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java.lang.Object | +--java.awt.Component | +--java.awt.Container | +--java.awt.Window | +--java.awt.Frame | +--javax.swing.JFrame | +--org.emboss.jemboss.editor.AlignJFrame
Displays a grapical representation of a collection of sequences.
Nested Class Summary | |
(package private) class |
AlignJFrame.winExit
Extends WindowAdapter to close window |
Field Summary | |
private java.awt.Cursor |
cbusy
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private java.awt.Cursor |
cdone
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private java.util.Hashtable |
currentColour
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private java.util.Vector |
graphicSequence
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private GraphicSequenceCollection |
gsc
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private javax.swing.JScrollPane |
jspSequence
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private Matrix |
mat
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private javax.swing.JCheckBoxMenuItem |
residueColor
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private java.util.Vector |
seqs
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private java.io.File |
sequenceFile
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private javax.swing.JTextField |
statusField
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private boolean |
useExitMenu
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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 |
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Fields inherited from class java.awt.Container |
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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()
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AlignJFrame(boolean useExitMenu)
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AlignJFrame(java.io.File seqFile)
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AlignJFrame(java.lang.String seqString,
java.lang.String name)
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AlignJFrame(java.util.Vector vseqs)
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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 |
private java.util.Vector seqs
private java.util.Vector graphicSequence
private javax.swing.JScrollPane jspSequence
private GraphicSequenceCollection gsc
private Matrix mat
private javax.swing.JTextField statusField
private java.io.File sequenceFile
private java.awt.Cursor cbusy
private java.awt.Cursor cdone
private javax.swing.JCheckBoxMenuItem residueColor
private java.util.Hashtable currentColour
private boolean useExitMenu
Constructor Detail |
public AlignJFrame(java.util.Vector vseqs)
vseqs
- vector containing Sequence objectspublic AlignJFrame(java.io.File seqFile)
seqFile
- sequence filepublic AlignJFrame(java.lang.String seqString, java.lang.String name)
seqString
- formatted sequence stringname
- name of sequence setpublic AlignJFrame()
public AlignJFrame(boolean useExitMenu)
useExitMenu
- true if an exit menu is to be displayed
otherwise a close menu is usedMethod Detail |
public void setMatrix(Matrix mat)
mat
- scoring matrix to usepublic void repaintSequences(java.util.Hashtable hash)
hash
- hash of the colour schemeprotected void openMethod(java.util.Vector seqVector)
seqVector
- vector containing Sequence objectsprivate void colourScheme(java.lang.String colScheme)
colScheme
- name of colour schemeprivate void colourMenus(javax.swing.JMenu viewMenu)
public static void main(java.lang.String[] args)
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