- ABOUT_DIALOG_ABOUT_TAB_TITLE - Static variable in interface org.mdanderson.biostat.util.DefaultAboutDialogKeys
-
- ABOUT_DIALOG_CONTACT_EMAIL_ADDRESS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_EMAIL_ADDRESS_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_EMAIL_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_PANEL_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_TAB_TITLE - Static variable in interface org.mdanderson.biostat.util.DefaultAboutDialogKeys
-
- ABOUT_DIALOG_CONTACT_USPS_ADDRESS_CITY_STATE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_USPS_ADDRESS_NAME - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_USPS_ADDRESS_STREET - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_USPS_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_WEB_ADDRESS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_WEB_ADDRESS_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CONTACT_WEB_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CREDITS_COLLABORATOR_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CREDITS_DEVELOPER_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CREDITS_RESEARCHER_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_DIALOG_CREDITS_TAB_TITLE - Static variable in interface org.mdanderson.biostat.util.DefaultAboutDialogKeys
-
- ABOUT_DIALOG_OK_BUTTON_LABEL - Static variable in interface org.mdanderson.biostat.util.DefaultAboutDialogKeys
-
- ABOUT_DIALOG_OK_BUTTON_TOOLTIP - Static variable in interface org.mdanderson.biostat.util.DefaultAboutDialogKeys
-
- ABOUT_DIALOG_SYSINFO_TAB_TITLE - Static variable in interface org.mdanderson.biostat.util.DefaultAboutDialogKeys
-
- ABOUT_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_MENUITEM_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_MENUITEM_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_MENUITEM_MNEMONIC - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_MENUITEM_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- ABOUT_PANEL_APP_NAME_VERSION_DESCRIPTION - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_APP_NAME_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_BANNER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_BANNER_LABEL - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_COPYRIGHT_DESCRIPTION - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_COPYRIGHT_LABEL - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_LEGALITIES_DESCRIPTION - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_LEGALITIES_LABEL - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_RELEASE_DATE_DESCRIPTION - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- ABOUT_PANEL_RELEASE_DATE_LABEL - Static variable in interface org.mdanderson.biostat.util.DefaultAboutPanelKeys
-
- AboutPanel - Interface in org.mdanderson.biostat.util
-
AboutPanel - Interface for panel settings.
- aboutPanel - Variable in class org.mdanderson.biostat.util.DefaultAboutDialog
-
- aboutPanel - Variable in class org.mdanderson.biostat.util.DefaultSplashScreen
-
- AbstractAboutDialog - Class in org.mdanderson.biostat.util
-
AbstractAboutDialog - Creates a generic ABOUT dialog.
- AbstractAboutDialog(String) - Constructor for class org.mdanderson.biostat.util.AbstractAboutDialog
-
Class constructor specifying title
- AbstractAboutDialog(Frame, String) - Constructor for class org.mdanderson.biostat.util.AbstractAboutDialog
-
Class constructor specifying owner and title
- AbstractAboutPanel - Class in org.mdanderson.biostat.util
-
AbstractAboutPanel - Creates an abstract ABOUT panel
- AbstractAboutPanel() - Constructor for class org.mdanderson.biostat.util.AbstractAboutPanel
-
Class constructor
- AbstractDialog - Class in org.mdanderson.biostat.util
-
AbstractDialog - Creates an abstract dialog class
- AbstractDialog(String) - Constructor for class org.mdanderson.biostat.util.AbstractDialog
-
Class constructor specifying title
- AbstractDialog(Frame, String) - Constructor for class org.mdanderson.biostat.util.AbstractDialog
-
Class constructor specifying owner and title
- AbstractStateMonitor - Class in org.mdanderson.biostat.util
-
AbstractStateMonitor - Responsible for enabling or disabling GUI components
whenever application state changes.
- AbstractStateMonitor() - Constructor for class org.mdanderson.biostat.util.AbstractStateMonitor
-
Class constructor
- accept(File) - Method in class org.mdanderson.biostat.geneclust.GCFileFilter
-
Tests whether or not the specified abstract pathname should be
included in a pathname list.
- accepts(Object) - Static method in class org.mdanderson.biostat.util.NonWhitespaceValidator
-
Convenience function that determines whether the data is blank without
the caller having to have an instance of this class available.
- accepts(Object) - Static method in class org.mdanderson.biostat.util.NumericValidator
-
Convenience function that determines the validity of numeric data
without the caller having to have an instance of this class available.
- accepts(Object) - Static method in class org.mdanderson.biostat.util.PathnameValidator
-
Convenience function that determines the validity of pathname data
without the caller having to have an instance of this class available.
- actionArea - Variable in class org.mdanderson.biostat.util.AbstractDialog
-
- activate(Component, Object) - Method in class org.mdanderson.biostat.util.AbstractStateMonitor
-
Returns the data that was checked
- active - Variable in class org.mdanderson.biostat.util.AbstractStateMonitor
-
Maps states to components
- addAboutPanelItems() - Method in class org.mdanderson.biostat.geneclust.GCAboutPanel
-
Overrides the parent routine to place things differently.
