org.mdanderson.biostat.geneclust
public class GeneClustPanel extends JPanel implements GeneClustKeys
JPanel.AccessibleJPanel
JComponent.AccessibleJComponent
Container.AccessibleAWTContainer
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
ABOUT_DIALOG_CONTACT_EMAIL_ADDRESS, ABOUT_DIALOG_CONTACT_EMAIL_ADDRESS_DESCRIPTION, ABOUT_DIALOG_CONTACT_EMAIL_LABEL, ABOUT_DIALOG_CONTACT_PANEL_TITLE, ABOUT_DIALOG_CONTACT_USPS_ADDRESS_CITY_STATE, ABOUT_DIALOG_CONTACT_USPS_ADDRESS_NAME, ABOUT_DIALOG_CONTACT_USPS_ADDRESS_STREET, ABOUT_DIALOG_CONTACT_USPS_LABEL, ABOUT_DIALOG_CONTACT_WEB_ADDRESS, ABOUT_DIALOG_CONTACT_WEB_ADDRESS_DESCRIPTION, ABOUT_DIALOG_CONTACT_WEB_LABEL, ABOUT_DIALOG_CREDITS_COLLABORATOR_LABEL, ABOUT_DIALOG_CREDITS_DEVELOPER_LABEL, ABOUT_DIALOG_CREDITS_RESEARCHER_LABEL, ABOUT_DIALOG_TITLE, ABOUT_MENUITEM_DESCRIPTION, ABOUT_MENUITEM_LABEL, ABOUT_MENUITEM_MNEMONIC, ABOUT_MENUITEM_TOOLTIP, AMPLITUDE_LABEL, AMPLITUDE_TEXTFIELD_COLUMNS, AMPLITUDE_TEXTFIELD_DEFAULT_VALUE, AMPLITUDE_TEXTFIELD_DESCRIPTION, AMPLITUDE_TEXTFIELD_MAXIMUM_VALUE, AMPLITUDE_TEXTFIELD_MINIMUM_VALUE, AMPLITUDE_TEXTFIELD_TOOLTIP, APPLICATION_COPYRIGHT, APPLICATION_DESCRIPTION, APPLICATION_LEGALITIES, APPLICATION_NAME, APPLICATION_RELEASE_DATE, APPLICATION_USAGE, APPLICATION_VERSION, APPLICATION_WINDOW_TITLE, CHOOSE_CLASSIFICATION_FILE_SELECTION_DIALOG_TITLE, CHOOSE_DATA_FILE_SELECTION_DIALOG_TITLE, CHOOSE_FILE_SELECTION_DIALOG_OK_BUTTON_LABEL, CHOOSE_FILE_SELECTION_DIALOG_OK_BUTTON_TOOLTIP, CLASSIFICATION_FILENAME_CHOOSER_BUTTON_DESCRIPTION, CLASSIFICATION_FILENAME_CHOOSER_BUTTON_LABEL, CLASSIFICATION_FILENAME_CHOOSER_BUTTON_TOOLTIP, CLASSIFICATION_FILENAME_LABEL, CLASSIFICATION_FILENAME_TEXTFIELD_COLUMNS, CLASSIFICATION_FILENAME_TEXTFIELD_DEFAULT_VALUE, CLASSIFICATION_FILENAME_TEXTFIELD_DESCRIPTION, CLASSIFICATION_FILENAME_TEXTFIELD_TOOLTIP, DEGREES_FREEDOM_LABEL, DEGREES_FREEDOM_TEXTFIELD_COLUMNS, DEGREES_FREEDOM_TEXTFIELD_DEFAULT_VALUE, DEGREES_FREEDOM_TEXTFIELD_DESCRIPTION, DEGREES_FREEDOM_TEXTFIELD_MAXIMUM_VALUE, DEGREES_FREEDOM_TEXTFIELD_MINIMUM_VALUE, DEGREES_FREEDOM_TEXTFIELD_TOOLTIP, DEMO_DATA_TAB_TITLE, DISPLAY_BUTTON_DESCRIPTION, DISPLAY_BUTTON_LABEL, DISPLAY_BUTTON_TOOLTIP, DISPLAY_DATA_MATRIX_CHECKBOX_DEFAULT_VALUE, DISPLAY_DATA_MATRIX_CHECKBOX_DESCRIPTION, DISPLAY_DATA_MATRIX_CHECKBOX_LABEL, DISPLAY_DATA_MATRIX_CHECKBOX_TOOLTIP, DISPLAY_GENES_GRAPH_CHECKBOX_DEFAULT_VALUE, DISPLAY_GENES_GRAPH_CHECKBOX_DESCRIPTION, DISPLAY_GENES_GRAPH_CHECKBOX_LABEL, DISPLAY_GENES_GRAPH_CHECKBOX_TOOLTIP, DISPLAY_PANEL_TITLE, DISPLAY_SAMPLES_GRAPH_CHECKBOX_DEFAULT_VALUE, DISPLAY_SAMPLES_GRAPH_CHECKBOX_DESCRIPTION, DISPLAY_SAMPLES_GRAPH_CHECKBOX_LABEL, DISPLAY_SAMPLES_GRAPH_CHECKBOX_TOOLTIP, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_DEFAULT_VALUE, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_DESCRIPTION, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_LABEL, DISPLAY_SHAVING_CLUSTERS_CHECKBOX_TOOLTIP, ENABLE_DEMO_CHECKBOX_DESCRIPTION, ENABLE_DEMO_CHECKBOX_TOOLTIP, ENABLE_DEMO_LABEL, ERR_EXTRACT_CLUSTERS_TOO_BIG, ERR_FILE_VERSION_MISMATCH, ERR_JVM_PREREQUISITE, ERR_LOAD_FILE, ERR_NO_PROPERTY_ITEMS_FOUND, ERR_SIMULATION_FAILED, ERROR_DIALOG_TITLE, EXIT_MENUITEM_DESCRIPTION, EXIT_MENUITEM_LABEL, EXIT_MENUITEM_MNEMONIC, EXIT_MENUITEM_TOOLTIP, FILE_MENU_DESCRIPTION, FILE_MENU_LABEL, GAP_TOLERANCE_LABEL, GAP_TOLERANCE_TEXTFIELD_COLUMNS, GAP_TOLERANCE_TEXTFIELD_DEFAULT_VALUE, GAP_TOLERANCE_TEXTFIELD_DESCRIPTION, GAP_TOLERANCE_TEXTFIELD_MAXIMUM_VALUE, GAP_TOLERANCE_TEXTFIELD_MINIMUM_VALUE, GAP_TOLERANCE_TEXTFIELD_TOOLTIP, HELP_MENU_DESCRIPTION, HELP_MENU_LABEL, INFO_LOAD_FILE, INFO_STARTUP, LOGO_DESCRIPTION, MENUBAR_DESCRIPTION, MODEL_COMBOBOX_DESCRIPTION, MODEL_COMBOBOX_ITEM_LABEL_1, MODEL_COMBOBOX_ITEM_LABEL_10, MODEL_COMBOBOX_ITEM_LABEL_2, MODEL_COMBOBOX_ITEM_LABEL_3, MODEL_COMBOBOX_ITEM_LABEL_4, MODEL_COMBOBOX_ITEM_LABEL_5, MODEL_COMBOBOX_ITEM_LABEL_6, MODEL_COMBOBOX_ITEM_LABEL_7, MODEL_COMBOBOX_ITEM_LABEL_8, MODEL_COMBOBOX_ITEM_LABEL_9, MODEL_COMBOBOX_TOOLTIP, MODEL_LABEL, NO_EXCEPTION_DETAIL_MESSAGE, NOISE_COMBOBOX_DESCRIPTION, NOISE_COMBOBOX_ITEM_LABEL_1, NOISE_COMBOBOX_ITEM_LABEL_2, NOISE_COMBOBOX_ITEM_LABEL_3, NOISE_COMBOBOX_ITEM_LABEL_4, NOISE_COMBOBOX_TOOLTIP, NOISE_LABEL, NUM_CLUSTERS_TO_EXTRACT_LABEL, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_COLUMNS, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_DEFAULT_VALUE, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_DESCRIPTION, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_MAXIMUM_VALUE, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_MINIMUM_VALUE, NUM_CLUSTERS_TO_EXTRACT_TEXTFIELD_TOOLTIP, NUM_COLUMNS_LABEL, NUM_COLUMNS_TEXTFIELD_COLUMNS, NUM_COLUMNS_TEXTFIELD_DEFAULT_VALUE, NUM_COLUMNS_TEXTFIELD_DESCRIPTION, NUM_COLUMNS_TEXTFIELD_MAXIMUM_VALUE, NUM_COLUMNS_TEXTFIELD_MINIMUM_VALUE, NUM_COLUMNS_TEXTFIELD_TOOLTIP, NUM_PERMUTATIONS_LABEL, NUM_PERMUTATIONS_TEXTFIELD_COLUMNS, NUM_PERMUTATIONS_TEXTFIELD_DEFAULT_VALUE, NUM_PERMUTATIONS_TEXTFIELD_DESCRIPTION, NUM_PERMUTATIONS_TEXTFIELD_MAXIMUM_VALUE, NUM_PERMUTATIONS_TEXTFIELD_MINIMUM_VALUE, NUM_PERMUTATIONS_TEXTFIELD_TOOLTIP, NUM_ROWS_LABEL, NUM_ROWS_TEXTFIELD_COLUMNS, NUM_ROWS_TEXTFIELD_DEFAULT_VALUE, NUM_ROWS_TEXTFIELD_DESCRIPTION, NUM_ROWS_TEXTFIELD_MAXIMUM_VALUE, NUM_ROWS_TEXTFIELD_MINIMUM_VALUE, NUM_ROWS_TEXTFIELD_TOOLTIP, OPEN_MENUITEM_DESCRIPTION, OPEN_MENUITEM_LABEL, OPEN_MENUITEM_MNEMONIC, OPEN_MENUITEM_TOOLTIP, OPEN_SETTINGS_FILE_SELECTION_DIALOG_TITLE, OVERVIEW_DIALOG_MESSAGE, OVERVIEW_DIALOG_TITLE, OVERVIEW_MENUITEM_DESCRIPTION, OVERVIEW_MENUITEM_LABEL, OVERVIEW_MENUITEM_MNEMONIC, OVERVIEW_MENUITEM_TOOLTIP, OVERWRITE_DIALOG_MESSAGE, OVERWRITE_DIALOG_TITLE, PACKAGE_NAME, PERCENT_SUPERVISION_LABEL, PERCENT_SUPERVISION_TEXTFIELD_COLUMNS, PERCENT_SUPERVISION_TEXTFIELD_DEFAULT_VALUE, PERCENT_SUPERVISION_TEXTFIELD_DESCRIPTION, PERCENT_SUPERVISION_TEXTFIELD_MAXIMUM_VALUE, PERCENT_SUPERVISION_TEXTFIELD_MINIMUM_VALUE, PERCENT_SUPERVISION_TEXTFIELD_TOOLTIP, PERCENT_TO_SHAVE_LABEL, PERCENT_TO_SHAVE_TEXTFIELD_COLUMNS, PERCENT_TO_SHAVE_TEXTFIELD_DEFAULT_VALUE, PERCENT_TO_SHAVE_TEXTFIELD_DESCRIPTION, PERCENT_TO_SHAVE_TEXTFIELD_MAXIMUM_VALUE, PERCENT_TO_SHAVE_TEXTFIELD_MINIMUM_VALUE, PERCENT_TO_SHAVE_TEXTFIELD_TOOLTIP, PERFORM_SUPERVISED_CHECKBOX_DEFAULT_VALUE, PERFORM_SUPERVISED_CHECKBOX_DESCRIPTION, PERFORM_SUPERVISED_CHECKBOX_LABEL, PERFORM_SUPERVISED_CHECKBOX_TOOLTIP, RAW_DATA_FILENAME_CHOOSER_BUTTON_DESCRIPTION, RAW_DATA_FILENAME_CHOOSER_BUTTON_LABEL, RAW_DATA_FILENAME_CHOOSER_BUTTON_TOOLTIP, RAW_DATA_FILENAME_LABEL, RAW_DATA_FILENAME_TEXTFIELD_COLUMNS, RAW_DATA_FILENAME_TEXTFIELD_DEFAULT_VALUE, RAW_DATA_FILENAME_TEXTFIELD_DESCRIPTION, RAW_DATA_FILENAME_TEXTFIELD_TOOLTIP, RAW_DATA_TAB_TITLE, SAVE_MENUITEM_DESCRIPTION, SAVE_MENUITEM_LABEL, SAVE_MENUITEM_MNEMONIC, SAVE_MENUITEM_TOOLTIP, SAVE_SETTINGS_FILE_SELECTION_DIALOG_TITLE, SHAVING_PANEL_TITLE, SIMULATION_DIALOG_BUTTON_LABEL, SIMULATION_DIALOG_MESSAGE, SIMULATION_DIALOG_TITLE, USER_GUIDE_DIALOG_TITLE, USER_GUIDE_FILE_URL, USER_GUIDE_HTTP_URL, USER_GUIDE_MENUITEM_DESCRIPTION, USER_GUIDE_MENUITEM_LABEL, USER_GUIDE_MENUITEM_MNEMONIC, USER_GUIDE_MENUITEM_TOOLTIP
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
Constructor and Description |
---|
GeneClustPanel(JFrame frame)
Class constructor
|
Modifier and Type | Method and Description |
---|---|
double |
getAmplitude()
Returns the maximum value of signal used when generating matrix
|
String |
getClassificationFileName()
Returns the string representing the classification filename
|
int |
getDegreesFreedom()
Returns the degrees of freedom (used by certain noise distributions)
|
int |
getGapTolerance()
Returns the gap tolerance
|
String |
getModel(boolean removeWhitespace)
Returns the string representing the data model
