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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
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
ASCII_FILE_FILTER_DESCRIPTION
- Static variable in interface org.mdanderson.biostat.geneclust.
GCFileFilterKeys
AboutPanel
- interface org.mdanderson.biostat.util.
AboutPanel
.
AboutPanel - Interface for panel settings.
AbstractAboutDialog
- class org.mdanderson.biostat.util.
AbstractAboutDialog
.
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 org.mdanderson.biostat.util.
AbstractAboutPanel
.
AbstractAboutPanel - Creates an abstract ABOUT panel
AbstractAboutPanel()
- Constructor for class org.mdanderson.biostat.util.
AbstractAboutPanel
Class constructor
AbstractDialog
- class org.mdanderson.biostat.util.
AbstractDialog
.
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 org.mdanderson.biostat.util.
AbstractStateMonitor
.
AbstractStateMonitor - Responsible for enabling or disabling GUI components whenever application state changes.
AbstractStateMonitor()
- Constructor for class org.mdanderson.biostat.util.
AbstractStateMonitor
Class constructor
AutoSelectEventHandler
- class org.mdanderson.biostat.util.
AutoSelectEventHandler
.
AutoSelectEventHandler - Responds to focus events.
AutoSelectEventHandler()
- Constructor for class org.mdanderson.biostat.util.
AutoSelectEventHandler
aboutPanel
- Variable in class org.mdanderson.biostat.util.
DefaultAboutDialog
aboutPanel
- Variable in class org.mdanderson.biostat.util.
DefaultSplashScreen
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
appNameVersionLine
- Variable in class org.mdanderson.biostat.util.
DefaultAboutPanel
B
BrowserLauncher
- class edu.stanford.ejalbert.
BrowserLauncher
.
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.
bannerLine
- Variable in class org.mdanderson.biostat.util.
DefaultAboutPanel
buttonPane
- Variable in class org.mdanderson.biostat.util.
DefaultAboutDialog
C
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_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
CLASSIFICATION_FILE_FILTER_DESCRIPTION
- Static variable in interface org.mdanderson.biostat.geneclust.
GCFileFilterKeys
CONFIG_FILE_FILTER_DESCRIPTION
- Static variable in interface org.mdanderson.biostat.geneclust.
GCFileFilterKeys
CSV_FILE_FILTER_DESCRIPTION
- Static variable in interface org.mdanderson.biostat.geneclust.
GCFileFilterKeys
Callback
- class org.mdanderson.biostat.util.
Callback
.
Callback- Callback invocation.
Callback(ICallback)
- Constructor for class org.mdanderson.biostat.util.
Callback
Class constructor specifying callback to be sent.
ContentTextArea
- class org.mdanderson.biostat.util.
ContentTextArea
.
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 org.mdanderson.biostat.util.
ContentTextField
.
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
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
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
contactPanel
- Variable in class org.mdanderson.biostat.util.
DefaultAboutDialog
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
D
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
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
DefaultAboutDialog
- class org.mdanderson.biostat.util.
DefaultAboutDialog
.
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 org.mdanderson.biostat.util.
DefaultAboutDialogKeys
.
DefaultAboutDialogKeys - Interface for property keys.
DefaultAboutPanel
- class org.mdanderson.biostat.util.
DefaultAboutPanel
.
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 org.mdanderson.biostat.util.
DefaultAboutPanelKeys
.
DefaultAboutPanelKeys - Interface for property keys.
DefaultSplashScreen
- class org.mdanderson.biostat.util.
DefaultSplashScreen
.
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 org.mdanderson.biostat.util.
DefaultStreamMonitor
.
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 org.mdanderson.biostat.util.
DefaultStreamMonitorKeys
.
DefaultStreamMonitorKeys - Interface for property keys.
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
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
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
ERROR_DIALOG_TITLE
- Static variable in interface org.mdanderson.biostat.geneclust.
GeneClustKeys
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
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 org.mdanderson.biostat.util.
ExtendedOptionPane
.
NoticeDialog - Creates a generic NOTICE dialog.
ExtendedOptionPane()
- Constructor for class org.mdanderson.biostat.util.
ExtendedOptionPane
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
.
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.
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
FIVE_SECONDS
- Static variable in class org.mdanderson.biostat.util.
DefaultSplashScreen
FIVE_SECONDS
- Static variable in class org.mdanderson.biostat.util.
ExtendedOptionPane
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
Filter
- class org.mdanderson.biostat.util.
Filter
.
Filter - Abstracts filtering.
Filter(Component)
- Constructor for class org.mdanderson.biostat.util.
Filter
Class constructor specifying component
FilterAdapter
- class org.mdanderson.biostat.util.
FilterAdapter
.
FilterAdapter - Implements keyboard filtering.
FilterAdapter(Component)
- Constructor for class org.mdanderson.biostat.util.
