org.peace_tools.views.overlap
Class Ruler

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              org.peace_tools.views.overlap.Ruler

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

 class Ruler
extends javax.swing.JComponent

The overlap panel that displays the actual overlap image.

This panel performs the core task of drawing the various fragments illustrating the overlap. The fragments are drawn row-by-row using the data from a given (specified in the constructor) OverlapModel object. The size and location of the rectangles for each fragment depend on the current scaling factors set for this component (via call to setScale() method). The scaling factors also control the preferred size reported by this panel. The color map maintained by this class is used to color the fragments based on their cluster ID.

NoteThis class is meant to be instantiated and used only by the OverlapView class. Consequently it has been made package private.

Nested Class Summary

static class

Ruler.Orientation Enumerations to define the two types of rulers that this class can be used for.

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

private double	colScale The scale to be applies when rendering a single column.
private java.awt.Dimension	modelSize The Dimension that provides the necessary information for rendering the ruler displayed in this class.
private Ruler.Orientation	orientation The orientation being used for this ruler.
private double	rowScale The scale to be applies when rendering a single row.
private int	RULE_HEIGHT The preferred height of the horizontal ruler.
private static int	RULE_WIDTH The preferred width of the vertical ruler.
private static long	serialVersionUID A generated serialization UID just to keep the compiler happy.

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.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

Ruler(int modelWidth, int modelHeight, Ruler.Orientation orientation)
The only constructor.

Method Summary

void	paintComponent(java.awt.Graphics g)
private void	paintHorizRule(java.awt.Graphics g) Helper method to paint the horizontal ruler.
private void	paintVerticalRule(java.awt.Graphics g) Helper method to paint the horizontal ruler.
void	setScale(double rowScale, double colScale) Method to set the current scales used by this component.

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, paramString, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update, updateUI

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, 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, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

rowScale

private double rowScale

The scale to be applies when rendering a single row. This value represents the maximum height of each row. Once the row height is above 3 at least one blank line is allocated for each row to clearly delineate one row from the other. This value is initialized in the constructor and can be changed via a call to the setScale() method in this class. Typically this value is in integral units without any fractions. However, it is maintained as a double to accommodate non-integral scales in the future. However, this value should never be set to zero.

colScale

private double colScale

The scale to be applies when rendering a single column. This value represents the maximum width of each column. This value is initialized in the constructor and can be changed via a call to the setScale() method in this class. Typically this value is in integral units when columns occupy more than 1 pixel. If a column occupies fewer than one pixel then this value is a fractional value. This value should never be set to zero.

modelSize

private final java.awt.Dimension modelSize

The Dimension that provides the necessary information for rendering the ruler displayed in this class. Horizontal ruler uses the modelWidth while the vertical ruler uses modelHeight value from this instance variable. This instance variable is initialized by the constructor and is never changed during the life time of this object.

orientation

private final Ruler.Orientation orientation

The orientation being used for this ruler. This value is set in the constructor and is never changed for this model.

RULE_WIDTH

private static int RULE_WIDTH

The preferred width of the vertical ruler. This width is defined as a constant so that it is easy to set the size of the ruler appropriately.

RULE_HEIGHT

private int RULE_HEIGHT

The preferred height of the horizontal ruler. This height is defined as a constant so that it is easy to set the size of the ruler appropriately.

serialVersionUID

private static final long serialVersionUID

A generated serialization UID just to keep the compiler happy.

See Also:

Constant Field Values

Constructor Detail

Ruler

public Ruler(int modelWidth,
             int modelHeight,
             Ruler.Orientation orientation)

The only constructor.

Parameters:

modelWidth - The total width of the model in nucleotides. This value is typically the OverlapModel.getMaxCol().

modelHeight - The total height of the model in number of rows of nucleotides. This value is typically OverlapModel.getMaxRow().

orientation - The orientation that defines the type of ruler that this instance is to represent. The orientation determines the overall behavior of this class.

Method Detail

paintComponent

public void paintComponent(java.awt.Graphics g)

Overrides:

paintComponent in class javax.swing.JComponent

paintHorizRule

private void paintHorizRule(java.awt.Graphics g)

Helper method to paint the horizontal ruler. This method is invoked from the main paint component method in order to draw a horizontal rule with the necessary ticks and labels. This method assumes that this ruler will always be added to the top of the overlap view panel.

Parameters:

g - The graphics object to be used for drawing the ticks.

paintVerticalRule

private void paintVerticalRule(java.awt.Graphics g)

Helper method to paint the horizontal ruler. This method is invoked from the main paint component method in order to draw a horizontal rule with the necessary ticks and labels. This method assumes that the vertical ruler will always be displayed to the left of the overlap panel.

Parameters:

g - The graphics object to be used for drawing the ticks.

setScale

public void setScale(double rowScale,
                     double colScale)

Method to set the current scales used by this component.

This method must be used to set the scales to be used for painting rows and columns in this panel. The scales also determine the overall size of this component.

Note: The containing component my repaint itself to ensure that changes in bounds are correctly refreshed on screen.

Parameters:

rowScale - The scale that determines the number of pixels occupied by each row. This value cannot be zero. However, no checks are performed on the scale. Consequently, the behavior of this component with a zero scale is undefined.

colScale - The scale that determines the number of pixels occupied by each row. This value cannot be zero. However, no checks are performed on the scale. Consequently, the behavior of this component with a zero scale is undefined.