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edu.stanford.genetics.treeview.karyoview
Class KaryoPanel  

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  edu.stanford.genetics.treeview.DragGridPanel
                      edu.stanford.genetics.treeview.karyoview.KaryoPanel

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.event.ComponentListener, java.awt.event.ContainerListener, java.util.EventListener, java.awt.event.FocusListener, java.awt.image.ImageObserver, edu.stanford.genetics.treeview.MainPanel, java.awt.MenuContainer, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.io.Serializable

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public class KaryoPanel

extends edu.stanford.genetics.treeview.DragGridPanel

implements edu.stanford.genetics.treeview.MainPanel

This class encapsulates a dendrogram view, which is the classic Eisen treeview. It uses a drag grid panel to lay out a bunch of linked visualizations of the data, a la Eisen. In addition to laying out components, it also manages the GlobalZoomMap. This is necessary since both the GTRView (gene tree) and GlobalView need to know where to lay out genes using the same map. The zoom map is managed by the ViewFrame- it represents the selected genes, and potentially forms a link between different views, only one of which is the DendroView.

Version:

$Revision: 1.19 $ $Date: 2003/09/23 17:43:47 $

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Nested Class Summary
(package private)  class	KaryoPanel.CoordinatesTask
(package private)  class	KaryoPanel.TimerListener

 

Nested classes inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

 

Nested classes inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

 

Nested classes inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

 

Nested classes inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

 

Field Summary
private  edu.stanford.genetics.treeview.ConfigNode	configNode
(package private)  javax.swing.ProgressMonitor	coordinatesMonitor
(package private)  CoordinatesSettingsPanel	coordinatesPanel
(package private)  KaryoPanel.CoordinatesTask	coordinatesTask
(package private)  javax.swing.Timer	coordinatesTimer
private  Genome	genome
private  KaryoDrawer	karyoDrawer
private  KaryoView	karyoView
private  boolean	loaded
private  KaryoViewParameterPanel	parameterPanel
private  Genome	startingGenome           store original coordinates here...
private  edu.stanford.genetics.treeview.MessagePanel	statusPanel
private  edu.stanford.genetics.treeview.ViewFrame	viewFrame
private  boolean	windowActive

 

Fields inherited from class edu.stanford.genetics.treeview.DragGridPanel

 

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.Container

 

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

 

Fields inherited from interface java.awt.image.ImageObserver

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

 

Constructor Summary

KaryoPanel(edu.stanford.genetics.treeview.DataModel tvmodel, edu.stanford.genetics.treeview.CdtSelection cdtSelection, edu.stanford.genetics.treeview.ViewFrame vFrame, edu.stanford.genetics.treeview.ConfigNode configNode)           Constructor for the DendroView object

 

Method Summary
void	addComponent(java.awt.Component component, java.awt.Rectangle rectangle)           Adds a component to the DendroView
void	addView(edu.stanford.genetics.treeview.ModelView modelView, java.awt.Rectangle rectangle)           Adds a ModelView to the KaryoPanel
void	bindConfig(edu.stanford.genetics.treeview.ConfigNode configNode)           Setter for configNode
edu.stanford.genetics.treeview.ConfigNode	getConfigNode()           Getter for configNode
private  edu.stanford.genetics.treeview.ConfigNode	getFirst(java.lang.String name)           always returns an instance of the node, even if it has to create it.
Genome	getGenome()           Getter for genome
void	getGenome(edu.stanford.genetics.treeview.DataModel newModel)
void	getGenome(edu.stanford.genetics.treeview.FileSet fileSet)
KaryoDrawer	getKaryoDrawer()           Getter for karyoDrawer
KaryoView	getKaryoView()           Getter for karyoView
void	populateAnalysisMenu(java.awt.Menu menu)           Add items which do some kind of analysis
void	populateExportMenu(java.awt.Menu menu)           Add items which allow for export, if any.
void	populateSettingsMenu(java.awt.Menu menu)           Add items related to settings
void	scrollToIndex(int i)           ensure a particular index is visible.
void	setGenome(Genome genome)           Setter for genome
void	setKaryoDrawer(KaryoDrawer karyoDrawer)           Setter for karyoDrawer
void	setKaryoView(KaryoView karyoView)           Setter for karyoView
private  void	setupViews()           This method should be called only during initial setup of the modelview It sets up the views, which are reinitialized if the model changes.
private  void	setWindowActive(boolean flag)           Sets the windowActive attribute of the DendroView object
void	showAveragingPopup()
void	showCoordinatesPopup()
void	showDisplayPopup()
void	syncConfig()           This makes the persistent storage resemble the compnents, if it doesn't already.
void	useOriginal()
boolean	windowActive()           Determines if window is currently active

 

Methods inherited from class edu.stanford.genetics.treeview.DragGridPanel

addComponent, componentAdded, componentHidden, componentMoved, componentRemoved, componentResized, componentShown, doLayout, focusGained, focusLost, getBorderHeight, getBorderWidth, getFocusHeight, getFocusWidth, getHeights, getMinimumHeight, getMinimumWidth, getPreferredSize, getWidths, isAdjustable, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, paintComponent, removeComponent, setAdjustable, setBorderHeight, setBorderWidth, setFocusHeight, setFocusWidth, setHeights, setMinimumHeight, setMinimumWidth, setWidths, toString

