apollo.gui.genomemap
Class StrandedZoomableApolloPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.gui.ControlledPanel
                      apollo.gui.genomemap.StrandedZoomableApolloPanel

All Implemented Interfaces:

DataLoadListener, ControlledObjectI, DrawableAnnotationConstants, BaseFocusListener, NamedFeatureSelectionListener, OrientationListener, ReverseComplementListener, RubberbandListener, ScrollListener, SetActiveCurStateListener, ZoomListener, ApolloPanelHolderI, java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

public class StrandedZoomableApolloPanel
extends ControlledPanel
implements java.awt.event.ActionListener, java.awt.event.AdjustmentListener, ApolloPanelHolderI, BaseFocusListener, ControlledObjectI, DrawableAnnotationConstants, NamedFeatureSelectionListener, SetActiveCurStateListener, OrientationListener, DataLoadListener, RubberbandListener, ScrollListener, ReverseComplementListener, ZoomListener

The class which controls and renders the main feature display panel, containing an AnnotationView, ResultView and SiteView for each strand. This class contains ApolloPanel which contains all the views, but it also contains the views as well, which seems confusing. Shouldnt either this or ApolloPanel contain all the views but not both? SiteViews should not be created unless there is sequence - change this. In addition to ApolloPanel this also has scrollbars, zoom buttons, & nav bar.

See Also:

Serialized Form

Nested Class Summary

class

StrandedZoomableApolloPanel.ShiftAwareButton My zoom-buttons are aware of when they are pressed with a shift-key.

Nested classes/interfaces inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

static java.lang.String	CUSTOM
AnnotationView	forwardAnnotView
protected static org.apache.log4j.Logger	logger
static java.lang.String	RESET
AnnotationView	reverseAnnotView
static java.lang.String	ZOOMIN
static java.lang.String	ZOOMIN2
static java.lang.String	ZOOMOUT
static java.lang.String	ZOOMOUT2

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 apollo.gui.drawable.DrawableAnnotationConstants

ALLSTOPS, BOTHENDS, END, NOSTOPS, ONESTOP, START

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

StrandedZoomableApolloPanel(GuiCurationState curationState, java.lang.String zoomPosition)
Makes zoomable scrollable szap