- addAboutPanelItems() - Method in class org.mdanderson.biostat.util.AbstractAboutPanel
-
Adds items to about panel.
- addAboutPanelItems() - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Adds items to about panel.
- addHyperlinkListener(HyperlinkListener) - Method in interface org.mdanderson.biostat.util.HyperlinkSource
-
Adds a hyperlink listener for notification of any changes,
for example when a link is selected and entered.
- addHyperlinkListener(HyperlinkListener) - Method in class org.mdanderson.biostat.util.UrlLabel
-
Adds a hyperlink listener for notification of any changes,
for example when a link is selected and entered.
- addLayoutComponent(String, Component) - Method in class org.mdanderson.biostat.util.VerticalFlowLayout
-
If the layout manager uses a per-component string, adds the component
to the layout, associating it with the string argument.
- addState(Object) - Method in class org.mdanderson.biostat.util.AbstractStateMonitor
-
Adds a state to the list of monitored states and updates
:TODO: , if it doesn't already exist
- addStatusListener(StatusListener) - Method in class org.mdanderson.biostat.util.ContentTextArea
-
Adds its non whitespace validator as a status listener for
notification of state of data changes
- addStatusListener(StatusListener) - Method in class org.mdanderson.biostat.util.ContentTextField
-
Adds its non whitespace validator as a status listener for
notification of state of data changes
- addStatusListener(StatusListener) - Method in class org.mdanderson.biostat.util.NumericTextField
-
Adds its numeric validator as a status listener for
notification of state of data changes
- addStatusListener(StatusListener) - Method in class org.mdanderson.biostat.util.PathnameTextField
-
Adds its pathname validator as a status listener for
notification of state of data changes
- addStatusListener(StatusListener) - Method in interface org.mdanderson.biostat.util.StatusSource
-
Adds a status listener for notification of state of data changes
- addStatusListener(StatusListener) - Method in class org.mdanderson.biostat.util.ValidationAdapter
-
Adds a status listener for notification of state of data changes
- addStatusListener(StatusListener) - Method in interface org.mdanderson.biostat.util.Validator
-
Adds a status listener for notification of state of data changes
- addTitledBorder(JComponent, String) - Static method in class org.mdanderson.biostat.util.GuiUtil
-
Adds a titled border to a container
- AMPLITUDE_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- AMPLITUDE_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- AMPLITUDE_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- AMPLITUDE_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- AMPLITUDE_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- AMPLITUDE_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- AMPLITUDE_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_COPYRIGHT - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_LEGALITIES - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_NAME - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_RELEASE_DATE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_USAGE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_VERSION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- APPLICATION_WINDOW_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- appNameVersionLine - Variable in class org.mdanderson.biostat.util.DefaultAboutPanel
-
- ASCII_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
-
- AutoSelectEventHandler - Class in org.mdanderson.biostat.util
-
AutoSelectEventHandler - Responds to focus events.
- AutoSelectEventHandler() - Constructor for class org.mdanderson.biostat.util.AutoSelectEventHandler
-
- Callback - Class in org.mdanderson.biostat.util
-
Callback- Callback invocation.
- Callback(ICallback) - Constructor for class org.mdanderson.biostat.util.Callback
-
Class constructor specifying callback to be sent.
- centerOnParent() - Method in class org.mdanderson.biostat.geneclust.SimulationDialog
-
Centers the dialog on its parent
- centerOnParent() - Method in class org.mdanderson.biostat.util.AbstractDialog
-
Centers this dialog on its parent
- centerOnScreen() - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Centers the splashscreen in the middle of the screen
- changedUpdate(DocumentEvent) - Method in class org.mdanderson.biostat.util.ValidationAdapter
-
Gives notification that an attribute or set of attributes changed
- changedUpdate(DocumentEvent) - Method in interface org.mdanderson.biostat.util.Validator
-
Gives notification that an attribute or set of attributes changed
- CHOOSE_CLASSIFICATION_FILE_SELECTION_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CHOOSE_DATA_FILE_SELECTION_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CHOOSE_FILE_SELECTION_DIALOG_OK_BUTTON_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CHOOSE_FILE_SELECTION_DIALOG_OK_BUTTON_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
-
- CLASSIFICATION_FILENAME_CHOOSER_BUTTON_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILENAME_CHOOSER_BUTTON_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILENAME_CHOOSER_BUTTON_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILENAME_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILENAME_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILENAME_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILENAME_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- CLASSIFICATION_FILENAME_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- classificationFileName - Variable in class org.mdanderson.biostat.geneclust.Simulation
-
- close() - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Closes the splashscreen and releases all native screen resources
- components - Variable in class org.mdanderson.biostat.util.AbstractStateMonitor
-
Maps components to activity count
- CONFIG_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
-
- contactPanel - Variable in class org.mdanderson.biostat.util.DefaultAboutDialog
-
- ContentTextArea - Class in org.mdanderson.biostat.util
-
ContentTextArea - Allows non whitespace validation of a textfield.
