org.biojava.nbio.structure.gui.util

Class SequenceScalePanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

org.biojava.nbio.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

Fields

Modifier and Type	Field and Description
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

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

accessibleContext, 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

Constructors

Constructor and Description
SequenceScalePanel(int position)

Method Summary

Modifier and Type	Method and Description
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, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, 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, 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