Method Summary

void	actionPerformed(java.awt.event.ActionEvent evt) Action event listener
void	addGraph(ScoreCalculator s, boolean isDiscrete, java.awt.Color color)
void	addHighlightRegion(BaseScrollable scroller, java.awt.Color color, boolean reverse)
void	adjustmentValueChanged(java.awt.event.AdjustmentEvent e)
void	applyLayout(misc.JIniFile iniFile, java.lang.String section, boolean updateBaseLocation)
void	applyVisibilityFromLayout(misc.JIniFile iniFile, java.lang.String section)
boolean	areAnnotationViewsVisible()
boolean	areResultViewsVisible()
java.awt.Rectangle	calculateHighlightRect(apollo.gui.genomemap.StrandedZoomableApolloPanel.HighlightWrapper hw)
void	changeYOrientation()
void	clearData()
Drawable	findDrawableForFeatureInResultViews(SeqFeatureI sf)
FeatureSetI	getAnnotations()
AnnotationView	getAnnotView(int strand)
ApolloPanel	getApolloPanel() I think this will need to change to: ApolloPanel[] getApolloPanels()
int	getCentreBase()
java.awt.Component	getComponent()
Controller	getController() Gets the Controller for the object
CurationSet	getCurationSet()
FeatureSetI	getForwardAnnotations()
FeatureSetI	getForwardResults()
java.util.List<GraphView>	getGraphs()
GraphView	getGraphView()
boolean	getGraphVisibility() true if GraphView is visible
javax.swing.JLabel	getOrganismLabel() A label that's stamped with a curation set's organism name and range whenever I'm informed of a new curation set.
FeatureSetI	getResults()
RevCompListener	getRevCompListener()
FeatureSetI	getReverseAnnotations()
FeatureSetI	getReverseResults()
ScaleView	getScaleView()
SelectionManager	getSelectionManager()
boolean	getSiteViewVisibleOnZoom() This does not return whther the sites are actually visible but whether they are capable of being visible.
Transformer	getTransformer()
ResultView	getViewForFeature(SeqFeatureI sf)
boolean	handleBaseFocusEvent(BaseFocusEvent evt)
boolean	handleDataLoadEvent(DataLoadEvent evt)
boolean	handleNamedFeatureSelectionEvent(NamedFeatureSelectionEvent theEvent) If we are handed a feature selected only by name, then - as long as we are not the source of the event, we will try to find the features in our result set which correspond to the named features.
boolean	handleOrientationEvent(OrientationEvent evt)
boolean	handleReverseComplementEvent(ReverseComplementEvent evt)
boolean	handleRubberbandEvent(RubberbandEvent evt)
boolean	handleScrollEvent(ScrollEvent event)
boolean	handleSetActiveCurStateEvent(SetActiveCurStateEvent evt)
boolean	handleZoomEvent(ZoomEvent event)
boolean	haveSequence()
boolean	isControlPanelVisible()
boolean	isForwardStrandVisible()
boolean	isReverseComplement() Single stranded holder return false?
boolean	isReverseStrandVisible()
boolean	isScaleViewVisible()
boolean	isScrollingPropagated()
boolean	isShowingEdgeMatches()
void	paint(java.awt.Graphics g)
void	paintComponent(java.awt.Graphics g)
void	putVerticalScrollbarsAtStart() This sets all the views scrollbars at start position.
void	removeAllGraphs()
void	removeGraph(GraphView graph)
void	removeHighlightRegion(BaseScrollable scroller)
void	repaint()
void	repaintHighlights()
void	resetViews()
void	saveLayout(misc.JIniFile iniFile, java.lang.String section)
void	scrollToSelection()
boolean	selectFeaturesByName(java.lang.String name, int window) Searches features for name and selects all that are found, does nothing if none are found.
boolean	selectFeaturesByName(java.lang.String name, int window, boolean useRegExp) window is how much padding to allow in the zoom.
void	setAnnotations(CurationSet curation)
void	setAnnotationViewsVisible(boolean state)
void	setCentreBase(int location)
void	setController(Controller controller) Sets the Controller for the object
void	setControlPanelVisibility(boolean state)
void	setCurationSet(CurationSet set)
void	setEdgeMatching(boolean state)
void	setFeatureSet(CurationSet cset)
void	setForwardVisible(boolean state)
void	setGraphVisibility(boolean state)
void	setGuideLine(boolean state)
void	setResultViewsVisible(boolean state)
void	setRevCompListener(RevCompListener l) For now only one listener, if need more then one listener in future make this addStrandVisibilyListener and add to vector
void	setReverseComplement(boolean state)
void	setReverseVisible(boolean state)
void	setScaleViewVisible(boolean state)
void	setScrollingPropagated(boolean value)
void	setScrollValues()
void	setSelectionManager(SelectionManager sm)
void	setShiftForLockedZooming(boolean state)
void	setSiteViewVisibleOnZoom(boolean state) If state is false hide site view, even if zoomed in.
void	setStatusBar(StatusBar sb)
void	setTextAvoidance(boolean state)
void	setViewColours()
void	setVisible(boolean state) setVisible calls setTextAvoidance(true).
void	setZoomFactor(double factor)
void	updateHighlightRegion(BaseScrollable scroller, java.awt.Color color, boolean reverse)
void	zoomToSelection()
void	zoomToSelectionWithWindow(int window) If zoomToSelectionWithWindow is called with no centerBase argument, make centerBase -1 to let the real method know that.
void	zoomToSelectionWithWindow(int window, int centerBase)
void	zoomToWidth(double dispWidth, int[] limits)