- ContentTextArea() - Constructor for class org.mdanderson.biostat.util.ContentTextArea
-
Class constructor
- ContentTextArea(String) - Constructor for class org.mdanderson.biostat.util.ContentTextArea
-
Class constructor specifying text
- ContentTextArea(int, int) - Constructor for class org.mdanderson.biostat.util.ContentTextArea
-
Class constructor specifying number of rows and columns
- ContentTextArea(String, int, int) - Constructor for class org.mdanderson.biostat.util.ContentTextArea
-
Class constructor specifying text, and number of rows and columns
- ContentTextField - Class in org.mdanderson.biostat.util
-
ContentTextField - Allows non whitespace validation of a textfield.
- ContentTextField() - Constructor for class org.mdanderson.biostat.util.ContentTextField
-
Class constructor
- ContentTextField(String) - Constructor for class org.mdanderson.biostat.util.ContentTextField
-
Class constructor specifying text
- ContentTextField(int) - Constructor for class org.mdanderson.biostat.util.ContentTextField
-
Class constructor specifying number of columns
- ContentTextField(String, int) - Constructor for class org.mdanderson.biostat.util.ContentTextField
-
Class constructor specifying text and number of columns
- controlArea - Variable in class org.mdanderson.biostat.util.AbstractDialog
-
- copyrightLine - Variable in class org.mdanderson.biostat.util.DefaultAboutPanel
-
- createAboutPanel() - Method in class org.mdanderson.biostat.geneclust.GCAboutDialog
-
Creates the banner panel displayed as the main pane
in the tabbed pane.
- createAboutPanel() - Method in class org.mdanderson.biostat.util.AbstractAboutDialog
-
Creates the banner panel displayed as the main pane
in the tabbed pane.
- createAboutPanel() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Creates the banner panel displayed as the main pane
in the tabbed pane.
- createActionArea() - Method in class org.mdanderson.biostat.util.AbstractDialog
-
Creates the dialog's action area, where user initiates action on input.
- createActionArea() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Creates the dialog's action area, where user initiates action on input.
- createBannerPanel() - Method in class org.mdanderson.biostat.geneclust.GCAboutPanel
-
Overrides the parent routine to add a microarray border under
the banner name.
- createBannerPanel() - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Creates a pane for displaying banner
- createButtonPane() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Implements the dialog action area.
- createContactPanel() - Method in class org.mdanderson.biostat.geneclust.GCAboutDialog
-
Creates a pane for displaying contact information
- createContactPanel() - Method in class org.mdanderson.biostat.util.AbstractAboutDialog
-
Creates a pane for displaying contact information
- createContactPanel() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Creates a pane for displaying contact information
- createControlArea() - Method in class org.mdanderson.biostat.util.AbstractDialog
-
Creates the dialog's control area, where user input is gathered.
- createControlArea() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Creates the dialog's control area, where user input is gathered.
- createCreditsPanel() - Method in class org.mdanderson.biostat.geneclust.GCAboutDialog
-
Creates a pane for displaying developer credits, et cetera.
- createCreditsPanel() - Method in class org.mdanderson.biostat.util.AbstractAboutDialog
-
Creates a pane for displaying developer credits, et cetera.
- createCreditsPanel() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Creates a pane for displaying developer credits, et cetera.
- createImagePanel() - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Creates a pane for displaying image
- createInfoPanel() - Method in class org.mdanderson.biostat.geneclust.GCAboutPanel
-
Overrides the parent routine to change the labels.
- createInfoPanel() - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Creates a pane for displaying application information
- createMenuItem(String, String, String, String, ActionListener) - Static method in class org.mdanderson.biostat.util.GuiUtil
-
Creates a generic menu item
- createNoticeDialog(Container, String, String, long) - Method in class org.mdanderson.biostat.util.ExtendedOptionPane
-
- createRadioButtonMenuItem(String, String, String, String, ActionListener) - Static method in class org.mdanderson.biostat.util.GuiUtil
-
Creates a radiobutton menu item
- createStatusPanel() - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Creates a pane for displaying status information
- createSysInfoPanel() - Method in class org.mdanderson.biostat.util.AbstractAboutDialog
-
Creates a pane for displaying information about the
Java Runtime Environment.
- createSysInfoPanel() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Creates a System Information panel that provides information
about the Java Runtime Environment.
- createTabbedPane() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Implements the dialog control area.
- creditsPanel - Variable in class org.mdanderson.biostat.util.DefaultAboutDialog
-
- CSV_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
-
- DefaultAboutDialog - Class in org.mdanderson.biostat.util
-
DefaultAboutDialog - Creates a generic ABOUT dialog.
