MDACC
Biostatistics
A B C D E F G H I K L M N O P R S T U V W 

A

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
 

B

bannerLine - Variable in class org.mdanderson.biostat.util.DefaultAboutPanel
 
BrowserLauncher - Class in edu.stanford.ejalbert
BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
buttonPane - Variable in class org.mdanderson.biostat.util.DefaultAboutDialog
 

C

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
 

D

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
 

E

echoOutput(String) - Method in class org.mdanderson.biostat.util.DefaultStreamMonitor
Echoes processed input from external process to 'stdout' stream.
edu.stanford.ejalbert - package edu.stanford.ejalbert
Provides class which allows use of your system's default web browser to display any URL.
ENABLE_DEMO_CHECKBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ENABLE_DEMO_CHECKBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ENABLE_DEMO_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
enableAudio() - Method in class org.mdanderson.biostat.util.FilterAdapter
Enable audio feedback
enableEcho() - Method in class org.mdanderson.biostat.util.DefaultStreamMonitor
Enable echo of processed input from external process to 'stdout' stream.
endSimulation() - Method in class org.mdanderson.biostat.geneclust.Sinterpreter
Ends the simulation by invoking simulation termination, and performs some thread management cleanup.
enhanceBanner(String) - Method in class org.mdanderson.biostat.util.DefaultAboutPanel
Enhances the original banner string.
ERR_EXTRACT_CLUSTERS_TOO_BIG - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ERR_FILE_VERSION_MISMATCH - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ERR_JVM_PREREQUISITE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ERR_LOAD_FILE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ERR_NEGATIVE_MEMORY_AMOUNT - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
ERR_NO_PROPERTY_ITEMS_FOUND - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ERR_SIMULATION_FAILED - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ERR_TRANSLATE_KEY - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
ERROR_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
EXEC_PSEUDO_TERMINAL - Static variable in interface org.mdanderson.biostat.geneclust.SinterpreterKeys
 
EXIT_MENUITEM_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
EXIT_MENUITEM_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
EXIT_MENUITEM_MNEMONIC - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
EXIT_MENUITEM_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
ExtendedOptionPane - Class in org.mdanderson.biostat.util
NoticeDialog - Creates a generic NOTICE dialog.
ExtendedOptionPane() - Constructor for class org.mdanderson.biostat.util.ExtendedOptionPane
 

F

FILE_MENU_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
FILE_MENU_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
Filter - Class in org.mdanderson.biostat.util
Filter - Abstracts filtering.
Filter(Component) - Constructor for class org.mdanderson.biostat.util.Filter
Class constructor specifying component
FilterAdapter - Class in org.mdanderson.biostat.util
FilterAdapter - Implements keyboard filtering.
FilterAdapter(Component) - Constructor for class org.mdanderson.biostat.util.FilterAdapter
Class constructor specifying component
FIVE_SECONDS - Static variable in class org.mdanderson.biostat.util.DefaultSplashScreen
 
FIVE_SECONDS - Static variable in class org.mdanderson.biostat.util.ExtendedOptionPane
 
focusGained(FocusEvent) - Method in class org.mdanderson.biostat.util.AutoSelectEventHandler
Invoked when component gains the keyboard focus.
focusLost(FocusEvent) - Method in class org.mdanderson.biostat.util.AutoSelectEventHandler
Invoked when component loses the keyboard focus.
FORMATTED_ASCII_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
 
FOUR_SECONDS - Static variable in class org.mdanderson.biostat.util.DefaultSplashScreen
 
FOUR_SECONDS - Static variable in class org.mdanderson.biostat.util.ExtendedOptionPane
 

G

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
 

H

handleActivated() - Method in class org.mdanderson.biostat.util.UrlLabel
Handles Hyperlink ACTIVATED events.
handleEntered() - Method in class org.mdanderson.biostat.util.UrlLabel
Handles Hyperlink ENTERED events.
handleExited() - Method in class org.mdanderson.biostat.util.UrlLabel
Handles Hyperlink EXITED events.
HELP_MENU_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
HELP_MENU_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
HyperlinkSource - Interface in org.mdanderson.biostat.util
HyperlinkSource - Documents hyperlink event producer.
hyperlinkUpdate(HyperlinkEvent) - Method in class org.mdanderson.biostat.util.InetProtocolHandler
Called when a hypertext link is updated.

I

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.