Methods inherited from class apollo.gui.ControlledPanel

addNotify, getControllerWindow, needsAutoRemoval

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, 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, isPaintingTile, isRequestFocusEnabled, isValidateRoot, 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, 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, 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, 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, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface apollo.gui.genomemap.ApolloPanelHolderI

setPreferredSize

Methods inherited from interface apollo.gui.ControlledObjectI

getControllerWindow, needsAutoRemoval

Field Detail

logger

protected static final org.apache.log4j.Logger logger

ZOOMIN

public static java.lang.String ZOOMIN

ZOOMIN2

public static java.lang.String ZOOMIN2

ZOOMOUT

public static java.lang.String ZOOMOUT

ZOOMOUT2

public static java.lang.String ZOOMOUT2

RESET

public static java.lang.String RESET

CUSTOM

public static java.lang.String CUSTOM

forwardAnnotView

public AnnotationView forwardAnnotView

reverseAnnotView

public AnnotationView reverseAnnotView

Constructor Detail

StrandedZoomableApolloPanel

public StrandedZoomableApolloPanel(GuiCurationState curationState,
                                   java.lang.String zoomPosition)

Makes zoomable scrollable szap

Method Detail

setGraphVisibility

public void setGraphVisibility(boolean state)

setGuideLine

public void setGuideLine(boolean state)

getCurationSet

public CurationSet getCurationSet()

setCurationSet

public void setCurationSet(CurationSet set)

Specified by:

setCurationSet in interface ApolloPanelHolderI

handleSetActiveCurStateEvent

public boolean handleSetActiveCurStateEvent(SetActiveCurStateEvent evt)

Specified by:

handleSetActiveCurStateEvent in interface SetActiveCurStateListener

getForwardResults

public FeatureSetI getForwardResults()

getReverseResults

public FeatureSetI getReverseResults()

setFeatureSet

public void setFeatureSet(CurationSet cset)

setVisible

public void setVisible(boolean state)

setVisible calls setTextAvoidance(true). It's done here because it was waiting for graphics. Setting textAvoidance to true causes a new layout to happen which will probably have more tiers, thus a side effect of setVisible is to get a larger view.

Specified by:

setVisible in interface ApolloPanelHolderI

Overrides:

setVisible in class javax.swing.JComponent

putVerticalScrollbarsAtStart

public void putVerticalScrollbarsAtStart()

This sets all the views scrollbars at start position. This is called after setVisible(true) which causes the views to grow (see note above) and throws any previous attempt at setting the scrollbars at start position. Im not sure whether to go through the views that szap has or to tell apollo panel to go through the views, as both have the views - confusing.

Specified by:

putVerticalScrollbarsAtStart in interface ApolloPanelHolderI

getApolloPanel

public ApolloPanel getApolloPanel()

Description copied from interface: ApolloPanelHolderI

I think this will need to change to: ApolloPanel[] getApolloPanels()

Specified by:

getApolloPanel in interface ApolloPanelHolderI

getForwardAnnotations

public FeatureSetI getForwardAnnotations()

getReverseAnnotations

public FeatureSetI getReverseAnnotations()

setAnnotations

public void setAnnotations(CurationSet curation)

findDrawableForFeatureInResultViews

public Drawable findDrawableForFeatureInResultViews(SeqFeatureI sf)

getAnnotations

public FeatureSetI getAnnotations()

getResults

public FeatureSetI getResults()

zoomToSelection

public void zoomToSelection()

zoomToSelectionWithWindow

public void zoomToSelectionWithWindow(int window)

If zoomToSelectionWithWindow is called with no centerBase argument, make centerBase -1 to let the real method know that.

zoomToSelectionWithWindow

public void zoomToSelectionWithWindow(int window,
                                      int centerBase)

setRevCompListener

public void setRevCompListener(RevCompListener l)

For now only one listener, if need more then one listener in future make this addStrandVisibilyListener and add to vector

getRevCompListener

public RevCompListener getRevCompListener()

scrollToSelection

public void scrollToSelection()

zoomToWidth

public void zoomToWidth(double dispWidth,
                        int[] limits)

selectFeaturesByName

public boolean selectFeaturesByName(java.lang.String name,
                                    int window)

Searches features for name and selects all that are found, does nothing if none are found. Zooms to the new selection. Should scroll to it as well Returns false if no features are found by name This code was taken from FindPanel and modified window is how much padding to allow in the zoom.

