jebl.gui.trees.treeviewer
Class TreePane

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              jebl.gui.trees.treeviewer.TreePane

All Implemented Interfaces:

ImageObserver, MenuContainer, Printable, Serializable, PainterListener, ControlsProvider

public class TreePane
extends JComponent
implements ControlsProvider, PainterListener, Printable

Author:

Andrew Rambaut

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.print.Printable

NO_SUCH_PAGE, PAGE_EXISTS

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

TreePane()

Method Summary

void	addSelectedClade(Node selectedNode)
void	addSelectedNode(Node selectedNode)
void	addSelectedTaxa(Node selectedNode)
void	addSelectedTaxon(Taxon selectedTaxon)
void	addTreeSelectionListener(TreeSelectionListener treeSelectionListener)
void	annotateSelectedNodes(String name, Object value)
void	annotateSelectedTaxa(String name, Object value)
void	clearSelection()
protected void	drawTree(Graphics2D g2, double width, double height)
Painter<Node>	getBranchLabelPainter()
List<Controls>	getControls(boolean detachPrimaryCheckbox) Get a list of Controls handled by this provider.
Rectangle2D	getDragRectangle()
double	getHeightAt(Graphics2D graphics2D, Point2D point)
Node	getNodeAt(Graphics2D g2, Point point)
Painter<Node>	getNodeLabelPainter()
Set<Node>	getNodesAt(Graphics2D g2, Rectangle rect)
Painter<TreePane>	getScaleBarPainter()
Set<Node>	getSelectedNodes()
Set<Taxon>	getSelectedTaxa()
void	getSettings(ControlsSettings settings) Get the settings for a given Controls object.
Painter<Node>	getTaxonLabelPainter()
RootedTree	getTree()
Rectangle2D	getTreeBounds()
double	getTreeScale() This returns the scaling factor between the graphical image and the branch lengths of the tree
boolean	isShowingRootBranch()
boolean	isShowingTaxonCallouts()
boolean	maintainAspectRatio() Return whether the two axis scales should be maintained relative to each other
void	paint(Graphics graphics)
void	painterChanged()
int	print(Graphics graphics, PageFormat pageFormat, int pageIndex)
void	removeTreeSelectionListener(TreeSelectionListener treeSelectionListener)
void	scrollPointToVisible(Point point)
void	setBounds(int x, int y, int width, int height)
void	setBounds(Rectangle rectangle)
void	setBranchDecorator(BranchDecorator branchDecorator)
void	setBranchLabelPainter(Painter<Node> branchLabelPainter)
void	setBranchLineWeight(float weight)
void	setBranchOrdering(boolean orderBranches, SortedRootedTree.BranchOrdering branchOrdering)
void	setBranchTransform(boolean transformBranches, TransformedRootedTree.Transform branchTransform)
void	setControlPalette(ControlPalette controlPalette) Give the controls provider with a handle for the controlPalette object.
void	setDragRectangle(Rectangle2D dragRectangle)
void	setNodeLabelPainter(Painter<Node> nodeLabelPainter)
void	setPreferredSize(Dimension dimension)
void	setRuler(double rulerHeight)
void	setScaleBarPainter(Painter<TreePane> scaleBarPainter)
void	setSelectedClade(Node selectedNode)
void	setSelectedNode(Node selectedNode)
void	setSelectedTaxa(Node selectedNode)
void	setSelectedTaxon(Taxon selectedTaxon)
void	setSettings(ControlsSettings settings) Give the provider some settings.
void	setShowingRootBranch(boolean showingRootBranch)
void	setShowingTaxonCallouts(boolean showingTaxonCallouts)
void	setSize(Dimension dimension)
void	setSize(int width, int height)
void	setTaxonLabelPainter(Painter<Node> taxonLabelPainter)
void	setTree(RootedTree tree)
void	setTreeLayout(TreeLayout treeLayout)

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, 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, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, paramString, 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, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update, updateUI

Methods inherited from class java.awt.Container

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, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

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, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

TreePane

public TreePane()

Method Detail

getTree

public RootedTree getTree()

setTree

public void setTree(RootedTree tree)

setTreeLayout

public void setTreeLayout(TreeLayout treeLayout)

getTreeBounds

public Rectangle2D getTreeBounds()

getTreeScale

public double getTreeScale()

This returns the scaling factor between the graphical image and the branch lengths of the tree

Returns:

the tree scale

painterChanged

public void painterChanged()

