org.emboss.jemboss.editor
Class AlignJFrame

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

All Implemented Interfaces:

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

Direct Known Subclasses:

GroutAlignJFrame

public class AlignJFrame

extends javax.swing.JFrame

Displays a grapical representation of a collection of sequences.

See Also:

Serialized Form

Nested Class Summary

(package private) class

AlignJFrame.winExit Extends WindowAdapter to close window

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 java.awt.Cursor	cbusy
private java.awt.Cursor	cdone
protected java.util.Hashtable	currentColour
private java.util.Vector	graphicSequence
protected static GraphicSequenceCollection	gsc
protected javax.swing.JScrollPane	jspSequence
private static Matrix	mat
protected javax.swing.JMenuBar	menuBar
private PrettyPlotJFrame	ppj
protected javax.swing.JCheckBoxMenuItem	residueColor
private java.io.File	sequenceFile
protected static javax.swing.JTextField	statusField
protected boolean	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

AlignJFrame()

AlignJFrame(boolean useExitMenu)

AlignJFrame(java.io.File seqFile)

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

AlignJFrame(java.util.Vector vseqs)

Method Summary

private void	colourMenus(javax.swing.JMenu viewMenu) Constructs the colour menus
protected void	colourScheme(java.lang.String colScheme) Update the status bar with the selected colour scheme being used.
static float	getTotalWeight(java.util.Vector vseq)
static void	main(java.lang.String[] args)
protected void	openMethod(java.util.Vector seqVector) Given a Vector of Sequence display them in the editor
void	repaintSequences(java.util.Hashtable hash) Force a re-display of the sequences with a new colour scheme.
private static java.awt.Color	resolveColor(java.lang.String[] args, int index) red, blue, cyan, darkGray, gray , green, lightGray, magenta , orange, pink, white, yellow, black
void	setMatrix(Matrix mat) Set the scoring matrix

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

graphicSequence

private java.util.Vector graphicSequence

jspSequence

protected javax.swing.JScrollPane jspSequence

gsc

protected static GraphicSequenceCollection gsc

mat

private static Matrix mat

ppj

private PrettyPlotJFrame ppj

statusField

protected static javax.swing.JTextField statusField

sequenceFile

private java.io.File sequenceFile

cbusy

private java.awt.Cursor cbusy

cdone

private java.awt.Cursor cdone

residueColor

protected javax.swing.JCheckBoxMenuItem residueColor

currentColour

protected java.util.Hashtable currentColour

useExitMenu

protected boolean useExitMenu

menuBar

protected javax.swing.JMenuBar menuBar

Constructor Detail

AlignJFrame

public AlignJFrame(java.util.Vector vseqs)

Parameters:

vseqs - vector containing Sequence objects

AlignJFrame

public AlignJFrame(java.io.File seqFile)

Parameters:

seqFile - sequence file

AlignJFrame

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

Parameters:

seqString - formatted sequence string

name - name of sequence set

AlignJFrame

public AlignJFrame()

AlignJFrame

public AlignJFrame(boolean useExitMenu)

Parameters:

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

Method Detail

getTotalWeight

public static float getTotalWeight(java.util.Vector vseq)

setMatrix

public void setMatrix(Matrix mat)

Set the scoring matrix

Parameters:

mat - scoring matrix to use

repaintSequences

public void repaintSequences(java.util.Hashtable hash)

Force a re-display of the sequences with a new colour scheme.

Parameters:

hash - hash of the colour scheme

openMethod

protected void openMethod(java.util.Vector seqVector)

Given a Vector of Sequence display them in the editor

Parameters:

seqVector - vector containing Sequence objects

colourScheme

protected void colourScheme(java.lang.String colScheme)

Update the status bar with the selected colour scheme being used.

Parameters:

colScheme - name of colour scheme

colourMenus

private void colourMenus(javax.swing.JMenu viewMenu)

Constructs the colour menus

resolveColor

private static java.awt.Color resolveColor(java.lang.String[] args,
                                           int index)

red, blue, cyan, darkGray, gray , green, lightGray, magenta , orange, pink, white, yellow, black

main

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