K

keyPressed(KeyEvent) - Method in class org.mdanderson.biostat.util.FilterAdapter
Invoked when a key has been pressed.
keyReleased(KeyEvent) - Method in class org.mdanderson.biostat.util.FilterAdapter
Invoked when a key has been released.
keyTyped(KeyEvent) - Method in class org.mdanderson.biostat.util.FilterAdapter
Invoked when a key has been typed.

L

layoutContainer(Container) - Method in class org.mdanderson.biostat.util.VerticalFlowLayout
Lays out the specified container
legalitiesLine - Variable in class org.mdanderson.biostat.util.DefaultAboutPanel
 
LOGO_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
LOGO_DESCRIPTION - Static variable in interface org.mdanderson.biostat.util.MdaccIconKeys
 

M

main(String[]) - Static method in class org.mdanderson.biostat.geneclust.GCAboutDialog
Main entry-point for the GCAboutDialog class
main(String[]) - Static method in class org.mdanderson.biostat.geneclust.GCSplashScreen
Main entry-point for the GCSplashScreen class
main(String[]) - Static method in class org.mdanderson.biostat.geneclust.GeneClust
Main entry-point for the GeneClust class
main(String[]) - Static method in class org.mdanderson.biostat.util.DefaultSplashScreen
Main entry-point for the DefaultSplashScreen class
main(String[]) - Static method in class org.mdanderson.biostat.util.ExtendedOptionPane
Main entry-point for the ExtendedOptionPane class
MATLAB_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
 
MdaccIcon - Class in org.mdanderson.biostat.util
MdaccIcon - Create M.D. Anderson Cancer Center logo icons.
MdaccIcon() - Constructor for class org.mdanderson.biostat.util.MdaccIcon
Class constructor
MdaccIcon(URL) - Constructor for class org.mdanderson.biostat.util.MdaccIcon
Class constructor specifying url
MdaccIcon(String) - Constructor for class org.mdanderson.biostat.util.MdaccIcon
Class constructor specifying accessible description
MdaccIcon(URL, String) - Constructor for class org.mdanderson.biostat.util.MdaccIcon
Class constructor specifying url and accessible description
MdaccIconKeys - Interface in org.mdanderson.biostat.util
MdaccIconKeys - Interface for property keys.
MENUBAR_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MICROSOFT_EXCEL_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
 
minimumLayoutSize(Container) - Method in class org.mdanderson.biostat.util.VerticalFlowLayout
Calculates the minimum size dimensions for the specified container, given the components it contains.
MODEL_COMBOBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_1 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_10 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_2 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_3 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_4 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_5 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_6 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_7 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_8 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_ITEM_LABEL_9 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_COMBOBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MODEL_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
MONITOR_APP_PROCESSING_COMPLETE - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_APP_PROCESSING_INPUT - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_APP_TERMINATED - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_CREATE_MATRIX - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_DISPLAY_RESULTS - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_ERR_FATAL - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_ERR_NO_CLUSTERS_LEFT - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_ERR_RECOVERABLE - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_ESTIMATE_OPT_CLUSTER_SIZE - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_EXTRACT_CLUSTER - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_HIERARCHICAL_CLUSTERING - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_ORTHOGONALIZE_MATRIX - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_RANDOMIZE_MATRIX - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_READ_MATRIX - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_SHAVE_INIT_NESTED_SEQUENCE - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 
MONITOR_SHAVE_RAND_NESTED_SEQUENCE - Static variable in interface org.mdanderson.biostat.geneclust.GCStreamMonitorKeys
 

N

NO_EXCEPTION_DETAIL_MESSAGE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NOISE_COMBOBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NOISE_COMBOBOX_ITEM_LABEL_1 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NOISE_COMBOBOX_ITEM_LABEL_2 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NOISE_COMBOBOX_ITEM_LABEL_3 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NOISE_COMBOBOX_ITEM_LABEL_4 - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NOISE_COMBOBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NOISE_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NonWhitespaceValidator - Class in org.mdanderson.biostat.util
NonWhitespaceValidator - Implements non whitespace validation.
NonWhitespaceValidator() - Constructor for class org.mdanderson.biostat.util.NonWhitespaceValidator
 
NUM_CLUSTERS_TO_EXTRACT_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_COLUMNS_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_COLUMNS_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_COLUMNS_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_COLUMNS_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_COLUMNS_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_COLUMNS_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_COLUMNS_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_PERMUTATIONS_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_PERMUTATIONS_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_PERMUTATIONS_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_PERMUTATIONS_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_PERMUTATIONS_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_PERMUTATIONS_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_PERMUTATIONS_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_ROWS_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_ROWS_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_ROWS_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_ROWS_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_ROWS_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_ROWS_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
NUM_ROWS_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
numClustersToExtract - Variable in class org.mdanderson.biostat.geneclust.Simulation
 
