString() - Method in enum es.imim.DisGeNET.gui.GuiParameters.associationValues

getString() - Method in enum es.imim.DisGeNET.gui.GuiParameters.diseaseClassValues

getString() - Method in enum es.imim.DisGeNET.gui.GuiParameters.sourceValues

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

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

getTitle() - Method in class es.imim.DisGeNET.tool.DownloadDBTask

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

getValue() - Method in class es.imim.DisGeNET.tool.SwingWorker

Get the value produced by the worker thread, or null if it hasn't been constructed yet.

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

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

this class handles all the settings from the gui panel and is used to hand them over to the functions that create the networks

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

GuiParameters.associationValues - Enum in es.imim.DisGeNET.gui

GuiParameters.diseaseClassValues - Enum in es.imim.DisGeNET.gui

GuiParameters.sourceValues - Enum in es.imim.DisGeNET.gui

GuiProps - Class in es.imim.DisGeNET.gui

this class simply holds all strings used in gui panel

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

H

halt() - Method in class es.imim.DisGeNET.tool.DownloadDBTask

HelperFunctions - Class in es.imim.DisGeNET.tool

DisGeNET: A Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks Copyright (C) 2010 Michael Rautschka, Anna Bauer-Mehren This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

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

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

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

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

functions to sort string lists by line length

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

I

init() - Method in interface es.imim.DisGeNET.database.DatabaseManager

init()

init() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

init()

init() - Method in interface es.imim.DisGeNET.DatabaseManager

init()

initAdditionalStyleAttributes(GuiParameters) - Method in class es.imim.DisGeNET.network.NetworkBuilder

initCalculators() - Method in class es.imim.DisGeNET.network.DisGeNETVisualStyle

Reinitializes the calculators.

interrupt() - Method in class es.imim.DisGeNET.tool.SwingWorker

A new method that interrupts the worker thread.

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

isInterrupted() - Method in class es.imim.DisGeNET.internal.DisGeNetCyTablesTask

isInterrupted() - Static method in class es.imim.DisGeNET.tool.DownloadDBTask

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

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

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

K

keyReleased(KeyEvent) - Method in class es.imim.DisGeNET.search.MemComboAgent

L

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

M

m_browser - Variable in class es.imim.DisGeNET.search.SearchField

m_comboBox - Variable in class es.imim.DisGeNET.search.MemComboAgent

m_editor - Variable in class es.imim.DisGeNET.search.MemComboAgent

m_icons - Variable in class es.imim.DisGeNET.search.AnimatedLabel

m_index - Variable in class es.imim.DisGeNET.search.AnimatedLabel

m_isRunning - Variable in class es.imim.DisGeNET.search.AnimatedLabel

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

m_runner - Variable in class es.imim.DisGeNET.search.SearchField

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

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(DisGeNETVisualStyle, StartDisGeNETMenuAction) - Constructor for class es.imim.DisGeNET.gui.MainPanel

Creates new MainPanel

markNodes(String, String) - Method in class es.imim.DisGeNET.network.NetworkBuilder

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

MemComboAgent - Class in es.imim.DisGeNET.search

MemComboAgent(MemComboBox) - Constructor for class es.imim.DisGeNET.search.MemComboAgent

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

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

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

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

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

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

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, Integer) - 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

NetworkBuilder - Class in es.imim.DisGeNET.network

Main class for - creating the networks - creating networks with edge attributes - creating additional attributes - handle the progress listeners - retrieve all node names from current net for search - marking nodes from search

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

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

P

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

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

Q

Query - Class in es.imim.DisGeNET.database

Query() - Constructor for class es.imim.DisGeNET.database.Query

QueryExecutor - Class in es.imim.DisGeNET.database

This class defines the executeQuery() method, which is similar to Statement.executeQuery() method.

