edu.mssm.crover.domain2d
Class HelicalDomain

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--javax.swing.JComponent
                    |
                    +--javax.swing.JPanel
                          |
                          +--edu.mssm.crover.domain2d.PrintablePanel
                                |
                                +--edu.mssm.crover.domain2d.TwoEndsDomain
                                      |
                                      +--edu.mssm.crover.domain2d.TwoEndsDraggableDomain
                                            |
                                            +--edu.mssm.crover.domain2d.HelicalDomain

All Implemented Interfaces:

javax.accessibility.Accessible, CoolPrint, Domain2D, Drawing, java.awt.image.ImageObserver, java.awt.MenuContainer, java.util.Observer, java.io.Serializable

public class HelicalDomain

extends TwoEndsDraggableDomain

A helix secondary structure representation.

See Also:

HelixModel, Serialized Form

Field Summary

boolean	hideFirst
boolean	hideLast
static int	LEFT_HANDED
static int	RIGHT_HANDED

Fields inherited from class edu.mssm.crover.domain2d.TwoEndsDomain

delta_end, delta_start, end, first, last, position, quickDraw, rgf, rgra, rmf, solver, start

Fields inherited from class edu.mssm.crover.domain2d.PrintablePanel

SVG_ANCHOR_HREF_PROPERTY

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

HelicalDomain()

HelicalDomain(ResidueModelFactory rmf, ResidueGlyphFactory rgf, ResidueGlyphRenderingAttributes rgra)

Method Summary

java.awt.Point	centerOf(java.awt.Component comp)
java.awt.Image	getBackgroundImage()
java.awt.geom.Point2D	getDirection() gets the direction of the drawing of this loop.
void	hideFirst(boolean hs) Loop spacer adustements require that the last residue of the last domain and the first residue of the next domain not to be displayed/controlled by the other domains.
void	hideLast(boolean hs) see hideFirst.
boolean	isOptimizedDrawingEnabled()
void	layoutResidues() Layout the residues in the domain.
void	paintComponent(java.awt.Graphics g)
void	setDirection(java.awt.geom.Point2D direction) Domaind2D interface method to change the model direction.
void	setDragging(boolean state) Enable/disable the dragging of a domain.
void	setHelixModel(HelixModel hm)
void	setRange(BiologicalSequence seq, int start, int end) Instructs the domain to render the part of sequence seq made of the residues between start and end, extremities included.
void	setSpacer(java.awt.geom.Point2D spacer) This method has no effect on this implementation.

Methods inherited from class edu.mssm.crover.domain2d.TwoEndsDraggableDomain

dispose, setDBSDebug, setListener

Methods inherited from class edu.mssm.crover.domain2d.TwoEndsDomain

calculateDeltas, connectEnd, connectPosition, connectStart, finalize, firstResiduePos, getComp, getComponent, getId, getLocation, getSurface, getX, getY, lastResiduePos, paintBrushing, paintSelection, position, setId, setLocation, setLocation, suggestLocation, suggestLocation, syncLocation, update, useResidueModelFactory

Methods inherited from class edu.mssm.crover.domain2d.PrintablePanel

coolPrint, recurseSVGPrint, svgPrint

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, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, 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, 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, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface edu.mssm.crover.domain2d.Drawing

getParent

Field Detail

LEFT_HANDED

public static final int LEFT_HANDED

See Also:

Constant Field Values

RIGHT_HANDED

public static final int RIGHT_HANDED

See Also:

Constant Field Values

hideFirst

public boolean hideFirst

hideLast

public boolean hideLast

Constructor Detail

HelicalDomain

public HelicalDomain()

HelicalDomain

public HelicalDomain(ResidueModelFactory rmf,
                     ResidueGlyphFactory rgf,
                     ResidueGlyphRenderingAttributes rgra)

Method Detail

setDragging

public void setDragging(boolean state)

Description copied from interface: Domain2D

Enable/disable the dragging of a domain. Most of the time this is a convenient method to access the DBS model and turn the dragging on/off.

See Also:

domain2d.DBSModel

getDirection

public java.awt.geom.Point2D getDirection()

gets the direction of the drawing of this loop. The point is to be understood as the extremity of a unary vector which origin is (0,0).

paintComponent

public void paintComponent(java.awt.Graphics g)

Overrides:

paintComponent in class javax.swing.JComponent

centerOf

public java.awt.Point centerOf(java.awt.Component comp)

getBackgroundImage

public java.awt.Image getBackgroundImage()

isOptimizedDrawingEnabled

public boolean isOptimizedDrawingEnabled()

Overrides:

isOptimizedDrawingEnabled in class TwoEndsDomain

setHelixModel

public void setHelixModel(HelixModel hm)

setRange

public void setRange(BiologicalSequence seq,
                     int start,
                     int end)
              throws InvalidRange

Description copied from interface: Domain2D

Instructs the domain to render the part of sequence seq made of the residues between start and end, extremities included.
Calling this method could be expensive as the number of residues may be altered and the layout recalculated. Implementors are advised to optimize their code to enable a dynamic adjustement of the range of the domain provided by the diagram editor (yet to be written). Interestingly, it has to be noted that this kind of dynamic adjustement is likely to translate the range over the sequence, add or remove a residue from the range. So some implementations can be choosen to accomodate these local changes that will reuse the previous layout and residues (from the previous invocation of setRange()).

InvalidRange

hideFirst

public void hideFirst(boolean hs)

Description copied from interface: Domain2D

Loop spacer adustements require that the last residue of the last domain and the first residue of the next domain not to be displayed/controlled by the other domains. To do so, the loop domain uses hideFirst and hideLast on its previous and follower domain.

Specified by:

hideFirst in interface Domain2D

Overrides:

hideFirst in class TwoEndsDomain

hideLast

public void hideLast(boolean hs)

Description copied from interface: Domain2D

see hideFirst.

Specified by:

hideLast in interface Domain2D

Overrides:

hideLast in class TwoEndsDomain

setSpacer

public void setSpacer(java.awt.geom.Point2D spacer)

This method has no effect on this implementation.

setDirection

public void setDirection(java.awt.geom.Point2D direction)

Domaind2D interface method to change the model direction.

layoutResidues

public void layoutResidues()

Description copied from interface: Domain2D

Layout the residues in the domain. Determine the size of the domain and set it. After this method has executed the positions of the first and last residue are know relatively to the domain position.

See Also:

Domain2D.firstResiduePos(), Domain2D.lastResiduePos()