- DefaultAboutDialog(String) - Constructor for class org.mdanderson.biostat.util.DefaultAboutDialog
-
Class constructor specifying title
- DefaultAboutDialog(Frame, String) - Constructor for class org.mdanderson.biostat.util.DefaultAboutDialog
-
Class constructor specifying owner and title
- DefaultAboutDialogKeys - Interface in org.mdanderson.biostat.util
-
DefaultAboutDialogKeys - Interface for property keys.
- DefaultAboutPanel - Class in org.mdanderson.biostat.util
-
DefaultAboutPanel - Creates a generic ABOUT panel
- DefaultAboutPanel() - Constructor for class org.mdanderson.biostat.util.DefaultAboutPanel
-
Class constructor
- DefaultAboutPanel(byte[]) - Constructor for class org.mdanderson.biostat.util.DefaultAboutPanel
-
Class constructor specifying image buffer
- DefaultAboutPanel(String) - Constructor for class org.mdanderson.biostat.util.DefaultAboutPanel
-
Class constructor specifying image file name
- DefaultAboutPanel(URL) - Constructor for class org.mdanderson.biostat.util.DefaultAboutPanel
-
Class constructor specifying image URL
- DefaultAboutPanel(ImageIcon) - Constructor for class org.mdanderson.biostat.util.DefaultAboutPanel
-
Class constructor specifying image icon
- DefaultAboutPanelKeys - Interface in org.mdanderson.biostat.util
-
DefaultAboutPanelKeys - Interface for property keys.
- DefaultSplashScreen - Class in org.mdanderson.biostat.util
-
DefaultSplashScreen - Creates a generic splash screen for use at
application startup
- DefaultSplashScreen(String, Frame) - Constructor for class org.mdanderson.biostat.util.DefaultSplashScreen
-
Class constructor specifying image filename and frame
- DefaultSplashScreen(String, Frame, long) - Constructor for class org.mdanderson.biostat.util.DefaultSplashScreen
-
Class constructor specifying image filename, frame, and delay
- DefaultSplashScreen(ImageIcon, Frame) - Constructor for class org.mdanderson.biostat.util.DefaultSplashScreen
-
Class constructor specifying image and frame
- DefaultSplashScreen(ImageIcon, Frame, long) - Constructor for class org.mdanderson.biostat.util.DefaultSplashScreen
-
Class constructor specifying image, frame, and delay
- DefaultSplashScreen(AboutPanel, Frame, long) - Constructor for class org.mdanderson.biostat.util.DefaultSplashScreen
-
Class constructor specifying about panel, frame, and delay
- DefaultStreamMonitor - Class in org.mdanderson.biostat.util
-
DefaultStreamMonitor - Generic application stream monitoring
- DefaultStreamMonitor(InputStream, OutputStream) - Constructor for class org.mdanderson.biostat.util.DefaultStreamMonitor
-
Class constructor specifying input stream, and output stream
- DefaultStreamMonitorKeys - Interface in org.mdanderson.biostat.util
-
DefaultStreamMonitorKeys - Interface for property keys.
- DEGREES_FREEDOM_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DEGREES_FREEDOM_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DEGREES_FREEDOM_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DEGREES_FREEDOM_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DEGREES_FREEDOM_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DEGREES_FREEDOM_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DEGREES_FREEDOM_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DEMO_DATA_TAB_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- dialog - Variable in class org.mdanderson.biostat.geneclust.SProcess
-
- dialog - Variable in class org.mdanderson.biostat.util.ExtendedOptionPane
-
- disableAudio() - Method in class org.mdanderson.biostat.util.FilterAdapter
-
Disable audio feedback
- disableEcho() - Method in class org.mdanderson.biostat.util.DefaultStreamMonitor
-
Disable echo of processed input from external process to 'stdout' stream.
- display() - Method in class org.mdanderson.biostat.geneclust.GeneClust
-
Displays the user interface
- display() - Method in class org.mdanderson.biostat.util.AbstractAboutDialog
-
Displays the dialog on the screen, centered on its parent
- display() - Method in class org.mdanderson.biostat.util.AbstractDialog
-
Displays the dialog on the screen
- display() - Method in class org.mdanderson.biostat.util.DefaultAboutDialog
-
Displays the dialog on the screen, centered on its parent
- display() - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Displays the splashscreen on the screen, centered on its parent
- DISPLAY_BUTTON_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_BUTTON_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_BUTTON_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_DATA_MATRIX_CHECKBOX_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_DATA_MATRIX_CHECKBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_DATA_MATRIX_CHECKBOX_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_DATA_MATRIX_CHECKBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_GENES_GRAPH_CHECKBOX_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_GENES_GRAPH_CHECKBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_GENES_GRAPH_CHECKBOX_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_GENES_GRAPH_CHECKBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_PANEL_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SAMPLES_GRAPH_CHECKBOX_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SAMPLES_GRAPH_CHECKBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SAMPLES_GRAPH_CHECKBOX_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SAMPLES_GRAPH_CHECKBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SHAVING_CLUSTERS_CHECKBOX_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SHAVING_CLUSTERS_CHECKBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SHAVING_CLUSTERS_CHECKBOX_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- DISPLAY_SHAVING_CLUSTERS_CHECKBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- displayAndWait() - Method in class org.mdanderson.biostat.geneclust.SimulationDialog
-
Displays this model dialog.
