public class NeoAssemblerDemo extends JApplet implements com.affymetrix.genoviz.event.NeoRangeListener, WindowListener, MouseListener, ActionListener
JApplet.AccessibleJApplet
Applet.AccessibleApplet
Panel.AccessibleAWTPanel
Container.AccessibleAWTContainer
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
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 |
accessibleContext, rootPane, rootPaneCheckingEnabled
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
Constructor and Description |
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NeoAssemblerDemo() |
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() |
addImpl, createRootPane, getAccessibleContext, getContentPane, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isRootPaneCheckingEnabled, paramString, remove, repaint, setContentPane, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update
getAudioClip, getAudioClip, getImage, getImage, getLocale, getParameterInfo, init, isActive, isValidateRoot, newAudioClip, play, play, resize, resize, setStub, showStatus
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
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
public boolean tryUniString
public boolean simulateTrimmedEdges
public boolean no_reverse
public com.affymetrix.genoviz.bioviews.ResiduePainter bg_painter
public com.affymetrix.genoviz.bioviews.ResiduePainter fg_painter
public void NeoAssemblerDemo()
protected void getGoing()
public Object addBases(com.affymetrix.genoviz.datamodel.Mapping align)
public Object addGaps(com.affymetrix.genoviz.datamodel.Mapping align)
public com.affymetrix.genoviz.bioviews.GlyphI addUniAlignment(com.affymetrix.genoviz.datamodel.Mapping align)
public Object addAlign(com.affymetrix.genoviz.datamodel.Mapping align)
public void showProperties()
public void turnOffAddAlignMenus()
public void addAlignment()
public void removeSeq()
public void addGaps()
public void addBases()
public void addNext()
public void addTheRest()
public void addNeg()
public genoviz.demo.datamodel.Assembly loadData()
public void addConsensus()
public void switchFontType()
public void switchFontStyle()
public void switchFontSize()
public void zoomFrameSetup()
public void doExternalSort()
public void toggleExternalFontColoring()
public void toggleExternalRectColoring()
public String getAppletInfo()
getAppletInfo
in class Applet
public void setupMenus(Frame dock)
public void actionPerformed(ActionEvent evt)
actionPerformed
in interface ActionListener
public void windowActivated(WindowEvent e)
windowActivated
in interface WindowListener
public void windowDeactivated(WindowEvent e)
windowDeactivated
in interface WindowListener
public void windowIconified(WindowEvent e)
windowIconified
in interface WindowListener
public void windowDeiconified(WindowEvent e)
windowDeiconified
in interface WindowListener
public void windowOpened(WindowEvent e)
windowOpened
in interface WindowListener
public void windowClosed(WindowEvent e)
windowClosed
in interface WindowListener
public void windowClosing(WindowEvent e)
windowClosing
in interface WindowListener
public void mouseClicked(MouseEvent e)
mouseClicked
in interface MouseListener
public void mouseEntered(MouseEvent e)
mouseEntered
in interface MouseListener
public void mouseExited(MouseEvent e)
mouseExited
in interface MouseListener
public void mouseReleased(MouseEvent e)
mouseReleased
in interface MouseListener
public void mousePressed(MouseEvent e)
mousePressed
in interface MouseListener
public void rangeChanged(com.affymetrix.genoviz.event.NeoRangeEvent evt)
rangeChanged
in interface com.affymetrix.genoviz.event.NeoRangeListener
public void reportSelectedResidues()
public String getSelectedResidues(com.affymetrix.genoviz.glyph.AlignmentGlyph theGlyph)
public int[] getSelectedRange(com.affymetrix.genoviz.glyph.AlignmentGlyph theGlyph)
protected com.affymetrix.genoviz.glyph.AlignmentGlyph getSelectedGlyph(com.affymetrix.genoviz.widget.NeoAssembler theAssembler)
public URL getCodeBase()
getCodeBase
in class Applet
public AppletContext getAppletContext()
getAppletContext
in class Applet
public URL getDocumentBase()
getDocumentBase
in class Applet
public String getParameter(String name)
getParameter
in class Applet
public static void main(String[] args)
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