org.emboss.jemboss.editor
Class PrettyPlotJFrame

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      org.emboss.jemboss.editor.PrettyPlotJFrame

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.event.ActionListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, javax.swing.RootPaneContainer, java.io.Serializable, javax.swing.WindowConstants

public class PrettyPlotJFrame

extends javax.swing.JFrame

implements java.awt.event.ActionListener

JFrame to define the colour of residue if identical or a positive match.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.JFrame

javax.swing.JFrame.AccessibleJFrame

Nested classes inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Nested classes inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

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 GraphicSequenceCollection	gsc graphic sequence panel
private javax.swing.JColorChooser	idColour colour panel for identical matches
private javax.swing.JColorChooser	idColourBackground colour panel for identical matches background
private javax.swing.JColorChooser	matchColour colour panel for positive scoring matches
private javax.swing.JColorChooser	matchColourBackground colour panel for positive scoring matches background
private javax.swing.JCheckBox	prettyBox define if the identities and matches are to be boxed
private TextFieldFloat	textFloat field to define threshold for positive matches
private TextFieldInt	textInt field to define min number of identities

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.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 javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

PrettyPlotJFrame(GraphicSequenceCollection gsc)

PrettyPlotJFrame(int minID, float plurality, java.awt.Color colID, java.awt.Color colMatch, java.awt.Color colIDBack, java.awt.Color colMatchBack, boolean lboxPretty)

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ae)
java.awt.Color	getIDBackgroundColour() Get the users defined background colour to draw identical residues
java.awt.Color	getIDColour() Get the users defined colour to draw identical residues
java.awt.Color	getMatchBackgroundColour() Get the users defined background colour to draw positive match residues
java.awt.Color	getMatchColour() Get the users defined colour to draw positive match residues
double	getMatchThreshold() Get the match threshold value
int	getMinimumIdentity(int nseqs) Get the users defined identity limit
protected boolean	isPrettyBox() Determine if boxes are to be drawn around the identical matches
protected void	setGraphicSequenceCollection(GraphicSequenceCollection gsc) Set the current graphic display

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Frame

addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setIconImage, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isFocusableWindow, isFocusCycleRoot, isFocused, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationRelativeTo, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setFocusTraversalKeys, setFocusTraversalPolicy, setFont, transferFocusBackward, 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, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isOpaque, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

textInt

private TextFieldInt textInt

field to define min number of identities

textFloat

private TextFieldFloat textFloat

field to define threshold for positive matches

idColour

private javax.swing.JColorChooser idColour

colour panel for identical matches

matchColour

private javax.swing.JColorChooser matchColour

colour panel for positive scoring matches

idColourBackground

private javax.swing.JColorChooser idColourBackground

colour panel for identical matches background

matchColourBackground

private javax.swing.JColorChooser matchColourBackground

colour panel for positive scoring matches background

gsc

private GraphicSequenceCollection gsc

graphic sequence panel

prettyBox

private javax.swing.JCheckBox prettyBox

define if the identities and matches are to be boxed

Constructor Detail

PrettyPlotJFrame

public PrettyPlotJFrame(int minID,
                        float plurality,
                        java.awt.Color colID,
                        java.awt.Color colMatch,
                        java.awt.Color colIDBack,
                        java.awt.Color colMatchBack,
                        boolean lboxPretty)

PrettyPlotJFrame

public PrettyPlotJFrame(GraphicSequenceCollection gsc)

Parameters:

gsc - graphic sequence panel

Method Detail

getMinimumIdentity

public int getMinimumIdentity(int nseqs)

Get the users defined identity limit

getMatchThreshold

public double getMatchThreshold()

Get the match threshold value

Returns:

threshold value

getIDColour

public java.awt.Color getIDColour()

Get the users defined colour to draw identical residues

Returns:

colour

getIDBackgroundColour

public java.awt.Color getIDBackgroundColour()

Get the users defined background colour to draw identical residues

Returns:

colour

getMatchColour

public java.awt.Color getMatchColour()

Get the users defined colour to draw positive match residues

Returns:

colour

getMatchBackgroundColour

public java.awt.Color getMatchBackgroundColour()

Get the users defined background colour to draw positive match residues

Returns:

colour

isPrettyBox

protected boolean isPrettyBox()

Determine if boxes are to be drawn around the identical matches

setGraphicSequenceCollection

protected void setGraphicSequenceCollection(GraphicSequenceCollection gsc)

Set the current graphic display

Parameters:

gsc - Sequence graphic

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ae)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

ae - the action event generated