NumericFilter - Class in org.mdanderson.biostat.util
NumericFilter - Implements numeric keyboard filtering.
NumericFilter(Component) - Constructor for class org.mdanderson.biostat.util.NumericFilter
Class constructor specifying component
NumericTextField - Class in org.mdanderson.biostat.util
NumericTextField - Allows numeric validation of a textfield.
NumericTextField() - Constructor for class org.mdanderson.biostat.util.NumericTextField
Class constructor
NumericTextField(String) - Constructor for class org.mdanderson.biostat.util.NumericTextField
Class constructor specifying text
NumericTextField(int) - Constructor for class org.mdanderson.biostat.util.NumericTextField
Class constructor specifying number of columns
NumericTextField(String, int) - Constructor for class org.mdanderson.biostat.util.NumericTextField
Class constructor specifying text and number of columns
NumericValidator - Class in org.mdanderson.biostat.util
NumericValidator - Implements numeric validation.
NumericValidator() - Constructor for class org.mdanderson.biostat.util.NumericValidator
 
numPermutations - Variable in class org.mdanderson.biostat.geneclust.Simulation
 

O

ONE_SECOND - Static variable in class org.mdanderson.biostat.util.DefaultSplashScreen
 
ONE_SECOND - Static variable in class org.mdanderson.biostat.util.ExtendedOptionPane
 
OPEN_MENUITEM_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OPEN_MENUITEM_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OPEN_MENUITEM_MNEMONIC - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OPEN_MENUITEM_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OPEN_SETTINGS_FILE_SELECTION_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
openURL(String) - Static method in class edu.stanford.ejalbert.BrowserLauncher
Attempts to open the default web browser to the given URL.
openURL(URL) - Static method in class org.mdanderson.biostat.util.InetProtocolHandler
Opens the requested URL.
openURL(String) - Static method in class org.mdanderson.biostat.util.InetProtocolHandler
Opens the requested URL.
org.mdanderson.biostat.geneclust - package org.mdanderson.biostat.geneclust
This is the user interface for a software package which can be used as a tool for exploratory analysis of gene expression microarray data.
org.mdanderson.biostat.util - package org.mdanderson.biostat.util
Provides classes and interfaces used by applications written by the Biostatistics department of M.D. Anderson Cancer Center.
OVERVIEW_DIALOG_MESSAGE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OVERVIEW_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OVERVIEW_MENUITEM_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OVERVIEW_MENUITEM_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OVERVIEW_MENUITEM_MNEMONIC - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OVERVIEW_MENUITEM_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OVERWRITE_DIALOG_MESSAGE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
OVERWRITE_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 

P

PACKAGE_NAME - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
paint(Graphics) - Method in class org.mdanderson.biostat.util.UrlLabel
Invoked by Swing to draw components.
PathnameTextField - Class in org.mdanderson.biostat.util
PathnameTextField - Allows pathname validation of a textfield.
PathnameTextField() - Constructor for class org.mdanderson.biostat.util.PathnameTextField
Class constructor
PathnameTextField(String) - Constructor for class org.mdanderson.biostat.util.PathnameTextField
Class constructor specifying text
PathnameTextField(int) - Constructor for class org.mdanderson.biostat.util.PathnameTextField
Class constructor specifying number of columns
PathnameTextField(String, int) - Constructor for class org.mdanderson.biostat.util.PathnameTextField
Class constructor specifying text and number of columns
PathnameValidator - Class in org.mdanderson.biostat.util
PathnameValidator - Implements pathname validation.
PathnameValidator() - Constructor for class org.mdanderson.biostat.util.PathnameValidator
 
PERCENT_SUPERVISION_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_SUPERVISION_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_SUPERVISION_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_SUPERVISION_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_SUPERVISION_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_SUPERVISION_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_SUPERVISION_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_TO_SHAVE_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_TO_SHAVE_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_TO_SHAVE_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_TO_SHAVE_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_TO_SHAVE_TEXTFIELD_MAXIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_TO_SHAVE_TEXTFIELD_MINIMUM_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERCENT_TO_SHAVE_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
percentSupervision - Variable in class org.mdanderson.biostat.geneclust.Simulation
 
percentToShave - Variable in class org.mdanderson.biostat.geneclust.Simulation
 
PERFORM_SUPERVISED_CHECKBOX_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERFORM_SUPERVISED_CHECKBOX_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERFORM_SUPERVISED_CHECKBOX_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
PERFORM_SUPERVISED_CHECKBOX_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
performSupervised - Variable in class org.mdanderson.biostat.geneclust.Simulation
 
preferredLayoutSize(Container) - Method in class org.mdanderson.biostat.util.VerticalFlowLayout
Calculates the preferred size dimensions for the specified container, given the components it contains.
PROCESS_COMPLETED - Static variable in interface org.mdanderson.biostat.geneclust.SinterpreterKeys
 
