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

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
 
Field Summary
private  java.awt.Cursor cbusy
           
private  java.awt.Cursor cdone
           
private  java.util.Hashtable currentColour
           
private  java.util.Vector graphicSequence
           
private  GraphicSequenceCollection gsc
           
private  javax.swing.JScrollPane jspSequence
           
private  Matrix mat
           
private  javax.swing.JCheckBoxMenuItem residueColor
           
private  java.util.Vector seqs
           
private  java.io.File sequenceFile
           
private  javax.swing.JTextField statusField
           
private  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
private  void colourScheme(java.lang.String colScheme)
          Update the status bar with the selected colour scheme being used.
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.
 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

seqs

private java.util.Vector seqs

graphicSequence

private java.util.Vector graphicSequence

jspSequence

private javax.swing.JScrollPane jspSequence

gsc

private GraphicSequenceCollection gsc

mat

private Matrix mat

statusField

private javax.swing.JTextField statusField

sequenceFile

private java.io.File sequenceFile

cbusy

private java.awt.Cursor cbusy

cdone

private java.awt.Cursor cdone

residueColor

private javax.swing.JCheckBoxMenuItem residueColor

currentColour

private java.util.Hashtable currentColour

useExitMenu

private boolean useExitMenu
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

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

private 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


main

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