QueryExecutor() - Constructor for class es.imim.DisGeNET.database.QueryExecutor

R

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

run() - Method in class es.imim.DisGeNET.database.QueryExecutor

run(TaskMonitor) - Method in class es.imim.DisGeNET.internal.DisGeNetCyTablesTask

run() - Method in class es.imim.DisGeNET.search.AnimatedLabel

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

run(TaskMonitor) - Method in class es.imim.DisGeNET.tool.DownloadDBTask

runQuery(String) - Method in interface es.imim.DisGeNET.database.Database

runQuery(String) - Method in class es.imim.DisGeNET.database.DatabaseImpl

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

setDatabaseLocal() - Method in interface es.imim.DisGeNET.database.DatabaseManager

setDatabaseLocal() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

setDatabaseRemote() - Method in interface es.imim.DisGeNET.database.DatabaseManager

setDatabaseRemote() - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

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

setDisGeNETvisualStyle(DisGeNETVisualStyle) - Method in class es.imim.DisGeNET.gui.GuiParameters

setDisProjDisClass(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setDisProjSource(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

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

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

setGenDis_DisClass(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenDisAssociationType(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenDisDisSearchText(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenDisGenSearchText(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenDisLowScore(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenDisSource(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenDisUpScore(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenProjDisClass(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

setGenProjSource(String) - Method in class es.imim.DisGeNET.gui.GuiParameters

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

setGroupBy(String) - Method in class es.imim.DisGeNET.database.Query

setMySQLparameters(String, String, String, String) - Method in interface es.imim.DisGeNET.database.DatabaseManager

setMySQLparameters(String, String, String, String) - Method in class es.imim.DisGeNET.database.DatabaseManagerImpl

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

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

setParams(GuiParameters) - Method in class es.imim.DisGeNET.gui.MainPanel

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

setRunning(boolean) - Method in class es.imim.DisGeNET.search.AnimatedLabel

setTaskMonitor(TaskMonitor) - Method in class es.imim.DisGeNET.internal.DisGeNetCyTablesTask

SOURCE_OPTIONS - Static variable in class es.imim.DisGeNET.gui.GuiProps

start(BundleContext) - Method in class es.imim.DisGeNET.internal.CyActivator

start() - Method in class es.imim.DisGeNET.tool.SwingWorker

Start the worker thread.

StartDisGeNETMenuAction - Class in es.imim.DisGeNET.internal

Creates a new menu item under Apps menu section.

StartDisGeNETMenuAction(CyApplicationManager, CyServiceRegistrar, String) - Constructor for class es.imim.DisGeNET.internal.StartDisGeNETMenuAction

Status - Enum in es.imim.DisGeNET

just some error messages; only used for DB connection so far

SwingWorker - Class in es.imim.DisGeNET.tool

This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.

SwingWorker() - Constructor for class es.imim.DisGeNET.tool.SwingWorker

Start a thread that will call the construct method and then exit.

U

unpackFile(String, String) - Static method in class es.imim.DisGeNET.tool.DownloadDBTask

unpackFile(String, String) - Static method in class es.imim.DisGeNET.tool.FileDownloadTools

unregister() - Method in class es.imim.DisGeNET.internal.StartDisGeNETMenuAction

unregister_disgenet_panel(DisGeNETCytoPanel) - Method in class es.imim.DisGeNET.internal.CyActivator

untarFile(String, String) - Static method in class es.imim.DisGeNET.tool.DownloadDBTask

untarFile(String, String) - Static method in class es.imim.DisGeNET.tool.FileDownloadTools

update(String) - Method in class es.imim.DisGeNET.search.MemComboBox

V

valueOf(String) - Static method in enum es.imim.DisGeNET.gui.GuiParameters.associationValues

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum es.imim.DisGeNET.gui.GuiParameters.diseaseClassValues

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum es.imim.DisGeNET.gui.GuiParameters.sourceValues

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum es.imim.DisGeNET.Status

Returns the enum constant of this type with the specified name.

values() - Static method in enum es.imim.DisGeNET.gui.GuiParameters.associationValues

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum es.imim.DisGeNET.gui.GuiParameters.diseaseClassValues

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum es.imim.DisGeNET.gui.GuiParameters.sourceValues

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum es.imim.DisGeNET.Status

Returns an array containing the constants of this enum type, in the order they are declared.

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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