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edu.stanford.genetics.treeview.karyoview
Class KaryoView  

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

All Implemented Interfaces:

javax.accessibility.Accessible, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.event.MouseListener, java.util.Observer, java.io.Serializable

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public class KaryoView

extends edu.stanford.genetics.treeview.ModelView

implements java.util.Observer

This class is a model view that displays the karyoscope view for a single experiment in the dataset. There is really quite a lot of complexity involved. I have decided to factor out all knowledge of where things are positioned into the KaryoDrawer class. I have retained knowledge of averaging in this class, as well as most of the component mechanics. This is to facilitate the use of KaryoDrawer for drawing to images with configurable parameters.

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Nested Class Summary
private  class	KaryoView.AveragerSettingsPanel           Inner class to manage the settings of the extant averagers.
(package private)  class	KaryoView.AveragerTask
(package private)  class	KaryoView.MouseTracker           follows mouse around, communicates with KaryoView by calling drawBad and being called by paintComposite()
(package private)  class	KaryoView.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
(package private)  Averager	averager
(package private)  javax.swing.ProgressMonitor	averagerMonitor
private  KaryoView.AveragerSettingsPanel	averagerSettingsPanel
(package private)  KaryoView.AveragerTask	averagerTask
(package private)  javax.swing.Timer	averageTimer
(package private)  java.awt.Rectangle	clipRect
private  edu.stanford.genetics.treeview.ConfigNode	configNode
private  int	currentCol           current experiment column to view
private  edu.stanford.genetics.treeview.DataMatrix	dataMatrix
private  int	defaultAverager
private  edu.stanford.genetics.treeview.HeaderInfo	experimentInfo
private  edu.stanford.genetics.treeview.HeaderInfo	geneInfo
private  IntervalAverager	intervalAverager
private  boolean	justZoomed
private  KaryoDrawer	karyoDrawer
(package private)  KaryoView.MouseTracker	mouseTracker
private  NearestAverager	nearestAverager
private  NeighborAverager	neighborAverager
private  double	nodata
private  int	numRow
private  KaryoViewParameterPanel	parameterPanel
(package private)  java.awt.Rectangle	repaintRect           This method is called to make the karyoview fit on the screen.
private  javax.swing.JScrollPane	scrollPane
private  Averager	simpleAverager
private  java.lang.String[]	statusText
private  java.awt.Point	zoomPoint

 

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

hasMouse, hint, offscreenChanged, offscreenSize, offscreenValid, panel, status, viewFrame

 

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

KaryoView(KaryoDrawer karyoDrawer, edu.stanford.genetics.treeview.DataModel tvmodel)           for viewing DataModels

 

