public class GeneSetTreePanel extends GeneSetPanel
JScrollPane.AccessibleJScrollPane, JScrollPane.ScrollBar
JComponent.AccessibleJComponent
Container.AccessibleAWTContainer
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
Modifier and Type | Field and Description |
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protected GeneSetTerm |
currentlySelectedGeneSet |
callingFrame, DELETED, FDR_THRESHOLD_FOR_FILTER, geneData, hideEmpty, hideInsignificant, hideNonCustom, MAX_DEFINITION_LENGTH, messenger, NOACTION, RESOURCE_LOCATION, RESTORED, settings, USER_NODE_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 |
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GeneSetTreePanel(MainFrame callingFrame,
Settings settings) |
Modifier and Type | Method and Description |
---|---|
void |
addedGeneSet(GeneSetTerm id) |
void |
addRun() |
protected boolean |
deleteUserGeneSet(GeneSetTerm classID) |
protected void |
expandAll(boolean expand) |
protected void |
expandNode(TreePath parent,
boolean expand)
Fully expand or collapse a node.
|
boolean |
expandToGeneSet(GeneSetTerm classID) |
void |
filter(boolean propagate) |
void |
filter(Collection<GeneSetTerm> selectedTerms) |
TreePath |
find(GeneSetTerm id) |
void |
fireResultsChanged() |
GeneSetTerm |
getCurrentlySelectedGeneSet() |
Collection<GeneSetTreeNode> |
getLeaves() |
void |
initialize(GeneAnnotations gd)
Called after data files are read in.
|
void |
mouseReleased(MouseEvent e) |
protected GeneSetTerm |
popupRespondAndGetGeneSet(MouseEvent e) |
void |
refreshView()
Force to repaint, reapply filters.
|
protected void |
removedGeneSet(GeneSetTerm id)
Update the view to reflect changes
|
void |
removeRun(GeneSetPvalRun runToRemove)
Do any extra cleanup after a run has been deleted.
|
void |
resetView()
Restore view
|
void |
setHideInsignificant(boolean b)
Has no effect unless you call filter() afterwards
|
protected void |
showPopupMenu(MouseEvent e) |
addDependentPanel, configurePopup, configurePopupListener, findInTree, modMenuItem_actionPerformed, openUrlForGeneSet, setMessenger, showDetailsForGeneSet
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
protected GeneSetTerm currentlySelectedGeneSet
public void addedGeneSet(GeneSetTerm id)
addedGeneSet
in class GeneSetPanel
public void addRun()
addRun
in class GeneSetPanel
public boolean expandToGeneSet(GeneSetTerm classID)
classID
- a node somewhere in the tree; we expand the pathpublic void filter(boolean propagate)
filter
in class GeneSetPanel
public void filter(Collection<GeneSetTerm> selectedTerms)
selectedTerms
- public TreePath find(GeneSetTerm id)
tree
- names
- public void fireResultsChanged()
public GeneSetTerm getCurrentlySelectedGeneSet()
public Collection<GeneSetTreeNode> getLeaves()
public void initialize(GeneAnnotations gd)
goData
- geneData
- public void mouseReleased(MouseEvent e)
e
- public void refreshView()
refreshView
in class GeneSetPanel
public void removeRun(GeneSetPvalRun runToRemove)
GeneSetPanel
removeRun
in class GeneSetPanel
public void resetView()
GeneSetPanel
resetView
in class GeneSetPanel
public void setHideInsignificant(boolean b)
b
- protected boolean deleteUserGeneSet(GeneSetTerm classID)
deleteUserGeneSet
in class GeneSetPanel
protected void expandAll(boolean expand)
expand
- If false, collapses all nodes. If true, expands them all.protected void expandNode(TreePath parent, boolean expand)
parent
- expand
- protected GeneSetTerm popupRespondAndGetGeneSet(MouseEvent e)
popupRespondAndGetGeneSet
in class GeneSetPanel
e
- protected void removedGeneSet(GeneSetTerm id)
GeneSetPanel
removedGeneSet
in class GeneSetPanel
protected void showPopupMenu(MouseEvent e)
showPopupMenu
in class GeneSetPanel
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