com.affymetrix.genoviz.demo

Class NeoAssemblerDemo

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Panel

java.applet.Applet

javax.swing.JApplet

com.affymetrix.genoviz.demo.NeoAssemblerDemo

All Implemented Interfaces:

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

public class NeoAssemblerDemo
extends JApplet
implements com.affymetrix.genoviz.event.NeoRangeListener, WindowListener, MouseListener, ActionListener

A demo of the NeoAssembler widget. Uses "low-level" calls to NeoAssembler to construct visual representation of assembly (instead of a data adapter, which is used in NeoAssemblerDemo2)

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

Modifier and Type	Field and Description
com.affymetrix.genoviz.bioviews.ResiduePainter	bg_painter
com.affymetrix.genoviz.bioviews.ResiduePainter	fg_painter
boolean	no_reverse
boolean	simulateTrimmedEdges
boolean	tryUniString

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
NeoAssemblerDemo()

Method Summary

Modifier and Type	Method and Description
void	actionPerformed(ActionEvent evt) ActionListener Implementation
Object	addAlign(com.affymetrix.genoviz.datamodel.Mapping align)
void	addAlignment()
void	addBases()
Object	addBases(com.affymetrix.genoviz.datamodel.Mapping align)
void	addConsensus()
void	addGaps()
Object	addGaps(com.affymetrix.genoviz.datamodel.Mapping align)
void	addNeg()
void	addNext()
void	addTheRest()
com.affymetrix.genoviz.bioviews.GlyphI	addUniAlignment(com.affymetrix.genoviz.datamodel.Mapping align) Trying to get improved speed and memory usage.
void	destroy()
void	doExternalSort() An example of arbitrary sorting of alignments -- in this case, just reverse the order in which they are currently sorted General method for arbitrary sorting is: call NeoAssembler.getAlignmentGlyphs() to get vector of all alignment glyphs, ordered from top to bottom of NeoAssembler rearrange ordering in vector call NeoAssembler.pack() to repack from top to bottom as ordered in the vector
AppletContext	getAppletContext()
String	getAppletInfo()
URL	getCodeBase()
URL	getDocumentBase()
protected void	getGoing()
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)
genoviz.demo.datamodel.Assembly	loadData()
genoviz.demo.datamodel.Assembly	loadData(URL seq_URL, URL align_URL)
static void	main(String[] args)
void	mouseClicked(MouseEvent e) MouseListener implelementation and collecting mouse events
void	mouseEntered(MouseEvent e)
void	mouseExited(MouseEvent e)
void	mousePressed(MouseEvent e)
void	mouseReleased(MouseEvent e)
void	NeoAssemblerDemo()
void	paint(Graphics g)
void	rangeChanged(com.affymetrix.genoviz.event.NeoRangeEvent evt) RangeListener implelementation
void	removeSeq()
void	reportSelectedResidues()
void	setupMenus(Frame dock)
void	showProperties()
void	start()
void	stop()
void	switchFontSize()
void	switchFontStyle()
void	switchFontType()
void	toggleExternalFontColoring()
void	toggleExternalRectColoring()
void	turnOffAddAlignMenus()
void	windowActivated(WindowEvent e) WindowListener Implementation
void	windowClosed(WindowEvent e)
void	windowClosing(WindowEvent e)
void	windowDeactivated(WindowEvent e)
void	windowDeiconified(WindowEvent e)
void	windowIconified(WindowEvent e)
void	windowOpened(WindowEvent e)
void	zoomFrameSetup()

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

getAudioClip, getAudioClip, getImage, getImage, getLocale, getParameterInfo, init, isActive, isValidateRoot, newAudioClip, play, play, resize, resize, setStub, showStatus

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, 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

Field Detail

tryUniString

public boolean tryUniString

simulateTrimmedEdges

public boolean simulateTrimmedEdges

no_reverse

public boolean no_reverse

bg_painter

public com.affymetrix.genoviz.bioviews.ResiduePainter bg_painter

fg_painter

public com.affymetrix.genoviz.bioviews.ResiduePainter fg_painter

Constructor Detail

NeoAssemblerDemo

public NeoAssemblerDemo()

Method Detail

NeoAssemblerDemo

public void NeoAssemblerDemo()

getGoing

protected void getGoing()

addBases

public Object addBases(com.affymetrix.genoviz.datamodel.Mapping align)

addGaps

public Object addGaps(com.affymetrix.genoviz.datamodel.Mapping align)

addUniAlignment

public com.affymetrix.genoviz.bioviews.GlyphI addUniAlignment(com.affymetrix.genoviz.datamodel.Mapping align)

Trying to get improved speed and memory usage. Takes the aligned sequence and its mapping to the reference and builds a single "ungapped" alignment string, with spaces substituted for any gaps. This is then added to the NeoAssembler as a sequence with a single span.

addAlign

public Object addAlign(com.affymetrix.genoviz.datamodel.Mapping align)

showProperties

public void showProperties()

turnOffAddAlignMenus

public void turnOffAddAlignMenus()

addAlignment

public void addAlignment()

removeSeq

public void removeSeq()

addGaps

public void addGaps()

addBases

public void addBases()

addNext

public void addNext()

addTheRest

public void addTheRest()

addNeg

public void addNeg()

loadData

public genoviz.demo.datamodel.Assembly loadData()

loadData

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

addConsensus

public void addConsensus()

switchFontType

public void switchFontType()

switchFontStyle

public void switchFontStyle()

switchFontSize

public void switchFontSize()

zoomFrameSetup

public void zoomFrameSetup()

doExternalSort

public void doExternalSort()

An example of arbitrary sorting of alignments -- in this case, just reverse the order in which they are currently sorted General method for arbitrary sorting is: call NeoAssembler.getAlignmentGlyphs() to get vector of all alignment glyphs, ordered from top to bottom of NeoAssembler rearrange ordering in vector call NeoAssembler.pack() to repack from top to bottom as ordered in the vector

toggleExternalFontColoring

public void toggleExternalFontColoring()

toggleExternalRectColoring

public void toggleExternalRectColoring()

getAppletInfo

public String getAppletInfo()

Overrides:

getAppletInfo in class Applet

start

public void start()

Overrides:

start in class Applet

stop

public void stop()

Overrides:

stop in class Applet

destroy

public void destroy()

Overrides:

destroy in class Applet

paint

public void paint(Graphics g)

Overrides:

paint in class Container

setupMenus

public void setupMenus(Frame dock)

actionPerformed

public void actionPerformed(ActionEvent evt)

ActionListener Implementation

Specified by:

actionPerformed in interface ActionListener

windowActivated

public void windowActivated(WindowEvent e)

WindowListener Implementation

Specified by:

windowActivated in interface WindowListener

windowDeactivated

public void windowDeactivated(WindowEvent e)

Specified by:

windowDeactivated in interface WindowListener

windowIconified

public void windowIconified(WindowEvent e)

Specified by:

windowIconified in interface WindowListener

windowDeiconified

public void windowDeiconified(WindowEvent e)

Specified by:

windowDeiconified in interface WindowListener

windowOpened

public void windowOpened(WindowEvent e)

Specified by:

windowOpened in interface WindowListener

windowClosed

public void windowClosed(WindowEvent e)

Specified by:

windowClosed in interface WindowListener

windowClosing

public void windowClosing(WindowEvent e)

Specified by:

windowClosing in interface WindowListener

mouseClicked

public void mouseClicked(MouseEvent e)

MouseListener implelementation and collecting mouse events

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)

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)