edu.mssm.crover.domain2d
Class BetaStrandDomain

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.BetaStrandDomain

All Implemented Interfaces:

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

public class BetaStrandDomain

extends TwoEndsDraggableDomain

implements Domain2D, java.util.Observer

Graphical representation of a beta strand subunit.

Author:

Karel Konvicka

See Also:

Serialized Form

Field Summary

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

BetaStrandDomain()

BetaStrandDomain(ResidueModelFactory rmf, ResidueGlyphFactory rgf, ResidueGlyphRenderingAttributes rgra)

Method Summary

protected void	assignCRDcoordinates(double[] crd_x, double[] crd_y, int ncomp)
java.awt.Point	centerOf(java.awt.Component comp)
protected void	computeBetaStrandCoordinates(double[] crd_x, double[] crd_y, int ncomp, int width, int height)
protected void	computePreferredSize(double[] crd_x, double[] crd_y, int ncomp, int width, int height)
java.awt.geom.Point2D	getDirection() Returns the direction of drawing of this domain, defined as the vector tangent to the direction of drawing of the residue chain at the exit of the domain.
void	getSpacer(java.awt.geom.Point2D space)
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.
void	layoutResidues() Layout the residues in the domain.
void	paintComponent(java.awt.Graphics g)
void	setDirection(java.awt.geom.Point2D direction) Sets the direction vector for this domain.
void	setDragging(boolean state) Enable/disable the dragging of a domain.
void	setModel(BetaStrandModel model)
protected void	setOffset(double xmin, double ymin)
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 space) Sets the spacer vector for this domain.
void	Update(java.util.Observable o, java.lang.Object arg)

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, isOptimizedDrawingEnabled, 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.Domain2D

calculateDeltas, connectEnd, connectPosition, connectStart, dispose, firstResiduePos, getComp, getId, lastResiduePos, position, setId, useResidueModelFactory

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

getComponent, getParent, getSurface, suggestLocation, suggestLocation

Methods inherited from interface java.util.Observer

update

Constructor Detail

BetaStrandDomain

public BetaStrandDomain()

BetaStrandDomain

public BetaStrandDomain(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.

Specified by:

setDragging in interface Domain2D

See Also:

domain2d.DBSModel

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

setModel

public void setModel(BetaStrandModel model)

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)

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.

Specified by:

layoutResidues in interface Domain2D

See Also:

Domain2D.firstResiduePos(), Domain2D.lastResiduePos()

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()).

Specified by:

setRange in interface Domain2D

InvalidRange

setSpacer

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

Description copied from interface: Domain2D

Sets the spacer vector for this domain. The spacer is only indicative: different implementations of Domain2D can interpret it differently. For instance, loops will try to adjust to fit the spacer vector as closely as possible, helices will change the direction of their drawing to fit the direction of the indicated spacer.

Specified by:

setSpacer in interface Domain2D

getSpacer

public void getSpacer(java.awt.geom.Point2D space)

setDirection

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

Description copied from interface: Domain2D

Sets the direction vector for this domain. Some domain display depend on the value of direction (general direction of drawing), other do not. The choice is left to the domain implementor. Helices should adjust to allow rotations of the domain. Loops are highly constrained by surrounding domains and aesthetic constrained, so are unlikely to adjust their display to this parameter.

Specified by:

setDirection in interface Domain2D

getDirection

public java.awt.geom.Point2D getDirection()

Description copied from interface: Domain2D

Returns the direction of drawing of this domain, defined as the vector tangent to the direction of drawing of the residue chain at the exit of the domain.
This is used by loops to determine their tangential orientation when connecting two domains. Stricly, there should be two directions: a entry direction and an exit direction. At the moment, for helices and strands it is not expected that the directions will be different so we conveniently keep only one method. This could change as needed.

Specified by:

getDirection in interface Domain2D

Update

public void Update(java.util.Observable o,
                   java.lang.Object arg)

computePreferredSize

protected void computePreferredSize(double[] crd_x,
                                    double[] crd_y,
                                    int ncomp,
                                    int width,
                                    int height)

computeBetaStrandCoordinates

protected void computeBetaStrandCoordinates(double[] crd_x,
                                            double[] crd_y,
                                            int ncomp,
                                            int width,
                                            int height)

assignCRDcoordinates

protected void assignCRDcoordinates(double[] crd_x,
                                    double[] crd_y,
                                    int ncomp)

setOffset

protected void setOffset(double xmin,
                         double ymin)