 

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

 

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

 

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, 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, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, 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, 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, processMouseEvent, 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, transferFocus, transferFocusBackward, transferFocusUpCycle

 

Methods inherited from class java.lang.Object

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

 

Field Detail

coordinatesMonitor

javax.swing.ProgressMonitor coordinatesMonitor

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coordinatesTimer

javax.swing.Timer coordinatesTimer

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coordinatesTask

KaryoPanel.CoordinatesTask coordinatesTask

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coordinatesPanel

CoordinatesSettingsPanel coordinatesPanel

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configNode

private edu.stanford.genetics.treeview.ConfigNode configNode

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viewFrame

private edu.stanford.genetics.treeview.ViewFrame viewFrame

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loaded

private boolean loaded

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windowActive

private boolean windowActive

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startingGenome

private Genome startingGenome

store original coordinates here...

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genome

private Genome genome

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karyoDrawer

private KaryoDrawer karyoDrawer

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karyoView

private KaryoView karyoView

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parameterPanel

private KaryoViewParameterPanel parameterPanel

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statusPanel

private edu.stanford.genetics.treeview.MessagePanel statusPanel

Constructor Detail

KaryoPanel

public KaryoPanel(edu.stanford.genetics.treeview.DataModel tvmodel,
                  edu.stanford.genetics.treeview.CdtSelection cdtSelection,
                  edu.stanford.genetics.treeview.ViewFrame vFrame,
                  edu.stanford.genetics.treeview.ConfigNode configNode)

Constructor for the DendroView object

Method Detail

getGenome

public void getGenome(edu.stanford.genetics.treeview.FileSet fileSet)
               throws edu.stanford.genetics.treeview.LoadException

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getGenome

public void getGenome(edu.stanford.genetics.treeview.DataModel newModel)

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useOriginal

public void useOriginal()

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setWindowActive

private void setWindowActive(boolean flag)

Sets the windowActive attribute of the DendroView object

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setupViews

private void setupViews()

This method should be called only during initial setup of the modelview It sets up the views, which are reinitialized if the model changes.

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addComponent

public void addComponent(java.awt.Component component,
                         java.awt.Rectangle rectangle)

Adds a component to the DendroView

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addView

public void addView(edu.stanford.genetics.treeview.ModelView modelView,
                    java.awt.Rectangle rectangle)

Adds a ModelView to the KaryoPanel

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windowActive

public boolean windowActive()

Determines if window is currently active

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syncConfig

public void syncConfig()

This makes the persistent storage resemble the compnents, if it doesn't already.

Specified by:

syncConfig in interface edu.stanford.genetics.treeview.MainPanel

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showDisplayPopup

public void showDisplayPopup()

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showCoordinatesPopup

public void showCoordinatesPopup()

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showAveragingPopup

public void showAveragingPopup()

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populateSettingsMenu

public void populateSettingsMenu(java.awt.Menu menu)

Add items related to settings

Specified by:

populateSettingsMenu in interface edu.stanford.genetics.treeview.MainPanel

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populateAnalysisMenu

public void populateAnalysisMenu(java.awt.Menu menu)

Add items which do some kind of analysis

Specified by:

populateAnalysisMenu in interface edu.stanford.genetics.treeview.MainPanel

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populateExportMenu

public void populateExportMenu(java.awt.Menu menu)

Add items which allow for export, if any.

Specified by:

populateExportMenu in interface edu.stanford.genetics.treeview.MainPanel

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scrollToIndex

public void scrollToIndex(int i)

ensure a particular index is visible. Used by Find.

Specified by:

scrollToIndex in interface edu.stanford.genetics.treeview.MainPanel

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bindConfig

public void bindConfig(edu.stanford.genetics.treeview.ConfigNode configNode)

Setter for configNode

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getConfigNode

public edu.stanford.genetics.treeview.ConfigNode getConfigNode()

Getter for configNode

Specified by:

getConfigNode in interface edu.stanford.genetics.treeview.MainPanel

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setGenome

public void setGenome(Genome genome)

Setter for genome

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getGenome

public Genome getGenome()

Getter for genome

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setKaryoDrawer

public void setKaryoDrawer(KaryoDrawer karyoDrawer)

Setter for karyoDrawer

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getKaryoDrawer

public KaryoDrawer getKaryoDrawer()

Getter for karyoDrawer

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setKaryoView

public void setKaryoView(KaryoView karyoView)

Setter for karyoView

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getKaryoView

public KaryoView getKaryoView()

Getter for karyoView

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getFirst

private edu.stanford.genetics.treeview.ConfigNode getFirst(java.lang.String name)

always returns an instance of the node, even if it has to create it.

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> edu >> stanford >> genetics >> treeview >> [ karyoview overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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