FilterAdapter
Class constructor specifying component
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.
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
GCAboutDialog
- class org.mdanderson.biostat.geneclust.
GCAboutDialog
.
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 org.mdanderson.biostat.geneclust.
GCAboutPanel
.
GCAboutPanel - Creates an ABOUT panel for this application
GCAboutPanel()
- Constructor for class org.mdanderson.biostat.geneclust.
GCAboutPanel
Class constructor
GCFileFilter
- class org.mdanderson.biostat.geneclust.
GCFileFilter
.
GCFileFilter - Abstract application-specific file filter
GCFileFilter()
- Constructor for class org.mdanderson.biostat.geneclust.
GCFileFilter
GCFileFilterKeys
- interface org.mdanderson.biostat.geneclust.
GCFileFilterKeys
.
GCFileFilterKeys - Interface for property keys.
GCSplashScreen
- class org.mdanderson.biostat.geneclust.
GCSplashScreen
.
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 org.mdanderson.biostat.geneclust.
GCStreamMonitor
.
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 org.mdanderson.biostat.geneclust.
GCStreamMonitorKeys
.
GCStreamMonitorKeys - Interface for property keys.
GeneClust
- class org.mdanderson.biostat.geneclust.
GeneClust
.
A Java application for GeneClust research.
GeneClust()
- Constructor for class org.mdanderson.biostat.geneclust.
GeneClust
Class constructor
GeneClustFrame
- class org.mdanderson.biostat.geneclust.
GeneClustFrame
.
GeneClustFrame - Implements the user interface frame.
GeneClustFrame(String)
- Constructor for class org.mdanderson.biostat.geneclust.
GeneClustFrame
Class constructor specifying title
GeneClustKeys
- interface org.mdanderson.biostat.geneclust.
GeneClustKeys
.
GeneClustKeys - Interface for property keys.
GeneClustPanel
- class org.mdanderson.biostat.geneclust.
GeneClustPanel
.
GeneClustPanel - Implements the user interface of the application.
GeneClustPanel(JFrame)
- Constructor for class org.mdanderson.biostat.geneclust.
GeneClustPanel
Class constructor
GuiUtil
- class org.mdanderson.biostat.util.
GuiUtil
.
GuiUtil - Implements GUI utility routines.
GuiUtil()
- Constructor for class org.mdanderson.biostat.util.
GuiUtil
gapTolerance
- Variable in class org.mdanderson.biostat.geneclust.
Simulation
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
H
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 org.mdanderson.biostat.util.
HyperlinkSource
.
HyperlinkSource - Documents hyperlink event producer.
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.
hyperlinkUpdate(HyperlinkEvent)
- Method in class org.mdanderson.biostat.util.
InetProtocolHandler
Called when a hypertext link is updated.
I
ICallback
- interface org.mdanderson.biostat.util.
ICallback
.
ICallback - Invokes callback.
INFO_LOAD_FILE
- Static variable in interface org.mdanderson.biostat.geneclust.
GeneClustKeys
INFO_STARTUP
- Static variable in interface org.mdanderson.biostat.geneclust.
GeneClustKeys
InetProtocolHandler
- class org.mdanderson.biostat.util.
InetProtocolHandler
.
InetProtocolHandler - Routes internet protocol requests.
InetProtocolHandler()
- Constructor for class org.mdanderson.biostat.util.
InetProtocolHandler
imageIcon
- Variable in class org.mdanderson.biostat.util.
DefaultAboutPanel
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
LOGO_DESCRIPTION
- Static variable in interface org.mdanderson.biostat.geneclust.
GeneClustKeys
LOGO_DESCRIPTION
- Static variable in interface org.mdanderson.biostat.util.
MdaccIconKeys
layoutContainer(Container)
- Method in class org.mdanderson.biostat.util.
VerticalFlowLayout
Lays out the specified container
legalitiesLine
- Variable in class org.mdanderson.biostat.util.
DefaultAboutPanel
M
MATLAB_FILE_FILTER_DESCRIPTION
- Static variable in interface org.mdanderson.biostat.geneclust.
GCFileFilterKeys
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
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
MdaccIcon
- class org.mdanderson.biostat.util.
MdaccIcon
.
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 org.mdanderson.biostat.util.
MdaccIconKeys
.
MdaccIconKeys - Interface for property keys.
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
minimumLayoutSize(Container)
- Method in class org.mdanderson.biostat.util.
VerticalFlowLayout
Calculates the minimum size dimensions for the specified container, given the components it contains.
N
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
NO_EXCEPTION_DETAIL_MESSAGE
- Static variable in interface org.mdanderson.biostat.geneclust.
GeneClustKeys
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
NonWhitespaceValidator
- class org.mdanderson.biostat.util.
NonWhitespaceValidator
.
NonWhitespaceValidator - Implements non whitespace validation.