Method Summary
void	bindConfig(edu.stanford.genetics.treeview.ConfigNode configNode)           Setter for configNode
void	cleanup()           removes any pointers to exteral objects to aid GC
private  Averager	getAverager(int type)
edu.stanford.genetics.treeview.SettingsPanel	getAveragerSettingsPanel()
java.lang.String	getAveragingArg()
int	getAveragingType()
private  int	getClosest(int chr, int arm, double pos)
edu.stanford.genetics.treeview.ConfigNode	getConfigNode()           Getter for configNode
int	getCurrentCol()
edu.stanford.genetics.treeview.DataMatrix	getDataMatrix()           Getter for dataMatrix
java.lang.String[]	getExperiments()
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.
edu.stanford.genetics.treeview.HeaderInfo	getGeneInfo()           Getter for geneInfo
KaryoDrawer	getKaryoDrawer()           Getter for karyoDrawer
double	getNodata()           Getter for nodata
int	getNumCol()           Getter for numCol
KaryoViewParameterPanel	getParameterPanel()
java.awt.Dimension	getPreferredSize()           Get the component's preferred size.
java.lang.String[]	getStatus()           Strings describing status to user, suitable for display.
boolean	isChromosomeVisible(int i)
void	paintComponent(java.awt.Graphics g)           override parent so as to avoid running out of memory at high zooms.
void	paintComposite(java.awt.Graphics g)           This call is to be used to add a quick addition to the component which you don't want to put on the doublebuffer.
void	recalculateAverages()
void	redoScale()
void	setCurrentCol(int n)
void	setDataMatrix(edu.stanford.genetics.treeview.DataMatrix dataMatrix)           Setter for dataMatrix
void	setGeneInfo(edu.stanford.genetics.treeview.HeaderInfo geneInfo)           Setter for geneInfo
void	setIntervalAveraging(double width)
void	setKaryoDrawer(KaryoDrawer karyoDrawer)           Setter for karyoDrawer
void	setNearestAveraging(int num)
void	setNeighborAveraging(int num)
void	setNodata(double nodata)           Setter for nodata
void	setParameterPanel(KaryoViewParameterPanel p)
void	setSimpleAveraging()
void	update(java.util.Observable o, java.lang.Object arg)           This method is called whenever the observable object changes, and has called notifyObservers.
void	updateBuffer(java.awt.Graphics g)           Update the double buffer, if buffered Otherwise, just called by paintComponent to paint the main component.
private  void	updateStatus(ChromosomeLocus locus)
java.lang.String	viewName()           viewName, returns name of view suitable for printing perhaps this should be replaced by reflection?
private  void	zoomFactor(double factor, java.awt.Point point)           Zoom with the specified factor, keeping the specified point in the same relative place.
private  void	zoomRectangle(java.awt.Rectangle r)

 

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

addNotify, getComponent, getHints, getViewFrame, keyReleased, keyTyped, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, setHintPanel, setStatusPanel, setViewFrame

 

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

 

Methods inherited from class javax.swing.JComponent

addAncestorListener, 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, doLayout, 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, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

 

Methods inherited from class java.lang.Object

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

 

Field Detail

parameterPanel

private KaryoViewParameterPanel parameterPanel

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currentCol

private int currentCol

current experiment column to view

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karyoDrawer

private KaryoDrawer karyoDrawer

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averagerSettingsPanel

private KaryoView.AveragerSettingsPanel averagerSettingsPanel

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defaultAverager

private int defaultAverager

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simpleAverager

private Averager simpleAverager

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neighborAverager

private NeighborAverager neighborAverager

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nearestAverager

private NearestAverager nearestAverager

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intervalAverager

private IntervalAverager intervalAverager

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scrollPane

private javax.swing.JScrollPane scrollPane

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dataMatrix

private edu.stanford.genetics.treeview.DataMatrix dataMatrix

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numRow

private int numRow

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nodata

private double nodata

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experimentInfo

private edu.stanford.genetics.treeview.HeaderInfo experimentInfo

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geneInfo

private edu.stanford.genetics.treeview.HeaderInfo geneInfo

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averagerMonitor

javax.swing.ProgressMonitor averagerMonitor

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averageTimer

javax.swing.Timer averageTimer

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averagerTask

KaryoView.AveragerTask averagerTask

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averager

Averager averager

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mouseTracker

KaryoView.MouseTracker mouseTracker

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clipRect

java.awt.Rectangle clipRect

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repaintRect

java.awt.Rectangle repaintRect

This method is called to make the karyoview fit on the screen. It will set the desired width and height, and then ask the KaryoDrawer to adjust the pixels per value and pixels per row to something sensible.

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justZoomed

private boolean justZoomed

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zoomPoint

private java.awt.Point zoomPoint

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statusText

private java.lang.String[] statusText

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configNode

private edu.stanford.genetics.treeview.ConfigNode configNode

Constructor Detail

KaryoView

public KaryoView(KaryoDrawer karyoDrawer,
                 edu.stanford.genetics.treeview.DataModel tvmodel)

for viewing DataModels

Method Detail

getParameterPanel

public KaryoViewParameterPanel getParameterPanel()

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setParameterPanel

public void setParameterPanel(KaryoViewParameterPanel p)

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getCurrentCol

public int getCurrentCol()

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setCurrentCol

public void setCurrentCol(int n)

