org.biojava.bio.structure.gui.util
Class SequenceScalePanel

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by org.biojava.bio.structure.gui.util.SequenceScalePanel
All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible

public class SequenceScalePanel
extends JPanel

A class that draws a Sequence as a rectangle, a scale display over it.

Since:
1.7
Author:
Andreas Prlic
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class javax.swing.JPanel
JPanel.AccessibleJPanel
 
Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
 
Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer
 
Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
 
Field Summary
static Color BACKGROUND_COLOR
           
static int DEFAULT_X_RIGHT_BORDER
           
static int DEFAULT_X_START
           
static int DEFAULT_Y_BOTTOM
           
static int DEFAULT_Y_HEIGHT
           
static int DEFAULT_Y_START
           
static int DEFAULT_Y_STEP
           
static Color GAP_COLOR
           
static Color IDX_COLOR
           
static int LINE_HEIGHT
           
static int MINIMUM_HEIGHT
           
static Color SCALE_COLOR
           
static Font seqFont
           
static Color SEQUENCE_COLOR
           
static int SIZE
           
static Color TEXT_SCALE_COLOR
           
 
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
SequenceScalePanel(int position)
           
 
Method Summary
protected  void drawIdx(Graphics2D g2D, int y)
           
protected  int drawScale(Graphics2D g2D, int y)
          draw the Scale
protected  int drawSequence(Graphics2D g2D, int y)
          draw the Amino acid sequence
 Chain getChain()
           
 float getScale()
           
 void paintComponent(Graphics g)
           
 void setAligMap(List<AlignedPosition> apos)
           
 void setChain(Chain c)
           
protected  void setPaintDefaults(Graphics2D g2D)
          set some default rendering hints, like text antialiasing on
 void setScale(float scale)
           
 
Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
 
Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, 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, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, 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
 
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

DEFAULT_X_START

public static final int DEFAULT_X_START
See Also:
Constant Field Values

DEFAULT_X_RIGHT_BORDER

public static final int DEFAULT_X_RIGHT_BORDER
See Also:
Constant Field Values

DEFAULT_Y_START

public static final int DEFAULT_Y_START
See Also:
Constant Field Values

DEFAULT_Y_STEP

public static final int DEFAULT_Y_STEP
See Also:
Constant Field Values

DEFAULT_Y_HEIGHT

public static final int DEFAULT_Y_HEIGHT
See Also:
Constant Field Values

DEFAULT_Y_BOTTOM

public static final int DEFAULT_Y_BOTTOM
See Also:
Constant Field Values

LINE_HEIGHT

public static final int LINE_HEIGHT
See Also:
Constant Field Values

MINIMUM_HEIGHT

public static final int MINIMUM_HEIGHT
See Also:
Constant Field Values

SEQUENCE_COLOR

public static final Color SEQUENCE_COLOR

SCALE_COLOR

public static final Color SCALE_COLOR

TEXT_SCALE_COLOR

public static final Color TEXT_SCALE_COLOR

IDX_COLOR

public static final Color IDX_COLOR

GAP_COLOR

public static final Color GAP_COLOR

BACKGROUND_COLOR

public static final Color BACKGROUND_COLOR

seqFont

public static final Font seqFont

SIZE

public static final int SIZE
See Also:
Constant Field Values
Constructor Detail

SequenceScalePanel

public SequenceScalePanel(int position)
Method Detail

setAligMap

public void setAligMap(List<AlignedPosition> apos)

setChain

public void setChain(Chain c)

getChain

public Chain getChain()

getScale

public float getScale()

setScale

public void setScale(float scale)

setPaintDefaults

protected void setPaintDefaults(Graphics2D g2D)
set some default rendering hints, like text antialiasing on

Parameters:
g2D - the graphics object to set the defaults on

paintComponent

public void paintComponent(Graphics g)
Overrides:
paintComponent in class JComponent

drawScale

protected int drawScale(Graphics2D g2D,
                        int y)
draw the Scale

Parameters:
g2D -
y - the height on which to draw the scale
Returns:
the new y position

drawIdx

protected void drawIdx(Graphics2D g2D,
                       int y)

drawSequence

protected int drawSequence(Graphics2D g2D,
                           int y)
draw the Amino acid sequence

Parameters:
g2D -
y - .. height of line to draw the sequence onto
Returns:
the new y value