- displayError(String) - Method in class org.mdanderson.biostat.geneclust.GeneClust
-
Displays error message to user
- displayErrorDialog(Container, String, String) - Static method in class org.mdanderson.biostat.util.GuiUtil
-
Displays an error message dialog
- displayInfoDialog(Container, String, String) - Static method in class org.mdanderson.biostat.util.GuiUtil
-
Displays an information message dialog
- displayNoticeDialog(Container, String, String, long) - Static method in class org.mdanderson.biostat.util.GuiUtil
-
- GAP_TOLERANCE_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- GAP_TOLERANCE_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- GAP_TOLERANCE_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- GAP_TOLERANCE_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- GAP_TOLERANCE_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- GAP_TOLERANCE_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- GAP_TOLERANCE_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- gapTolerance - Variable in class org.mdanderson.biostat.geneclust.Simulation
-
- GCAboutDialog - Class in org.mdanderson.biostat.geneclust
-
GCAboutDialog - Creates an ABOUT dialog for this application.
- GCAboutDialog(String) - Constructor for class org.mdanderson.biostat.geneclust.GCAboutDialog
-
Class constructor specifying title
- GCAboutDialog(Frame, String) - Constructor for class org.mdanderson.biostat.geneclust.GCAboutDialog
-
Class constructor specifying owner and title
- GCAboutPanel - Class in org.mdanderson.biostat.geneclust
-
GCAboutPanel - Creates an ABOUT panel for this application
- GCAboutPanel() - Constructor for class org.mdanderson.biostat.geneclust.GCAboutPanel
-
Class constructor
- GCFileFilter - Class in org.mdanderson.biostat.geneclust
-
GCFileFilter - Abstract application-specific file filter
- GCFileFilter() - Constructor for class org.mdanderson.biostat.geneclust.GCFileFilter
-
- GCFileFilterKeys - Interface in org.mdanderson.biostat.geneclust
-
GCFileFilterKeys - Interface for property keys.
- GCSplashScreen - Class in org.mdanderson.biostat.geneclust
-
GCSplashScreen - Creates a splash screen for use at application startup
- GCSplashScreen() - Constructor for class org.mdanderson.biostat.geneclust.GCSplashScreen
-
Class constructor
- GCSplashScreen(Frame) - Constructor for class org.mdanderson.biostat.geneclust.GCSplashScreen
-
Class constructor specifying frame
- GCStreamMonitor - Class in org.mdanderson.biostat.geneclust
-
GCStreamMonitor - Implements application-specific stream monitoring
- GCStreamMonitor(InputStream, OutputStream, SimulationDialog) - Constructor for class org.mdanderson.biostat.geneclust.GCStreamMonitor
-
Class constructor specifying input stream, output stream, and dialog
where results should be displayed
- GCStreamMonitorKeys - Interface in org.mdanderson.biostat.geneclust
-
GCStreamMonitorKeys - Interface for property keys.
- GeneClust - Class in org.mdanderson.biostat.geneclust
-
A Java application for GeneClust research.
- GeneClust() - Constructor for class org.mdanderson.biostat.geneclust.GeneClust
-
Class constructor
- GeneClustFrame - Class in org.mdanderson.biostat.geneclust
-
GeneClustFrame - Implements the user interface frame.
- GeneClustFrame(String) - Constructor for class org.mdanderson.biostat.geneclust.GeneClustFrame
-
Class constructor specifying title
- GeneClustKeys - Interface in org.mdanderson.biostat.geneclust
-
GeneClustKeys - Interface for property keys.
- GeneClustPanel - Class in org.mdanderson.biostat.geneclust
-
GeneClustPanel - Implements the user interface of the application.
- GeneClustPanel(JFrame) - Constructor for class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Class constructor
- getAmplitude() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the maximum value of signal used when generating matrix
- getAmplitude() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the maximum value of signal used when generating matrix
- getClassificationFileName() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the string representing the classification filename
- getClassificationFileName() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the classification file to use for supervised shaving.
- getDegreesFreedom() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the degrees of freedom (used by certain noise distributions)
- getDegreesFreedom() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the degrees of freedom needed by certain algorithms
for noise generation
- getDescription() - Method in class org.mdanderson.biostat.geneclust.GCFileFilter
-
Returns the file filter's description
- getDialog() - Method in class org.mdanderson.biostat.geneclust.SProcess
-
Returns reference to dialog where simulation progress can be monitored.
- getGapTolerance() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the gap tolerance
- getGapTolerance() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the gap tolerance.
- getIsDisplayDataMatrix() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the flag used to determine if samples graph should be displayed.