|
String |
getNoise()
Returns the string representing the noise
|
int |
getNoiseIndex()
Returns the index of the selected noise
|
int |
getNumClustersToExtract()
Returns the number of clusters to extract
|
int |
getNumColumns()
Returns the number of samples in the gene expression matrix (cell lines)
|
int |
getNumPermutations()
Returns the number of permutations to find optimal
|
int |
getNumRows()
Returns the number of rows in the gene expression matrix (genes)
|
int |
getPercentSupervision()
Returns the percent supervision
|
int |
getPercentToShave()
Returns the percent to shave
|
String |
getRawDataFileName()
Returns the string representing the filename
|
boolean |
isDemoEnabled()
Returns boolean that tells whether data should be generated or not.
|
boolean |
isDisplayDataMatrix()
Returns boolean that tells whether to display graph of
hierarchial clustering of samples should be performed or not.
|
boolean |
isDisplayGenesGraph()
Returns boolean that tells whether to display graph of
hierarchial clustering of genes should be performed or not.
|
boolean |
isDisplaySamplesGraph()
Returns boolean that tells whether to display graph of
hierarchial clustering of samples should be performed or not.
|
boolean |
isDisplayShaving()
Returns boolean that tells whether to display graph of
hierarchial clustering of samples should be performed or not.
|
boolean |
isPerformSupervised()
Returns boolean that tells whether supervised shaving should be
performed or not.
|
boolean |
isWriteMatrix()
Returns boolean that tells whether original matrix should be
written to disk or not.
|
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTree
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle
public GeneClustPanel(JFrame frame)
frame
- parent componentpublic boolean isWriteMatrix()
public boolean isDisplayGenesGraph()
public boolean isDisplaySamplesGraph()
public boolean isDisplayDataMatrix()
public boolean isDisplayShaving()
public boolean isPerformSupervised()
public int getPercentSupervision()
public String getClassificationFileName()
public int getNumClustersToExtract()
public int getNumPermutations()
public int getGapTolerance()
public int getPercentToShave()
public int getNumRows()
public int getNumColumns()
public double getAmplitude()
public String getModel(boolean removeWhitespace)
removeWhitespace
- if true, remove any whitespace from entrypublic String getNoise()
public int getNoiseIndex()
public int getDegreesFreedom()
public String getRawDataFileName()
public boolean isDemoEnabled()
Copyright © 2002 M.D. Anderson Cancer Center. All Rights Reserved.