org.emboss.jemboss.editor
Class SequenceJPanel

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--javax.swing.JComponent
                    |
                    +--javax.swing.JPanel
                          |
                          +--org.emboss.jemboss.editor.SequenceJPanel
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.event.ActionListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

public class SequenceJPanel
extends javax.swing.JPanel
implements java.awt.event.ActionListener

Applet for drawing sequence

See Also:
Serialized Form

Nested Class Summary
(package private)  class SequenceJPanel.PopupListener
           
 
Field Summary
private  int boundWidth
           
private  int boundWidth2
           
private  java.awt.Color col
           
private  java.util.Hashtable colorTable
           
private  boolean drawBlackBox
           
private  boolean drawColorBox
           
private  boolean drawNumber
           
private  boolean drawSequence
           
private  java.awt.Font font
           
private  int fontSize
           
private  boolean highlightPattern
           
private  int interval
           
private  java.lang.String padChar
           
private  java.lang.String pattern
           
private  javax.swing.JPopupMenu popup
           
private  int pressedResidue
           
private  boolean prettyPlot
           
private  int resWidth
           
private  Sequence seq
           
private  int seqHeight
           
private  int seqLength
           
private  javax.swing.JComponent viewPane
           
private  int ypad
           
 
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
SequenceJPanel(int interval, int seqLength)
           
SequenceJPanel(Sequence seq, javax.swing.JComponent viewPane, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, java.util.Hashtable colorTable, int ypad)
          Constructor with default font size.
SequenceJPanel(Sequence seq, javax.swing.JComponent viewPane, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, java.util.Hashtable colorTable, int fontSize, int ypad)
           
 
Method Summary
 void actionPerformed(java.awt.event.ActionEvent e)
           
private  java.awt.Color getColor(java.lang.String s)
           
 java.lang.String getDescription()
           
 int getFontSize()
           
 void getNamePrintGraphic(java.awt.Graphics g2d)
           
private  java.util.Vector getPatternPositions(int istart, int istop, java.lang.String seqS)
          Find all occurences of the pattern in the sequence between the start and stop positions.
private  java.util.Vector getPatternPositions(int subseqStart, java.lang.String subseq)
          Find all occurences of the pattern in the sequence between the start and stop positions.
 java.awt.Dimension getPreferredSize()
           
 int getResidueWidth()
           
 int getSequenceHeight()
           
 void getSequencePrintGraphic(java.awt.Graphics g2d, int MAXSEQNAME, int istart, int istop)
           
 int getSequenceResidueWidth()
           
 int getSequenceWidth()
           
 java.awt.Point getToolTipLocation(java.awt.event.MouseEvent e)
           
 java.lang.String getToolTipText(java.awt.event.MouseEvent e)
           
 void init()
           
 void paintComponent(java.awt.Graphics g)
           
 void setColorScheme(java.util.Hashtable colorHash)
           
 void setDefaultColorHashtable()
           
 void setDrawBoxes(boolean drawBlackBox)
           
 void setDrawColor(boolean drawColorBox)
           
 void setFontSize(int size)
           
 void setPrettyPlot(boolean prettyPlot)
           
 void setSequenceLength(int s)
           
protected  void showPattern(java.lang.String pattern)
           
protected  void 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, getName, 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

col

private java.awt.Color col

seq

private Sequence seq

fontSize

private int fontSize

font

private java.awt.Font font

boundWidth

private int boundWidth

boundWidth2

private int boundWidth2

resWidth

private int resWidth

seqHeight

private int seqHeight

pressedResidue

private int pressedResidue

interval

private int interval

seqLength

private int seqLength

ypad

private int ypad

colorTable

private java.util.Hashtable colorTable

padChar

private java.lang.String padChar

pattern

private java.lang.String pattern

drawSequence

private boolean drawSequence

drawBlackBox

private boolean drawBlackBox

drawColorBox

private boolean drawColorBox

drawNumber

private boolean drawNumber

prettyPlot

private boolean prettyPlot

highlightPattern

private boolean highlightPattern

viewPane

private javax.swing.JComponent viewPane

popup

private javax.swing.JPopupMenu popup
Constructor Detail

SequenceJPanel

public SequenceJPanel(Sequence seq,
                      javax.swing.JComponent viewPane,
                      boolean drawSequence,
                      boolean drawBlackBox,
                      boolean drawColorBox,
                      java.util.Hashtable colorTable,
                      int fontSize,
                      int ypad)

SequenceJPanel

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


SequenceJPanel

public SequenceJPanel(int interval,
                      int seqLength)
Method Detail

init

public void init()

paintComponent

public void paintComponent(java.awt.Graphics g)
Overrides:
paintComponent in class javax.swing.JComponent

getPatternPositions

private java.util.Vector getPatternPositions(int istart,
                                             int istop,
                                             java.lang.String seqS)
Find all occurences of the pattern in the sequence between the start and stop positions. Returning all positions of these in a vector.


getPatternPositions

private java.util.Vector getPatternPositions(int subseqStart,
                                             java.lang.String subseq)
Find all occurences of the pattern in the sequence between the start and stop positions. Returning all positions of these in a vector.


showPattern

protected void showPattern(java.lang.String pattern)

setPrettyPlot

public void setPrettyPlot(boolean prettyPlot)

getToolTipText

public java.lang.String getToolTipText(java.awt.event.MouseEvent e)
Overrides:
getToolTipText in class javax.swing.JComponent

getToolTipLocation

public java.awt.Point getToolTipLocation(java.awt.event.MouseEvent e)
Overrides:
getToolTipLocation in class javax.swing.JComponent

getColor

private java.awt.Color getColor(java.lang.String s)

setDefaultColorHashtable

public void setDefaultColorHashtable()

setDrawBoxes

public void setDrawBoxes(boolean drawBlackBox)

setDrawColor

public void setDrawColor(boolean drawColorBox)

setFontSize

public void setFontSize(int size)

getResidueWidth

public int getResidueWidth()

setColorScheme

public void setColorScheme(java.util.Hashtable colorHash)

getFontSize

public int getFontSize()

getPreferredSize

public java.awt.Dimension getPreferredSize()
Overrides:
getPreferredSize in class javax.swing.JComponent

viewPaneResize

protected void viewPaneResize()

getSequenceHeight

public int getSequenceHeight()

getSequenceWidth

public int getSequenceWidth()

getSequenceResidueWidth

public int getSequenceResidueWidth()

setSequenceLength

public void setSequenceLength(int s)

getDescription

public java.lang.String getDescription()

getNamePrintGraphic

public void getNamePrintGraphic(java.awt.Graphics g2d)

getSequencePrintGraphic

public void getSequencePrintGraphic(java.awt.Graphics g2d,
                                    int MAXSEQNAME,
                                    int istart,
                                    int istop)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)
Specified by:
actionPerformed in interface java.awt.event.ActionListener