- getIsDisplayGenesGraph() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the flag used to determine if genes graph should be displayed.
- getIsDisplaySamplesGraph() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the flag used to determine if samples graph should be displayed.
- getIsDisplayShaving() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the flag used to determine if samples graph should be displayed.
- getIsPerformSupervised() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the flag used to determine if supervised shaving should be
performed.
- getModel(boolean) - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the string representing the data model
- getModel() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the model to use when generating matrix
- getNoise() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the string representing the noise
- getNoise() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the type of noise to use when generating matrix
- getNoiseIndex() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the index of the selected noise
- getNumClustersToExtract() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the number of clusters to extract
- getNumColumns() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the number of samples in the gene expression matrix (cell lines)
- getNumColumns() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the number of samples in the gene expression matrix (cell lines)
- getNumExtClusters() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the number of clusters to extract.
- getNumPermutations() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the number of permutations to find optimal
- getNumPermutations() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the number of permutations to find optimal cluster.
- getNumRows() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the number of rows in the gene expression matrix (genes)
- getNumRows() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the number of rows in the gene expression matrix (genes)
- getPercentSupervision() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the percent supervision
- getPercentSupervision() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the supervision percentage.
- getPercentToShave() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the percent to shave
- getPercentToShave() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the percent to shave.
- getPreferredSize() - Method in class org.mdanderson.biostat.geneclust.GCAboutDialog
-
Gets the preferred size of the component
- getPreferredSize() - Method in class org.mdanderson.biostat.geneclust.GCAboutPanel
-
Gets the preferred size of the component
- getProcessing() - Method in class org.mdanderson.biostat.geneclust.SimulationDialog
-
Returns the state of the simulation.
- getRawDataFileName() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns the string representing the filename
- getRawDataFileName() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the raw data file to process.
- getSelectedMode() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the selected simulation mode.
- getStatus() - Method in class org.mdanderson.biostat.util.StatusEvent
-
Returns the status of the data that was checked
- getUserInterface() - Method in class org.mdanderson.biostat.geneclust.GeneClust
-
Returns the user interface panel
- getValue() - Method in class org.mdanderson.biostat.util.StatusEvent
-
Returns the data that was checked
- GuiUtil - Class in org.mdanderson.biostat.util
-
GuiUtil - Implements GUI utility routines.
- GuiUtil() - Constructor for class org.mdanderson.biostat.util.GuiUtil
-
- ICallback - Interface in org.mdanderson.biostat.util
-
ICallback - Invokes callback.
- imageIcon - Variable in class org.mdanderson.biostat.util.DefaultAboutPanel
-
- InetProtocolHandler - Class in org.mdanderson.biostat.util
-
InetProtocolHandler - Routes internet protocol requests.
- InetProtocolHandler() - Constructor for class org.mdanderson.biostat.util.InetProtocolHandler
-
- INFO_LOAD_FILE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- INFO_STARTUP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- insertUpdate(DocumentEvent) - Method in class org.mdanderson.biostat.util.ValidationAdapter
-
Gives notification that there was an insert into the document
- insertUpdate(DocumentEvent) - Method in interface org.mdanderson.biostat.util.Validator
-
Gives notification that there was an insert into the document
- interrupt() - Method in class org.mdanderson.biostat.geneclust.Sinterpreter
-
Causes the S interpreter input required to interrupt the simulation to be
written to the output stream.
- invoke(Object) - Method in class org.mdanderson.biostat.util.Callback
-
Invokes the callback.
- invokeCallback(Object) - Method in interface org.mdanderson.biostat.util.ICallback
-
Invokes the callback
- isDemoEnabled() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns boolean that tells whether data should be generated or not.
- isDemoMode() - Method in class org.mdanderson.biostat.geneclust.Settings
-
Returns the selected simulation mode.
- isDisplayDataMatrix() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns boolean that tells whether to display graph of
hierarchial clustering of samples should be performed or not.
- isDisplayGenesGraph() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns boolean that tells whether to display graph of
hierarchial clustering of genes should be performed or not.
- isDisplaySamplesGraph() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns boolean that tells whether to display graph of
hierarchial clustering of samples should be performed or not.
- isDisplayShaving() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns boolean that tells whether to display graph of
hierarchial clustering of samples should be performed or not.
- isKeyValid(KeyEvent) - Method in class org.mdanderson.biostat.util.FilterAdapter
-
Determines if the key is valid in this context
- isKeyValid(KeyEvent) - Method in class org.mdanderson.biostat.util.NumericFilter
-
Determines if the key is valid in this context.
- isMatchingExtension(String) - Method in class org.mdanderson.biostat.geneclust.GCFileFilter
-
Tests whether or not the abstract pathname's file extension matches
this filter's expected extension(s).
- isPerformSupervised() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns boolean that tells whether supervised shaving should be
performed or not.
