edu.mssm.crover.domain2d
Class ProteinSegmentDomain

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.ProteinSegmentDomain

All Implemented Interfaces:

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

public class ProteinSegmentDomain

extends TwoEndsDraggableDomain

implements Domain2D, java.util.Observer

Graphical representation of a protein segment. This is actually meant to represent protein domains, but rbde already uses this name. The segment is represented by an large ellipse in which the name, and range of residues in the segment are written. The spacer of this domain enterely determines the dimension on the page. The size of the elipse that represent the protein segment is calculated directly from the spacer.

Author:

Fabien Campagne

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

ProteinSegmentDomain()

ProteinSegmentDomain(ResidueModelFactory rmf, ResidueGlyphFactory rgf, ResidueGlyphRenderingAttributes rgra)

Method Summary

java.awt.Point	centerOf(java.awt.Component comp)
protected void	computePreferredSize()
java.awt.geom.Point2D	getDirection() Returns the direction of the spacer (normalized).
int	getEndResidueIndex()
float	getRadius() Returns the radius of the circle that represents this domain.
java.awt.geom.Point2D	getSpacer()
int	getStartResidueIndex()
java.lang.String	getURL() URL of the document linked to this ProteinSegmentDomain.
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(ProteinSegmentModel model)
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) Sets the spacer of the protein domain.
void	setURL(java.lang.String URL) Sets the URL of a document to which this ProteinSegmentDomain links.
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

ProteinSegmentDomain

public ProteinSegmentDomain()

ProteinSegmentDomain

public ProteinSegmentDomain(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(ProteinSegmentModel model)

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

getStartResidueIndex

public int getStartResidueIndex()

getEndResidueIndex

public int getEndResidueIndex()

setSpacer

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

Sets the spacer of the protein domain. The spacer directly determines the dimensions of the rendering.

Specified by:

setSpacer in interface Domain2D

getSpacer

public java.awt.geom.Point2D getSpacer()

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

getURL

public java.lang.String getURL()

URL of the document linked to this ProteinSegmentDomain. A url can be linked to this segment in one of two ways:

setURL was called previously

the PrintablePanelSVG_ANCHOR_HREF_PROPERTY property has been set on this JComponent segment.

Returns:

null or String encoding an URL.

setURL

public void setURL(java.lang.String URL)

Sets the URL of a document to which this ProteinSegmentDomain links. Also sets the client property SVG_ANCHOR_HREF_PROPERTY on this component so that PrintablePanel can create a link when exporting to SVG.

getDirection

public java.awt.geom.Point2D getDirection()

Returns the direction of the spacer (normalized).

Specified by:

getDirection in interface Domain2D

getRadius

public float getRadius()

Returns the radius of the circle that represents this domain.

Update

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

paintComponent

public void paintComponent(java.awt.Graphics g)

Overrides:

paintComponent in class javax.swing.JComponent

computePreferredSize

protected void computePreferredSize()