com.affymetrix.genoviz.demo

Class NeoAssemblerDemo2

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Panel

java.applet.Applet

javax.swing.JApplet

com.affymetrix.genoviz.demo.NeoAssemblerDemo2

All Implemented Interfaces:

com.affymetrix.genoviz.event.NeoRangeListener, MouseListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer

public class NeoAssemblerDemo2
extends JApplet
implements com.affymetrix.genoviz.event.NeoRangeListener, MouseListener

This is a reworking of the old NeoAssemblerDemo It adds a button to clear and reload the NeoAssembler. This to check a bug reported by Genentech.

Version:

$Id: NeoAssemblerDemo2.java 6217 2010-06-22 14:54:18Z vbishnoi $

See Also:

Serialized Form

Nested Class Summary

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

JApplet.AccessibleJApplet

Nested classes/interfaces inherited from class java.applet.Applet

Applet.AccessibleApplet

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

Panel.AccessibleAWTPanel

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields inherited from class javax.swing.JApplet

accessibleContext, rootPane, rootPaneCheckingEnabled

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

Constructors

Constructor and Description
NeoAssemblerDemo2()

Method Summary

Modifier and Type	Method and Description
Panel	buttonSetup() puts buttons on a panel so the user can instigate actions.
AppletContext	getAppletContext()
URL	getCodeBase()
URL	getDocumentBase()
String	getParameter(String name)
protected com.affymetrix.genoviz.glyph.AlignmentGlyph	getSelectedGlyph(com.affymetrix.genoviz.widget.NeoAssembler theAssembler)
int[]	getSelectedRange(com.affymetrix.genoviz.glyph.AlignmentGlyph theGlyph)
String	getSelectedResidues(com.affymetrix.genoviz.glyph.AlignmentGlyph theGlyph)
void	init()
genoviz.demo.datamodel.Assembly	loadData(URL seq_URL, URL align_URL)
static void	main(String[] args)
void	mouseClicked(MouseEvent e)
void	mouseEntered(MouseEvent e)
void	mouseExited(MouseEvent e)
void	mousePressed(MouseEvent e)
void	mouseReleased(MouseEvent e)
void	rangeChanged(com.affymetrix.genoviz.event.NeoRangeEvent evt) RangeListener implelementation
void	reportSelectedResidues()

Methods inherited from class javax.swing.JApplet

addImpl, createRootPane, getAccessibleContext, getContentPane, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isRootPaneCheckingEnabled, paramString, remove, repaint, setContentPane, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.applet.Applet

destroy, getAppletInfo, getAudioClip, getAudioClip, getImage, getImage, getLocale, getParameterInfo, isActive, isValidateRoot, newAudioClip, play, play, resize, resize, setStub, showStatus, start, stop

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, revalidate, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Constructor Detail

NeoAssemblerDemo2

public NeoAssemblerDemo2()

Method Detail

init

public void init()

Overrides:

init in class Applet

buttonSetup

public Panel buttonSetup()

puts buttons on a panel so the user can instigate actions.

loadData

public genoviz.demo.datamodel.Assembly loadData(URL seq_URL,
                                                URL align_URL)

getCodeBase

public URL getCodeBase()

Overrides:

getCodeBase in class Applet

getAppletContext

public AppletContext getAppletContext()

Overrides:

getAppletContext in class Applet

getDocumentBase

public URL getDocumentBase()

Overrides:

getDocumentBase in class Applet

getParameter

public String getParameter(String name)

Overrides:

getParameter in class Applet

main

public static void main(String[] args)

mouseClicked

public void mouseClicked(MouseEvent e)

Specified by:

mouseClicked in interface MouseListener

mouseEntered

public void mouseEntered(MouseEvent e)

Specified by:

mouseEntered in interface MouseListener

mouseExited

public void mouseExited(MouseEvent e)

Specified by:

mouseExited in interface MouseListener

mouseReleased

public void mouseReleased(MouseEvent e)

Specified by:

mouseReleased in interface MouseListener

mousePressed

public void mousePressed(MouseEvent e)

Specified by:

mousePressed in interface MouseListener

rangeChanged

public void rangeChanged(com.affymetrix.genoviz.event.NeoRangeEvent evt)

RangeListener implelementation

Specified by:

rangeChanged in interface com.affymetrix.genoviz.event.NeoRangeListener

reportSelectedResidues

public void reportSelectedResidues()

getSelectedResidues

public String getSelectedResidues(com.affymetrix.genoviz.glyph.AlignmentGlyph theGlyph)

getSelectedRange

public int[] getSelectedRange(com.affymetrix.genoviz.glyph.AlignmentGlyph theGlyph)

getSelectedGlyph

protected com.affymetrix.genoviz.glyph.AlignmentGlyph getSelectedGlyph(com.affymetrix.genoviz.widget.NeoAssembler theAssembler)