- isValid(Object) - Method in class org.mdanderson.biostat.util.NonWhitespaceValidator
-
Determines whether the data is blank or not.
- isValid(Object) - Method in class org.mdanderson.biostat.util.NumericValidator
-
Determines the validity of numeric data.
- isValid(Object) - Method in class org.mdanderson.biostat.util.PathnameValidator
-
Determines the validity of pathname data.
- isValid(Object) - Method in class org.mdanderson.biostat.util.ValidationAdapter
-
Determines the validity of data
- isValid(Object) - Method in interface org.mdanderson.biostat.util.Validator
-
Determines the validity of data
- isWriteMatrix() - Method in class org.mdanderson.biostat.geneclust.GeneClustPanel
-
Returns boolean that tells whether original matrix should be
written to disk or not.
- SAS_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
-
- SAVE_MENUITEM_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- SAVE_MENUITEM_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- SAVE_MENUITEM_MNEMONIC - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- SAVE_MENUITEM_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- SAVE_SETTINGS_FILE_SELECTION_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- setAmplitude(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the maximum value of signal used when generating matrix
- setAppVersionLine(String, String) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Sets the application name and version to be displayed
- setAppVersionLine(String, String) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Sets the application name and version to be displayed
- setBannerLine(String) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Sets the banner to be displayed
- setBannerLine(String) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Sets the banner to be displayed
- setBannerLine(String) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Sets the banner to be displayed
- setClassificationFileName(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the classification file to use for supervised shaving.
- setCopyrightLine(String) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Sets the copyright to be displayed
- setCopyrightLine(String) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Sets the copyright to be displayed
- setCopyrightLine(String) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Sets the copyright to be displayed
- setCopyrightVisible(boolean) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Shows or hides the copyright information depending on the
value of parameter
- setCopyrightVisible(boolean) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Shows or hides the copyright information depending on the
value of parameter
- setCopyrightVisible(boolean) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Shows or hides the copyright information depending on the
value of parameter
- setDegreesFreedom(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the degrees of freedom nneded by certain algorithms
for noise generation
- setDescription(String) - Method in class org.mdanderson.biostat.geneclust.GCFileFilter
-
Sets the file filter's description
- setGapTolerance(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the gap tolerance.
- setIsDisplayDataMatrix(boolean) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the flag used to determine if samples graph should be displayed.
- setIsDisplayGenesGraph(boolean) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the flag used to determine if genes graph should be displayed.
- setIsDisplaySamplesGraph(boolean) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the flag used to determine if samples graph should be displayed.
- setIsDisplayShaving(boolean) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the flag used to determine if samples graph should be displayed.
- setIsPerformSupervised(boolean) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the flag used to determine if supervised shaving should be performed
- setLegalitiesLine(String) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Sets the legal text to be displayed
- setLegalitiesLine(String) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Sets the legal text to be displayed
- setLegalitiesLine(String) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Sets the legal text to be displayed
- setLegalitiesVisible(boolean) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Shows or hides the legal information depending on the
value of parameter
- setLegalitiesVisible(boolean) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Shows or hides the legal information depending on the
value of parameter
- setLegalitiesVisible(boolean) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Shows or hides the legal information depending on the
value of parameter
- setModel(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the model to use when generating matrix
- setNoise(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the type of noise to use when generating matrix
- setNumColumns(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the number of samples in the gene expression matrix (cell lines)
- setNumExtClusters(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the number of clusters to extract.
- setNumPermutations(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the number of permutations to find optimal cluster.
- setNumRows(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the number of rows in the gene expression matrix (genes)
- setPercentSupervision(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the supervision percentage.
- setPercentToShave(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the percent to shave.
- setProcessing(boolean) - Method in class org.mdanderson.biostat.geneclust.SimulationDialog
-
Sets the state of the simulation.
- setRange(double, double) - Method in class org.mdanderson.biostat.util.NumericTextField
-
Sets its numeric validator's allowed range of values
- setRange(double, double) - Method in class org.mdanderson.biostat.util.NumericValidator
-
Sets the allowed range of values
- setRawDataFileName(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the raw data file to process.
- setReleaseDateLine(Date) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Sets the release date to be displayed
- setReleaseDateLine(String) - Method in interface org.mdanderson.biostat.util.AboutPanel
-
Sets the release date to be displayed
- setReleaseDateLine(Date) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Sets the release date to be displayed
- setReleaseDateLine(String) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
-
Sets the release date to be displayed
- setSelectedMode(boolean) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the selected simulation mode.
- setSelectedMode(String) - Method in class org.mdanderson.biostat.geneclust.Settings
-
Sets the selected simulation mode.
- setStatusLine(String) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Sets the application status text to be displayed
- setStatusVisible(boolean) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Shows or hides the application status information depending on the
value of parameter
- setTimeOut(long) - Method in class org.mdanderson.biostat.util.DefaultSplashScreen
-
Sets the amount of time to display the splash screen.