PROCESS_DESTROYED - Static variable in interface org.mdanderson.biostat.geneclust.SinterpreterKeys
 
processLine(String) - Method in class org.mdanderson.biostat.geneclust.GCStreamMonitor
Processes the output from the input stream, checking for embedded messages destined for the GUI.
processLine(String) - Method in class org.mdanderson.biostat.util.DefaultStreamMonitor
Postprocesses the output from the input stream.
processLine(String) - Method in interface org.mdanderson.biostat.util.StreamMonitor
Postprocesses the output from the input stream.

R

RAW_DATA_FILENAME_CHOOSER_BUTTON_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_FILENAME_CHOOSER_BUTTON_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_FILENAME_CHOOSER_BUTTON_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_FILENAME_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_FILENAME_TEXTFIELD_COLUMNS - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_FILENAME_TEXTFIELD_DEFAULT_VALUE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_FILENAME_TEXTFIELD_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_FILENAME_TEXTFIELD_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
RAW_DATA_TAB_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
read(File) - Method in class org.mdanderson.biostat.geneclust.Settings
Reads the settings file and updates the associated GUI components with those values.
releaseDateLine - Variable in class org.mdanderson.biostat.util.DefaultAboutPanel
 
removeHyperlinkListener(HyperlinkListener) - Method in interface org.mdanderson.biostat.util.HyperlinkSource
Removes a hyperlink listener.
removeHyperlinkListener(HyperlinkListener) - Method in class org.mdanderson.biostat.util.UrlLabel
Removes a hyperlink listener.
removeLayoutComponent(Component) - Method in class org.mdanderson.biostat.util.VerticalFlowLayout
Removes the specified component from the layout.
removeState(Object) - Method in class org.mdanderson.biostat.util.AbstractStateMonitor
Removes a state from the list of monitored states, :TODO: if it doesn't already exist
removeStatusListener(StatusListener) - Method in interface org.mdanderson.biostat.util.StatusSource
Removes a status listener
removeStatusListener(StatusListener) - Method in class org.mdanderson.biostat.util.ValidationAdapter
Removes a status listener
removeStatusListener(StatusListener) - Method in interface org.mdanderson.biostat.util.Validator
Removes a status listener
removeUpdate(DocumentEvent) - Method in class org.mdanderson.biostat.util.ValidationAdapter
Gives notification that a portion of the document has been removed
removeUpdate(DocumentEvent) - Method in interface org.mdanderson.biostat.util.Validator
Gives notification that a portion of the document has been removed
run(String) - Method in class org.mdanderson.biostat.geneclust.SProcess
Runs the simulation, managing the S interpreter processing occuring in external process.
run() - Method in class org.mdanderson.biostat.util.DefaultStreamMonitor
Thread entry-point for DefaultStreamMonitor object.
runSimulation() - Method in class org.mdanderson.biostat.geneclust.Sinterpreter
Launches the external S interpreter process, sets up process monitoring and logging threads, then writes the simulation input to the output stream.

S

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
 
STREAMMONITOR_DONE - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
 
STREAMMONITOR_END_OF_INPUT - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
 
STREAMMONITOR_STARTED - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
 
STREAMMONITOR_TAG - Static variable in interface org.mdanderson.biostat.util.DefaultStreamMonitorKeys
 
SYSINFO_ARCHITECTURE_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_FREE_VM_MEMORY_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_JAVA_CLASS_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_JAVA_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_JIT_COMPILER_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_JVM_INFO_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_JVM_NAME_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_JVM_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_KILOBYTE_TEXT - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_MISSING_VALUE_TEXT - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_OS_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_OS_VERSION_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
SYSINFO_TOTAL_VM_MEMORY_LABEL - Static variable in interface org.mdanderson.biostat.util.SysInfoPanelKeys
 
sysInfoPanel - Variable in class org.mdanderson.biostat.util.DefaultAboutDialog
 
SysInfoPanelKeys - Interface in org.mdanderson.biostat.util
SysInfoPanelKeys - Interface for property keys.

