jebl.gui.trees.treeviewer_dev
Class TreePane

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

All Implemented Interfaces:

ImageObserver, MenuContainer, Printable, Serializable, PainterListener

public class TreePane
extends JComponent
implements 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

String

COLLAPSE_ATTRIBUTE_NAME

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	addSelectedTip(Node selectedTip)
void	addSelectedTips(Node selectedNode)
void	addTreePaneListener(TreePaneListener listener)
void	addTreeSelectionListener(TreeSelectionListener treeSelectionListener)
void	annotateSelectedNodes(String name, Object value)
void	annotateSelectedTips(String name, Object value)
void	clearSelection()
void	collapseSelectedNodes()
void	drawTree(Graphics2D g2, double width, double height)
void	fireTreePaneSettingsChanged()
Painter<Node>	getBranchLabelPainter()
SortedRootedTree.BranchOrdering	getBranchOrdering()
BasicStroke	getBranchStroke()
TransformedRootedTree.Transform	getBranchTransform()
BasicStroke	getCalloutStroke()
Rectangle2D	getDragRectangle()
double	getHeightAt(Graphics2D graphics2D, Point2D point)
Node	getNodeAt(Graphics2D g2, Point point)
Painter<Node>	getNodeBarPainter()
Painter<Node>	getNodeLabelPainter()
Set<Node>	getNodesAt(Graphics2D g2, Rectangle rect)
RootedTree	getOriginalTree()
Painter<TreePane>	getScaleBarPainter()
Set<Node>	getSelectedNodes()
Set<Node>	getSelectedTips()
Paint	getSelectionPaint()
Painter<Node>	getTipLabelPainter()
RootedTree	getTree()
Rectangle2D	getTreeBounds()
TreeLayout	getTreeLayout()
double	getTreeScale() This returns the scaling factor between the graphical image and the branch lengths of the tree
boolean	hasSelection()
boolean	isOrderBranchesOn()
boolean	isShowingTipCallouts()
boolean	isTransformBranchesOn()
boolean	maintainAspectRatio() Return whether the two axis scales should be maintained relative to each other
void	paint(Graphics graphics)
void	painterChanged()
void	painterSettingsChanged()
int	print(Graphics graphics, PageFormat pageFormat, int pageIndex)
void	removeTreePaneListener(TreePaneListener listener)
void	removeTreeSelectionListener(TreeSelectionListener treeSelectionListener)
void	scrollPointToVisible(Point point)
void	selectAllNodes()
void	selectAllTaxa()
void	selectCladesFromSelectedNodes()
void	selectNodesFromSelectedTips()
void	selectTipsFromSelectedNodes()
void	setBounds(int x, int y, int width, int height)
void	setBounds(Rectangle rectangle)
void	setBranchColouringDecorator(String branchColouringAttribute, Decorator branchColouringDecorator)
void	setBranchDecorator(Decorator branchDecorator)
void	setBranchLabelPainter(LabelPainter<Node> branchLabelPainter)
void	setBranchOrdering(SortedRootedTree.BranchOrdering branchOrdering)
void	setBranchStroke(BasicStroke stroke)
void	setBranchTransform(TransformedRootedTree.Transform branchTransform)
void	setCalloutStroke(BasicStroke calloutStroke)
void	setDragRectangle(Rectangle2D dragRectangle)
void	setNodeBarPainter(NodeBarPainter nodeBarPainter)
void	setNodeLabelPainter(LabelPainter<Node> nodeLabelPainter)
void	setOrderBranchesOn(boolean orderBranchesOn)
void	setPreferredSize(Dimension dimension)
void	setRuler(double rulerHeight)
void	setScaleBarPainter(Painter<TreePane> scaleBarPainter)
void	setSelectedClade(Node selectedNode)
void	setSelectedNode(Node selectedNode)
void	setSelectedTip(Node selectedTip)
void	setSelectedTips(Node selectedNode)
void	setSelectionPaint(Paint selectionPaint)
void	setShowingTipCallouts(boolean showingTipCallouts)
void	setSize(Dimension dimension)
void	setSize(int width, int height)
void	setTipLabelPainter(LabelPainter<Node> tipLabelPainter)
void	setTransformBranchesOn(boolean transformBranchesOn)
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

Field Detail

COLLAPSE_ATTRIBUTE_NAME

public final String COLLAPSE_ATTRIBUTE_NAME

See Also:

Constant Field Values

Constructor Detail

TreePane

public TreePane()

