org.emboss.jemboss.editor
Class GroutSequenceJPanel

java.lang.Object
  extended byjava.awt.Component
      extended byjava.awt.Container
          extended byjavax.swing.JComponent
              extended byjavax.swing.JPanel
                  extended byorg.emboss.jemboss.editor.SequenceJPanel
                      extended byorg.emboss.jemboss.editor.GroutSequenceJPanel
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.event.ActionListener, java.util.EventListener, GroutGraphicSequenceCollectionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

public class GroutSequenceJPanel
extends SequenceJPanel
implements GroutGraphicSequenceCollectionListener

Sequence panel for drawing a sequence or the sequence numbers

See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class org.emboss.jemboss.editor.SequenceJPanel
SequenceJPanel.PopupListener
 
Nested classes inherited from class javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
 
Nested classes inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
 
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
(package private)  int centreMarkerX
           
(package private)  int indent
           
 
Fields inherited from class org.emboss.jemboss.editor.SequenceJPanel
boundWidth2, drawNumber, interval, resWidth, seq, seqHeight, viewPane
 
Fields inherited from class javax.swing.JPanel
 
Fields inherited from class javax.swing.JComponent
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_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 java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
GroutSequenceJPanel(int interval, int seqLength)
          Constructor for sequence numbering
GroutSequenceJPanel(int indent, int interval, int seqLength)
          Constructor for sequence numbering and indenting the sequence
GroutSequenceJPanel(int indent, Sequence seq, javax.swing.JComponent viewPane, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, java.util.Hashtable colorTable, int ypad)
          Constructor with default font size and indenting the sequence
GroutSequenceJPanel(int indent, Sequence seq, javax.swing.JComponent viewPane, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, java.util.Hashtable colorTable, int fontSize, int ypad)
          Constructor for indenting the sequence
GroutSequenceJPanel(Sequence seq, javax.swing.JComponent viewPane, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, java.util.Hashtable colorTable, int ypad)
          Constructor with default font size
GroutSequenceJPanel(Sequence seq, javax.swing.JComponent viewPane, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, java.util.Hashtable colorTable, int fontSize, int ypad)
           
 
Method Summary
protected  void doDrawNumber(int i, java.awt.FontMetrics metrics, java.awt.Graphics g)
           
protected  void drawCentreMarker(java.awt.Graphics g)
           
 void groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent e)
           
 void init()
          Add the mouse listener's
 void setIndent(int indent)
          indents the sequence by specifed amount
 
Methods inherited from class org.emboss.jemboss.editor.SequenceJPanel
actionPerformed, attach, detach, detachAll, getFontSize, getName, getNamePrintGraphic, getPreferredSize, getResidueWidth, getSequenceHeight, getSequencePrintGraphic, getSequenceResidueWidth, getSequenceWidth, getToolTipLocation, getToolTipText, isPrettyPlot, notifyGroup, paintComponent, setColorScheme, setDefaultColorHashtable, setDrawBoxes, setDrawColor, setFontSize, setPrettyPlot, setSequenceLength, showPattern, update, viewPaneResize
 
Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
 
Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

centreMarkerX

int centreMarkerX

indent

int indent
Constructor Detail

GroutSequenceJPanel

public GroutSequenceJPanel(int indent,
                           Sequence seq,
                           javax.swing.JComponent viewPane,
                           boolean drawSequence,
                           boolean drawBlackBox,
                           boolean drawColorBox,
                           java.util.Hashtable colorTable,
                           int fontSize,
                           int ypad)
Constructor for indenting the sequence

Parameters:
indent - number of residues to indent this sequence
seq - sequence to display
viewPane - sequence alignment panel
drawSequence - draw the sequence if true
drawBlackBox - draw a black box around residues
drawColorBox - colour the residues
colorTable - colour scheme
fontSize - font size
ypad - sequence height pad

GroutSequenceJPanel

public GroutSequenceJPanel(int indent,
                           Sequence seq,
                           javax.swing.JComponent viewPane,
                           boolean drawSequence,
                           boolean drawBlackBox,
                           boolean drawColorBox,
                           java.util.Hashtable colorTable,
                           int ypad)
Constructor with default font size and indenting the sequence

Parameters:
indent - number of residues to indent this sequence
seq - sequence to display
viewPane - sequence alignment panel
drawSequence - draw the sequence if true
drawBlackBox - draw a black box around residues
drawColorBox - colour the residues
colorTable - colour scheme
ypad - sequence height pad

GroutSequenceJPanel

public GroutSequenceJPanel(int indent,
                           int interval,
                           int seqLength)
Constructor for sequence numbering and indenting the sequence

Parameters:
indent - number of residues to indent this sequence
interval - numbering interval
seqLength - length of the sequence

GroutSequenceJPanel

public GroutSequenceJPanel(Sequence seq,
                           javax.swing.JComponent viewPane,
                           boolean drawSequence,
                           boolean drawBlackBox,
                           boolean drawColorBox,
                           java.util.Hashtable colorTable,
                           int fontSize,
                           int ypad)
Parameters:
seq - sequence to display
viewPane - sequence alignment panel
drawSequence - draw the sequence if true
drawBlackBox - draw a black box around residues
drawColorBox - colour the residues
colorTable - colour scheme
fontSize - font size
ypad - sequence height pad

GroutSequenceJPanel

public GroutSequenceJPanel(Sequence seq,
                           javax.swing.JComponent viewPane,
                           boolean drawSequence,
                           boolean drawBlackBox,
                           boolean drawColorBox,
                           java.util.Hashtable colorTable,
                           int ypad)
Constructor with default font size

Parameters:
seq - sequence to display
viewPane - sequence alignment panel
drawSequence - draw the sequence if true
drawBlackBox - draw a black box around residues
drawColorBox - colour the residues
colorTable - colour scheme
ypad - sequence height pad

GroutSequenceJPanel

public GroutSequenceJPanel(int interval,
                           int seqLength)
Constructor for sequence numbering

Parameters:
interval - numbering interval
seqLength - length of the sequence
Method Detail

setIndent

public void setIndent(int indent)
indents the sequence by specifed amount

Parameters:
indent - number of residues to indent this sequence

init

public void init()
Add the mouse listener's

Overrides:
init in class SequenceJPanel

groutGraphicSequenceCollectionChanged

public void groutGraphicSequenceCollectionChanged(GroutGraphicSequenceCollectionEvent e)
Specified by:
groutGraphicSequenceCollectionChanged in interface GroutGraphicSequenceCollectionListener

doDrawNumber

protected void doDrawNumber(int i,
                            java.awt.FontMetrics metrics,
                            java.awt.Graphics g)

drawCentreMarker

protected void drawCentreMarker(java.awt.Graphics g)