- Settings - Class in org.mdanderson.biostat.geneclust
-
Settings - Load and store settings for user interface values.
- Settings() - Constructor for class org.mdanderson.biostat.geneclust.Settings
-
Class constructor
- Settings(boolean) - Constructor for class org.mdanderson.biostat.geneclust.Settings
-
Class constructor specifying if demo enabled
- setUnvisitedColor(Color) - Method in class org.mdanderson.biostat.util.UrlLabel
-
Sets the foreground color of an unvisited link
- setVisitedColor(Color) - Method in class org.mdanderson.biostat.util.UrlLabel
-
Sets the foreground color of a (previously) visited link
- SHAVING_PANEL_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- showInternalNoticeDialog(Container, String, String, long) - Static method in class org.mdanderson.biostat.util.ExtendedOptionPane
-
- showNoticeDialog(Container, String, String, long) - Static method in class org.mdanderson.biostat.util.ExtendedOptionPane
-
- Simulation - Class in org.mdanderson.biostat.geneclust
-
- Simulation(SimulationDialog, boolean, int, String, int, int, int, int, boolean) - Constructor for class org.mdanderson.biostat.geneclust.Simulation
-
Class constructor specifying (way too many) simulation parameters...
- SIMULATION_DIALOG_BUTTON_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- SIMULATION_DIALOG_MESSAGE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- SIMULATION_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
-
- SimulationDialog - Class in org.mdanderson.biostat.geneclust
-
SimulationDialog - UI bridge that displays simulation output in dialog
- SimulationDialog(Container) - Constructor for class org.mdanderson.biostat.geneclust.SimulationDialog
-
Class constructor specifying parent.
- Sinterpreter - Class in org.mdanderson.biostat.geneclust
-
Sinterpreter - Data processing portion of the application.
- Sinterpreter(SProcess) - Constructor for class org.mdanderson.biostat.geneclust.Sinterpreter
-
Class constructor specifying simulation
- SinterpreterKeys - Interface in org.mdanderson.biostat.geneclust
-
SinterpreterKeys - Interface for property keys.
- splashLabel - Variable in class org.mdanderson.biostat.util.DefaultAboutPanel
-
- SProcess - Class in org.mdanderson.biostat.geneclust
-
SProcess - Abstract data passing between the user interface and Sinterpreter.
- SProcess(SimulationDialog) - Constructor for class org.mdanderson.biostat.geneclust.SProcess
-
- states - Variable in class org.mdanderson.biostat.util.AbstractStateMonitor
-
Currently active states
- statusChanged(StatusEvent) - Method in class org.mdanderson.biostat.util.ContentTextArea
-
Notifies observers when the state of the data changes.
- statusChanged(StatusEvent) - Method in class org.mdanderson.biostat.util.ContentTextField
-
Notifies observers when the state of the data changes.
- statusChanged(StatusEvent) - Method in class org.mdanderson.biostat.util.NumericTextField
-
Notifies observers when the state of the data changes.
- statusChanged(StatusEvent) - Method in class org.mdanderson.biostat.util.PathnameTextField
-
Notifies observers when the state of the data changes.
- statusChanged(StatusEvent) - Method in interface org.mdanderson.biostat.util.StatusListener
-
Notifies observers when the state of the data changes
- StatusEvent - Class in org.mdanderson.biostat.util
-
StatusEvent - Event to notify listener of status change.
- StatusEvent(Object, Object, boolean) - Constructor for class org.mdanderson.biostat.util.StatusEvent
-
Class constructor specifying source, value, and status
- statusLine - Variable in class org.mdanderson.biostat.util.DefaultSplashScreen
-
- StatusListener - Interface in org.mdanderson.biostat.util
-
StatusListener - Notifies observers when state of data changes.
- statusPanel - Variable in class org.mdanderson.biostat.util.DefaultSplashScreen
-
- StatusSource - Interface in org.mdanderson.biostat.util
-
StatusSource - Documents status event producer.
- StreamMonitor - Interface in org.mdanderson.biostat.util
-
StreamMonitor - Allows postprocessing of data read from stream.
- STREAMMONITOR_AWAITING_INPUT - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
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- STREAMMONITOR_DONE - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
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- STREAMMONITOR_END_OF_INPUT - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
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- STREAMMONITOR_STARTED - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
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- STREAMMONITOR_TAG - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
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- SYSINFO_ARCHITECTURE_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_FREE_VM_MEMORY_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_JAVA_CLASS_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_JAVA_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_JIT_COMPILER_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_JVM_INFO_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_JVM_NAME_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_JVM_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_KILOBYTE_TEXT - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_MISSING_VALUE_TEXT - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_OS_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_OS_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- SYSINFO_TOTAL_VM_MEMORY_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
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- sysInfoPanel - Variable in class org.mdanderson.biostat.util.DefaultAboutDialog
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- SysInfoPanelKeys - Interface in org.mdanderson.biostat.util
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SysInfoPanelKeys - Interface for property keys.