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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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getAveragerSettingsPanel

public edu.stanford.genetics.treeview.SettingsPanel getAveragerSettingsPanel()

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getAveragingType

public int getAveragingType()

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getAveragingArg

public java.lang.String getAveragingArg()

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setSimpleAveraging

public void setSimpleAveraging()

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setNearestAveraging

public void setNearestAveraging(int num)

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setNeighborAveraging

public void setNeighborAveraging(int num)

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setIntervalAveraging

public void setIntervalAveraging(double width)

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getAverager

private Averager getAverager(int type)

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setDataMatrix

public void setDataMatrix(edu.stanford.genetics.treeview.DataMatrix dataMatrix)

Setter for dataMatrix

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getDataMatrix

public edu.stanford.genetics.treeview.DataMatrix getDataMatrix()

Getter for dataMatrix

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getNumCol

public int getNumCol()

Getter for numCol

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setNodata

public void setNodata(double nodata)

Setter for nodata

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getNodata

public double getNodata()

Getter for nodata

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setGeneInfo

public void setGeneInfo(edu.stanford.genetics.treeview.HeaderInfo geneInfo)

Setter for geneInfo

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getGeneInfo

public edu.stanford.genetics.treeview.HeaderInfo getGeneInfo()

Getter for geneInfo

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cleanup

public void cleanup()

removes any pointers to exteral objects to aid GC

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update

public void update(java.util.Observable o,
                   java.lang.Object arg)

Description copied from interface: java.util.Observer

This method is called whenever the observable object changes, and has called notifyObservers. The Observable object can pass arbitrary information in the second parameter.

Specified by:

update in interface java.util.Observer

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recalculateAverages

public void recalculateAverages()

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paintComposite

public void paintComposite(java.awt.Graphics g)

Description copied from class: edu.stanford.genetics.treeview.ModelView

This call is to be used to add a quick addition to the component which you don't want to put on the doublebuffer. The composite could potentially be another buffer. Currently, this is only used by globalview for adding the zoom rect and focus rect.

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paintComponent

public void paintComponent(java.awt.Graphics g)

override parent so as to avoid running out of memory at high zooms.

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updateBuffer

public void updateBuffer(java.awt.Graphics g)

Description copied from class: edu.stanford.genetics.treeview.ModelView

Update the double buffer, if buffered Otherwise, just called by paintComponent to paint the main component. called only when offscreen buffer is marked as invalid, or if the onscreen size has changed. note: now actually called by paintcomponent to update the swing double buffer.

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viewName

public java.lang.String viewName()

Description copied from class: edu.stanford.genetics.treeview.ModelView

viewName, returns name of view suitable for printing perhaps this should be replaced by reflection?

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redoScale

public void redoScale()

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getExperiments

public java.lang.String[] getExperiments()

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getPreferredSize

public java.awt.Dimension getPreferredSize()

Description copied from class: javax.swing.JComponent

Get the component's preferred size. If the JComponent.preferredSize>JComponent.preferredSize 55 property has been explicitly set, it is returned. If the JComponent.preferredSize>JComponent.preferredSize 55 property has not been set but the JComponent.ui>JComponent.ui 55 property has been, the result of ComponentUI.getPreferredSize(javax.swing.JComponent)>ComponentUI.getPreferredSize(javax.swing.JComponent) 55 is returned. If neither property has been set, the result of Container.getPreferredSize()>Container.getPreferredSize() 55 is returned.

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isChromosomeVisible

public boolean isChromosomeVisible(int i)

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zoomRectangle

private void zoomRectangle(java.awt.Rectangle r)

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zoomFactor

private void zoomFactor(double factor,
                        java.awt.Point point)

Zoom with the specified factor, keeping the specified point in the same relative place. If the point is null, it keeps the center in the same place.

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updateStatus

private void updateStatus(ChromosomeLocus locus)

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getStatus

public java.lang.String[] getStatus()

Description copied from class: edu.stanford.genetics.treeview.ModelView

Strings describing status to user, suitable for display.

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getClosest

private int getClosest(int chr,
                       int arm,
                       double pos)

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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

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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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