org.emboss.jemboss.editor
Class GroutAlignJFrame

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

All Implemented Interfaces:

javax.accessibility.Accessible, GroutGraphicSequenceCollectionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, javax.swing.RootPaneContainer, java.io.Serializable, javax.swing.WindowConstants

public class GroutAlignJFrame

extends AlignJFrame

implements GroutGraphicSequenceCollectionListener

Displays a grapical representation of a collection of sequences.

See Also:

Serialized Form

Nested Class Summary

(package private) class

GroutAlignJFrame.winExit Extends WindowAdapter to handle disposal of the occurance

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 int	position
private java.util.Vector	targets

Fields inherited from class org.emboss.jemboss.editor.AlignJFrame

currentColour, gsc, jspSequence, menuBar, residueColor, statusField, useExitMenu

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

GroutAlignJFrame()

GroutAlignJFrame(boolean useExitMenu)

GroutAlignJFrame(java.io.File seqFile)

GroutAlignJFrame(java.lang.String seqString, java.lang.String name)

GroutAlignJFrame(java.util.Vector vseqs)

GroutAlignJFrame(java.util.Vector vseqs, java.util.Vector indents)
This constructor is for Grout.

Method Summary

void	addGroutAlignJFrameListener(GroutAlignJFrameListener listener)
private void	addMenuItems()
protected void	addWindowCloser() when you close the window, should remove lines from Grout
void	groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent e) Responds to the groutGraphicSequenceCollectionChanged event
static void	main(java.lang.String[] args) Test main really
protected void	notifyTargets(java.lang.String propertyName, java.lang.Object oldValue, java.lang.Object newValue)
protected void	openMethod(java.util.Vector seqVector) Given a Vector of Sequence display them in the editor
protected void	openMethod(java.util.Vector seqVector, java.util.Vector indents) Given a Vector of Sequence and the indent for each display them in the editor
void	removeGroutAlignJFrameListener(GroutAlignJFrameListener listener)
void	setIndents(java.util.Vector indents) Sets the indents to these values
void	setPosition(int position) Moves the view position to this point

Methods inherited from class org.emboss.jemboss.editor.AlignJFrame

colourScheme, getTotalWeight, repaintSequences, setMatrix

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

targets

private java.util.Vector targets

position

private int position

Constructor Detail

GroutAlignJFrame

public GroutAlignJFrame(java.util.Vector vseqs,
                        java.util.Vector indents)

This constructor is for Grout. It includes the indent for each sequence

Parameters:

vseqs - vector containing Sequence objects

GroutAlignJFrame

public GroutAlignJFrame(java.util.Vector vseqs)

Parameters:

vseqs - vector containing Sequence objects

GroutAlignJFrame

public GroutAlignJFrame(java.io.File seqFile)

Parameters:

seqFile - sequence file

GroutAlignJFrame

public GroutAlignJFrame(java.lang.String seqString,
                        java.lang.String name)

Parameters:

seqString - formatted sequence string

name - name of sequence set

GroutAlignJFrame

public GroutAlignJFrame()

GroutAlignJFrame

public GroutAlignJFrame(boolean useExitMenu)

Parameters:

useExitMenu - true if an exit menu is to be displayed otherwise a close menu is used

Method Detail

openMethod

protected void openMethod(java.util.Vector seqVector)

Given a Vector of Sequence display them in the editor

Overrides:

openMethod in class AlignJFrame

Parameters:

seqVector - vector containing Sequence objects

openMethod

protected void openMethod(java.util.Vector seqVector,
                          java.util.Vector indents)

Given a Vector of Sequence and the indent for each display them in the editor

Parameters:

seqVector - vector containing Sequence objects

indents - vector containing ints giving indents

addGroutAlignJFrameListener

public void addGroutAlignJFrameListener(GroutAlignJFrameListener listener)

removeGroutAlignJFrameListener

public void removeGroutAlignJFrameListener(GroutAlignJFrameListener listener)

notifyTargets

protected void notifyTargets(java.lang.String propertyName,
                             java.lang.Object oldValue,
                             java.lang.Object newValue)

setPosition

public void setPosition(int position)

Moves the view position to this point

Parameters:

position - the position to view

setIndents

public void setIndents(java.util.Vector indents)

Sets the indents to these values

addWindowCloser

protected void addWindowCloser()

when you close the window, should remove lines from Grout

addMenuItems

private void addMenuItems()

groutGraphicSequenceCollectionChanged

public void groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent e)

Responds to the groutGraphicSequenceCollectionChanged event

Specified by:

groutGraphicSequenceCollectionChanged in interface GroutGraphicSequenceCollectionListener

Parameters:

e - the event

main

public static void main(java.lang.String[] args)

Test main really