NonWhitespaceValidator()
- Constructor for class org.mdanderson.biostat.util.
NonWhitespaceValidator
NumericFilter
- class org.mdanderson.biostat.util.
NumericFilter
.
NumericFilter - Implements numeric keyboard filtering.
NumericFilter(Component)
- Constructor for class org.mdanderson.biostat.util.
NumericFilter
Class constructor specifying component
NumericTextField
- class org.mdanderson.biostat.util.
NumericTextField
.
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 org.mdanderson.biostat.util.
NumericValidator
.
NumericValidator - Implements numeric validation.
NumericValidator()
- Constructor for class org.mdanderson.biostat.util.
NumericValidator
numClustersToExtract
- Variable in class org.mdanderson.biostat.geneclust.
Simulation
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
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
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.
P
PACKAGE_NAME
- Static variable in interface org.mdanderson.biostat.geneclust.
GeneClustKeys
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
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
PROCESS_COMPLETED
- Static variable in interface org.mdanderson.biostat.geneclust.
SinterpreterKeys
PROCESS_DESTROYED
- Static variable in interface org.mdanderson.biostat.geneclust.
SinterpreterKeys
PathnameTextField
- class org.mdanderson.biostat.util.
PathnameTextField
.
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 org.mdanderson.biostat.util.
PathnameValidator
.
PathnameValidator - Implements pathname validation.
PathnameValidator()
- Constructor for class org.mdanderson.biostat.util.
PathnameValidator
paint(Graphics)
- Method in class org.mdanderson.biostat.util.
UrlLabel
Invoked by Swing to draw components.
percentSupervision
- Variable in class org.mdanderson.biostat.geneclust.
Simulation
percentToShave
- Variable in class org.mdanderson.biostat.geneclust.
Simulation
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.
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
SHAVING_PANEL_TITLE
- Static variable in interface org.mdanderson.biostat.geneclust.
GeneClustKeys
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
SProcess
- class org.mdanderson.biostat.geneclust.
SProcess
.
SProcess - Abstract data passing between the user interface and Sinterpreter.
SProcess(SimulationDialog)
- Constructor for class org.mdanderson.biostat.geneclust.
SProcess
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
Settings
- class org.mdanderson.biostat.geneclust.
Settings
.
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
Simulation
- class org.mdanderson.biostat.geneclust.
Simulation
.
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...
SimulationDialog
- class org.mdanderson.biostat.geneclust.
SimulationDialog
.
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 org.mdanderson.biostat.geneclust.
Sinterpreter
.
Sinterpreter - Data processing portion of the application.
Sinterpreter(SProcess)
- Constructor for class org.mdanderson.biostat.geneclust.
Sinterpreter
Class constructor specifying simulation
SinterpreterKeys
- interface org.mdanderson.biostat.geneclust.
SinterpreterKeys
.
SinterpreterKeys - Interface for property keys.
StatusEvent
- class org.mdanderson.biostat.util.
StatusEvent
.
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
StatusListener
- interface org.mdanderson.biostat.util.
StatusListener
.
StatusListener - Notifies observers when state of data changes.
StatusSource
- interface org.mdanderson.biostat.util.
StatusSource
.
StatusSource - Documents status event producer.
StreamMonitor
- interface org.mdanderson.biostat.util.
StreamMonitor
.
StreamMonitor - Allows postprocessing of data read from stream.
SysInfoPanelKeys
- interface org.mdanderson.biostat.util.
SysInfoPanelKeys
.
SysInfoPanelKeys - Interface for property keys.
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.
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
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
splashLabel
- Variable in class org.mdanderson.biostat.util.
DefaultAboutPanel
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
statusLine
- Variable in class org.mdanderson.biostat.util.
DefaultSplashScreen
statusPanel
- Variable in class org.mdanderson.biostat.util.
DefaultSplashScreen
sysInfoPanel
- Variable in class org.mdanderson.biostat.util.
DefaultAboutDialog
T
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
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.
U
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
UrlLabel
- class org.mdanderson.biostat.util.
UrlLabel
.
UrlLabel - Simulates a link on a webpage.
UrlLabel(String, URL)
- Constructor for class org.mdanderson.biostat.util.
UrlLabel
Class constructor specifying text and url
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.
V
ValidationAdapter
- class org.mdanderson.biostat.util.
ValidationAdapter
.
ValidationAdapter - Textfield validation adapter
ValidationAdapter()
- Constructor for class org.mdanderson.biostat.util.
ValidationAdapter
Validator
- interface org.mdanderson.biostat.util.
Validator
.
Validator - Interface for validation.
VerticalFlowLayout
- class org.mdanderson.biostat.util.
VerticalFlowLayout
.
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
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
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.
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Copyright © 2002 M.D. Anderson Cancer Center. All Rights Reserved.