Specified by:

painterChanged in interface PainterListener

setBranchOrdering

public void setBranchOrdering(boolean orderBranches,
                              SortedRootedTree.BranchOrdering branchOrdering)

setBranchTransform

public void setBranchTransform(boolean transformBranches,
                               TransformedRootedTree.Transform branchTransform)

isShowingRootBranch

public boolean isShowingRootBranch()

setShowingRootBranch

public void setShowingRootBranch(boolean showingRootBranch)

isShowingTaxonCallouts

public boolean isShowingTaxonCallouts()

setShowingTaxonCallouts

public void setShowingTaxonCallouts(boolean showingTaxonCallouts)

setSelectedNode

public void setSelectedNode(Node selectedNode)

setSelectedTaxon

public void setSelectedTaxon(Taxon selectedTaxon)

setSelectedClade

public void setSelectedClade(Node selectedNode)

setSelectedTaxa

public void setSelectedTaxa(Node selectedNode)

addSelectedNode

public void addSelectedNode(Node selectedNode)

addSelectedTaxon

public void addSelectedTaxon(Taxon selectedTaxon)

addSelectedClade

public void addSelectedClade(Node selectedNode)

addSelectedTaxa

public void addSelectedTaxa(Node selectedNode)

clearSelection

public void clearSelection()

annotateSelectedNodes

public void annotateSelectedNodes(String name,
                                  Object value)

annotateSelectedTaxa

public void annotateSelectedTaxa(String name,
                                 Object value)

maintainAspectRatio

public boolean maintainAspectRatio()

Return whether the two axis scales should be maintained relative to each other

Returns:

a boolean

setTaxonLabelPainter

public void setTaxonLabelPainter(Painter<Node> taxonLabelPainter)

getTaxonLabelPainter

public Painter<Node> getTaxonLabelPainter()

setNodeLabelPainter

public void setNodeLabelPainter(Painter<Node> nodeLabelPainter)

getNodeLabelPainter

public Painter<Node> getNodeLabelPainter()

setBranchLabelPainter

public void setBranchLabelPainter(Painter<Node> branchLabelPainter)

getBranchLabelPainter

public Painter<Node> getBranchLabelPainter()

setScaleBarPainter

public void setScaleBarPainter(Painter<TreePane> scaleBarPainter)

getScaleBarPainter

public Painter<TreePane> getScaleBarPainter()

setBranchDecorator

public void setBranchDecorator(BranchDecorator branchDecorator)

setBranchLineWeight

public void setBranchLineWeight(float weight)

setPreferredSize

public void setPreferredSize(Dimension dimension)

Overrides:

setPreferredSize in class JComponent

getHeightAt

public double getHeightAt(Graphics2D graphics2D,
                          Point2D point)

getNodeAt

public Node getNodeAt(Graphics2D g2,
                      Point point)

getNodesAt

public Set<Node> getNodesAt(Graphics2D g2,
                            Rectangle rect)

getSelectedNodes

public Set<Node> getSelectedNodes()

getSelectedTaxa

public Set<Taxon> getSelectedTaxa()

getDragRectangle

public Rectangle2D getDragRectangle()

setDragRectangle

public void setDragRectangle(Rectangle2D dragRectangle)

setRuler

public void setRuler(double rulerHeight)

scrollPointToVisible

public void scrollPointToVisible(Point point)

setControlPalette

public void setControlPalette(ControlPalette controlPalette)

Description copied from interface: ControlsProvider

Give the controls provider with a handle for the controlPalette object.

Specified by:

setControlPalette in interface ControlsProvider

getControls

public List<Controls> getControls(boolean detachPrimaryCheckbox)

Description copied from interface: ControlsProvider

Get a list of Controls handled by this provider.

Specified by:

getControls in interface ControlsProvider

Parameters:

detachPrimaryCheckbox - When false, do nothing. When true, if controls have a "main" on/off switch (implemented as a JCheckBox), that checkbox should not be included in the controls panel but returned in

Returns:

A list of Controls

See Also:

Controls.getPrimaryCheckbox()

setSettings

public void setSettings(ControlsSettings settings)

Description copied from interface: ControlsProvider

Give the provider some settings.

Specified by:

setSettings in interface ControlsProvider

getSettings

public void getSettings(ControlsSettings settings)

Description copied from interface: ControlsProvider

Get the settings for a given Controls object.

Specified by:

getSettings in interface ControlsProvider

addTreeSelectionListener

public void addTreeSelectionListener(TreeSelectionListener treeSelectionListener)

removeTreeSelectionListener

public void removeTreeSelectionListener(TreeSelectionListener treeSelectionListener)

paint

public void paint(Graphics graphics)

Overrides:

paint in class JComponent

print

public int print(Graphics graphics,
                 PageFormat pageFormat,
                 int pageIndex)
          throws PrinterException

Specified by:

print in interface Printable

Throws:

PrinterException

drawTree

protected void drawTree(Graphics2D g2,
                        double width,
                        double height)

setBounds

public void setBounds(int x,
                      int y,
                      int width,
                      int height)

Overrides:

setBounds in class Component

setBounds

public void setBounds(Rectangle rectangle)

Overrides:

setBounds in class Component

setSize

public void setSize(Dimension dimension)

Overrides:

setSize in class Component

setSize

public void setSize(int width,
                    int height)

Overrides:

setSize in class Component