T

tabbedPane - Variable in class org.mdanderson.biostat.util.DefaultAboutDialog
 
terminate(int) - Static method in class org.mdanderson.biostat.geneclust.GeneClust
Causes termination of the Java Virtual Machine.
THREAD_JOINED - Static variable in interface org.mdanderson.biostat.geneclust.SinterpreterKeys
 
THREE_SECONDS - Static variable in class org.mdanderson.biostat.util.DefaultSplashScreen
 
THREE_SECONDS - Static variable in class org.mdanderson.biostat.util.ExtendedOptionPane
 
TSV_FILE_FILTER_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GCFileFilterKeys
 
TWO_SECONDS - Static variable in class org.mdanderson.biostat.util.DefaultSplashScreen
 
TWO_SECONDS - Static variable in class org.mdanderson.biostat.util.ExtendedOptionPane
 

U

update(Observable, Object) - Method in class org.mdanderson.biostat.util.AbstractDialog
Receives notice of look and feel changes
updateExtract(String) - Method in class org.mdanderson.biostat.geneclust.SimulationDialog
Updates the primary message label for simulation progress and blanks the secondary message label.
updateProgress(String) - Method in class org.mdanderson.biostat.geneclust.SimulationDialog
Updates the secondary message label for simulation progress.
UrlLabel - Class in org.mdanderson.biostat.util
UrlLabel - Simulates a link on a webpage.
UrlLabel(String, URL) - Constructor for class org.mdanderson.biostat.util.UrlLabel
Class constructor specifying text and url
USER_GUIDE_DIALOG_TITLE - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
USER_GUIDE_FILE_URL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
USER_GUIDE_HTTP_URL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
USER_GUIDE_MENUITEM_DESCRIPTION - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
USER_GUIDE_MENUITEM_LABEL - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
USER_GUIDE_MENUITEM_MNEMONIC - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 
USER_GUIDE_MENUITEM_TOOLTIP - Static variable in interface org.mdanderson.biostat.geneclust.GeneClustKeys
 

V

validate(Object) - Method in class org.mdanderson.biostat.util.ValidationAdapter
Determines the validity of data and fires an event if state has changed
validate(Object) - Method in interface org.mdanderson.biostat.util.Validator
Determines the validity of data and fires an event if state has changed
ValidationAdapter - Class in org.mdanderson.biostat.util
ValidationAdapter - Textfield validation adapter
ValidationAdapter() - Constructor for class org.mdanderson.biostat.util.ValidationAdapter
 
Validator - Interface in org.mdanderson.biostat.util
Validator - Interface for validation.
VerticalFlowLayout - Class in org.mdanderson.biostat.util
VerticalFlowLayout - Vertical flow layout manager
VerticalFlowLayout() - Constructor for class org.mdanderson.biostat.util.VerticalFlowLayout
Class constructor
VerticalFlowLayout(int) - Constructor for class org.mdanderson.biostat.util.VerticalFlowLayout
Class constructor specifying vertical gap

W

WAITING_FOR_PROCESS - Static variable in interface org.mdanderson.biostat.geneclust.SinterpreterKeys
 
WAITING_FOR_THREAD_JOIN - Static variable in interface org.mdanderson.biostat.geneclust.SinterpreterKeys
 
write(File) - Method in class org.mdanderson.biostat.geneclust.Settings
Writes the current GUI component values to a settings file.
writeMatrix - Variable in class org.mdanderson.biostat.geneclust.Simulation
 
writeSinterpreterGenericInput(SBufferedWriter) - Method in class org.mdanderson.biostat.geneclust.Simulation
Writes mode-indifferent S interpreter input data to the output stream.
writeSinterpreterInit(SBufferedWriter) - Method in class org.mdanderson.biostat.geneclust.Simulation
Writes the S interpreter initialization code.
writeSinterpreterInput(SBufferedWriter) - Method in class org.mdanderson.biostat.geneclust.SProcess
Writes all S interpreter input to the output stream.
writeSinterpreterInterrupt(SBufferedWriter) - Method in class org.mdanderson.biostat.geneclust.SProcess
Writes the S interpreter input required to interrupt the simulation to the output stream.
writeSinterpreterTermination(SBufferedWriter) - Method in class org.mdanderson.biostat.geneclust.SProcess
Writes the S interpreter input required to close the graphics device and terminate the external process.
A B C D E F G H I K L M N O P R S T U V W 
MDACC
Biostatistics

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