Method Detail

getTree

public RootedTree getTree()

setTree

public void setTree(RootedTree tree)

getTreeLayout

public TreeLayout getTreeLayout()

setTreeLayout

public void setTreeLayout(TreeLayout treeLayout)

setBranchDecorator

public void setBranchDecorator(Decorator branchDecorator)

setBranchColouringDecorator

public void setBranchColouringDecorator(String branchColouringAttribute,
                                        Decorator branchColouringDecorator)

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

painterSettingsChanged

public void painterSettingsChanged()

Specified by:

painterSettingsChanged in interface PainterListener

getBranchStroke

public BasicStroke getBranchStroke()

setBranchStroke

public void setBranchStroke(BasicStroke stroke)

getCalloutStroke

public BasicStroke getCalloutStroke()

setCalloutStroke

public void setCalloutStroke(BasicStroke calloutStroke)

getSelectionPaint

public Paint getSelectionPaint()

setSelectionPaint

public void setSelectionPaint(Paint selectionPaint)

isTransformBranchesOn

public boolean isTransformBranchesOn()

setTransformBranchesOn

public void setTransformBranchesOn(boolean transformBranchesOn)

getBranchTransform

public TransformedRootedTree.Transform getBranchTransform()

setBranchTransform

public void setBranchTransform(TransformedRootedTree.Transform branchTransform)

isOrderBranchesOn

public boolean isOrderBranchesOn()

setOrderBranchesOn

public void setOrderBranchesOn(boolean orderBranchesOn)

getBranchOrdering

public SortedRootedTree.BranchOrdering getBranchOrdering()

setBranchOrdering

public void setBranchOrdering(SortedRootedTree.BranchOrdering branchOrdering)

getOriginalTree

public RootedTree getOriginalTree()

isShowingTipCallouts

public boolean isShowingTipCallouts()

setShowingTipCallouts

public void setShowingTipCallouts(boolean showingTipCallouts)

setSelectedNode

public void setSelectedNode(Node selectedNode)

setSelectedTip

public void setSelectedTip(Node selectedTip)

setSelectedClade

public void setSelectedClade(Node selectedNode)

setSelectedTips

public void setSelectedTips(Node selectedNode)

addSelectedNode

public void addSelectedNode(Node selectedNode)

addSelectedTip

public void addSelectedTip(Node selectedTip)

addSelectedClade

public void addSelectedClade(Node selectedNode)

addSelectedTips

public void addSelectedTips(Node selectedNode)

selectCladesFromSelectedNodes

public void selectCladesFromSelectedNodes()

selectTipsFromSelectedNodes

public void selectTipsFromSelectedNodes()

selectNodesFromSelectedTips

public void selectNodesFromSelectedTips()

selectAllTaxa

public void selectAllTaxa()

selectAllNodes

public void selectAllNodes()

clearSelection

public void clearSelection()

hasSelection

public boolean hasSelection()

collapseSelectedNodes

public void collapseSelectedNodes()

annotateSelectedNodes

public void annotateSelectedNodes(String name,
                                  Object value)

annotateSelectedTips

public void annotateSelectedTips(String name,
                                 Object value)

maintainAspectRatio

public boolean maintainAspectRatio()

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

Returns:

a boolean

setTipLabelPainter

public void setTipLabelPainter(LabelPainter<Node> tipLabelPainter)

getTipLabelPainter

public Painter<Node> getTipLabelPainter()

setNodeLabelPainter

public void setNodeLabelPainter(LabelPainter<Node> nodeLabelPainter)

getNodeLabelPainter

public Painter<Node> getNodeLabelPainter()

setBranchLabelPainter

public void setBranchLabelPainter(LabelPainter<Node> branchLabelPainter)

getBranchLabelPainter

public Painter<Node> getBranchLabelPainter()

setNodeBarPainter

public void setNodeBarPainter(NodeBarPainter nodeBarPainter)

getNodeBarPainter

public Painter<Node> getNodeBarPainter()

setScaleBarPainter

public void setScaleBarPainter(Painter<TreePane> scaleBarPainter)

getScaleBarPainter

public Painter<TreePane> getScaleBarPainter()

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()

getSelectedTips

public Set<Node> getSelectedTips()

getDragRectangle

public Rectangle2D getDragRectangle()

setDragRectangle

public void setDragRectangle(Rectangle2D dragRectangle)

setRuler

public void setRuler(double rulerHeight)

scrollPointToVisible

public void scrollPointToVisible(Point point)

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

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

addTreePaneListener

public void addTreePaneListener(TreePaneListener listener)

removeTreePaneListener

public void removeTreePaneListener(TreePaneListener listener)

fireTreePaneSettingsChanged

public void fireTreePaneSettingsChanged()

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