public abstract class GeneSetPanel extends JScrollPane
JScrollPane.AccessibleJScrollPane, JScrollPane.ScrollBar
JComponent.AccessibleJComponent
Container.AccessibleAWTContainer
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
Modifier and Type | Field and Description |
---|---|
protected MainFrame |
callingFrame |
static String |
DELETED |
static double |
FDR_THRESHOLD_FOR_FILTER |
protected GeneAnnotations |
geneData |
protected static boolean |
hideEmpty |
protected static boolean |
hideInsignificant |
protected static boolean |
hideNonCustom |
static int |
MAX_DEFINITION_LENGTH |
protected StatusViewer |
messenger |
static String |
NOACTION |
static String |
RESOURCE_LOCATION |
static String |
RESTORED |
protected Settings |
settings |
static Color |
USER_NODE_COLOR |
static Color |
USER_NODE_TEXT_COLOR |
columnHeader, horizontalScrollBar, horizontalScrollBarPolicy, lowerLeft, lowerRight, rowHeader, upperLeft, upperRight, verticalScrollBar, verticalScrollBarPolicy, viewport
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
COLUMN_HEADER, HORIZONTAL_SCROLLBAR, HORIZONTAL_SCROLLBAR_ALWAYS, HORIZONTAL_SCROLLBAR_AS_NEEDED, HORIZONTAL_SCROLLBAR_NEVER, HORIZONTAL_SCROLLBAR_POLICY, LOWER_LEADING_CORNER, LOWER_LEFT_CORNER, LOWER_RIGHT_CORNER, LOWER_TRAILING_CORNER, ROW_HEADER, UPPER_LEADING_CORNER, UPPER_LEFT_CORNER, UPPER_RIGHT_CORNER, UPPER_TRAILING_CORNER, VERTICAL_SCROLLBAR, VERTICAL_SCROLLBAR_ALWAYS, VERTICAL_SCROLLBAR_AS_NEEDED, VERTICAL_SCROLLBAR_NEVER, VERTICAL_SCROLLBAR_POLICY, VIEWPORT
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
Constructor and Description |
---|
GeneSetPanel(Settings settings,
MainFrame callingFrame) |
Modifier and Type | Method and Description |
---|---|
void |
addDependentPanel(GeneSetPanel panel) |
protected abstract void |
addedGeneSet(GeneSetTerm addedTerm) |
abstract void |
addRun() |
protected GeneSetPanelPopupMenu |
configurePopup(MouseEvent e)
Configure the base popup common to any compoment showing gene sets.
|
protected MouseListener |
configurePopupListener() |
protected boolean |
deleteUserGeneSet(GeneSetTerm classID) |
abstract void |
filter(boolean propagate) |
void |
findInTree(ActionEvent e) |
protected void |
modMenuItem_actionPerformed(ActionEvent e) |
protected void |
openUrlForGeneSet(String url,
GeneSetTerm term)
Forms a url like url + term.getId().
|
protected abstract GeneSetTerm |
popupRespondAndGetGeneSet(MouseEvent e) |
abstract void |
refreshView()
Updating, reapplying filters
|
protected abstract void |
removedGeneSet(GeneSetTerm addedTerm)
Update the view to reflect changes
|
abstract void |
removeRun(GeneSetPvalRun runToRemove)
Do any extra cleanup after a run has been deleted.
|
abstract void |
resetView()
Restore view
|
void |
setMessenger(StatusViewer messenger) |
protected void |
showDetailsForGeneSet(GeneSetTerm id,
GeneSetPvalRun run)
Create the popup window with the visualization for a specific gene set and results.
|
protected abstract void |
showPopupMenu(MouseEvent e) |
createHorizontalScrollBar, createVerticalScrollBar, createViewport, getAccessibleContext, getColumnHeader, getCorner, getHorizontalScrollBar, getHorizontalScrollBarPolicy, getRowHeader, getUI, getUIClassID, getVerticalScrollBar, getVerticalScrollBarPolicy, getViewport, getViewportBorder, getViewportBorderBounds, isValidateRoot, isWheelScrollingEnabled, paramString, setColumnHeader, setColumnHeaderView, setComponentOrientation, setCorner, setHorizontalScrollBar, setHorizontalScrollBarPolicy, setLayout, setRowHeader, setRowHeaderView, setUI, setVerticalScrollBar, setVerticalScrollBarPolicy, setViewport, setViewportBorder, setViewportView, setWheelScrollingEnabled, 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, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, 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, 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, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle
public static final double FDR_THRESHOLD_FOR_FILTER
public static final Color USER_NODE_COLOR
public static final Color USER_NODE_TEXT_COLOR
public static final String RESOURCE_LOCATION
protected MainFrame callingFrame
protected GeneAnnotations geneData
protected StatusViewer messenger
protected Settings settings
public static final String NOACTION
public static final String RESTORED
public static final String DELETED
public static final int MAX_DEFINITION_LENGTH
protected static boolean hideEmpty
protected static boolean hideInsignificant
protected static boolean hideNonCustom
public void addDependentPanel(GeneSetPanel panel)
public abstract void addRun()
public abstract void removeRun(GeneSetPvalRun runToRemove)
runToRemove
- public void findInTree(ActionEvent e)
e
- public abstract void resetView()
public abstract void refreshView()
public void setMessenger(StatusViewer messenger)
messenger
- protected abstract void addedGeneSet(GeneSetTerm addedTerm)
addedTerm
- protected GeneSetPanelPopupMenu configurePopup(MouseEvent e)
e
- protected MouseListener configurePopupListener()
protected boolean deleteUserGeneSet(GeneSetTerm classID)
classID
- public abstract void filter(boolean propagate)
protected void openUrlForGeneSet(String url, GeneSetTerm term)
url
- term
- protected void modMenuItem_actionPerformed(ActionEvent e)
protected abstract GeneSetTerm popupRespondAndGetGeneSet(MouseEvent e)
protected abstract void removedGeneSet(GeneSetTerm addedTerm)
addedTerm
- protected void showDetailsForGeneSet(GeneSetTerm id, GeneSetPvalRun run)
id
- run
- can be nullprotected abstract void showPopupMenu(MouseEvent e)
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