Specified by:

selectFeaturesByName in interface ApolloPanelHolderI

selectFeaturesByName

public boolean selectFeaturesByName(java.lang.String name,
                                    int window,
                                    boolean useRegExp)

window is how much padding to allow in the zoom.

setControlPanelVisibility

public void setControlPanelVisibility(boolean state)

isControlPanelVisible

public boolean isControlPanelVisible()

setViewColours

public void setViewColours()

setForwardVisible

public void setForwardVisible(boolean state)

setReverseVisible

public void setReverseVisible(boolean state)

getAnnotView

public AnnotationView getAnnotView(int strand)

isForwardStrandVisible

public boolean isForwardStrandVisible()

isReverseStrandVisible

public boolean isReverseStrandVisible()

setController

public void setController(Controller controller)

Description copied from interface: ControlledObjectI

Sets the Controller for the object

Specified by:

setController in interface ControlledObjectI

Specified by:

setController in class ControlledPanel

handleOrientationEvent

public boolean handleOrientationEvent(OrientationEvent evt)

Specified by:

handleOrientationEvent in interface OrientationListener

handleNamedFeatureSelectionEvent

public boolean handleNamedFeatureSelectionEvent(NamedFeatureSelectionEvent theEvent)

If we are handed a feature selected only by name, then - as long as we are not the source of the event, we will try to find the features in our result set which correspond to the named features. Then we create a FeatureSelectionEvent containing the features we found, and re-throw this event back at the controller.

Specified by:

handleNamedFeatureSelectionEvent in interface NamedFeatureSelectionListener

changeYOrientation

public void changeYOrientation()

setSelectionManager

public void setSelectionManager(SelectionManager sm)

Specified by:

setSelectionManager in interface ApolloPanelHolderI

paintComponent

public void paintComponent(java.awt.Graphics g)

Overrides:

paintComponent in class javax.swing.JComponent

getScaleView

public ScaleView getScaleView()

getGraphView

public GraphView getGraphView()

getGraphVisibility

public boolean getGraphVisibility()

true if GraphView is visible

getGraphs

public java.util.List<GraphView> getGraphs()

addGraph

public void addGraph(ScoreCalculator s,
                     boolean isDiscrete,
                     java.awt.Color color)

calculateHighlightRect

public java.awt.Rectangle calculateHighlightRect(apollo.gui.genomemap.StrandedZoomableApolloPanel.HighlightWrapper hw)

repaintHighlights

public void repaintHighlights()

paint

public void paint(java.awt.Graphics g)

Overrides:

paint in class javax.swing.JComponent

addHighlightRegion

public void addHighlightRegion(BaseScrollable scroller,
                               java.awt.Color color,
                               boolean reverse)

removeHighlightRegion

public void removeHighlightRegion(BaseScrollable scroller)

updateHighlightRegion

public void updateHighlightRegion(BaseScrollable scroller,
                                  java.awt.Color color,
                                  boolean reverse)

isReverseComplement

public boolean isReverseComplement()

Description copied from interface: ApolloPanelHolderI

Single stranded holder return false?

Specified by:

isReverseComplement in interface ApolloPanelHolderI

setReverseComplement

public void setReverseComplement(boolean state)

Specified by:

setReverseComplement in interface ApolloPanelHolderI

handleScrollEvent

public boolean handleScrollEvent(ScrollEvent event)

Specified by:

handleScrollEvent in interface ScrollListener

adjustmentValueChanged

public void adjustmentValueChanged(java.awt.event.AdjustmentEvent e)

Specified by:

adjustmentValueChanged in interface java.awt.event.AdjustmentListener

handleBaseFocusEvent

public boolean handleBaseFocusEvent(BaseFocusEvent evt)

Specified by:

handleBaseFocusEvent in interface BaseFocusListener

handleReverseComplementEvent

public boolean handleReverseComplementEvent(ReverseComplementEvent evt)

Specified by:

handleReverseComplementEvent in interface ReverseComplementListener

getCentreBase

public int getCentreBase()

setCentreBase

public void setCentreBase(int location)

setScrollValues

public void setScrollValues()

getController

public Controller getController()

Description copied from interface: ControlledObjectI

Gets the Controller for the object

Specified by:

getController in interface ControlledObjectI

Specified by:

getController in class ControlledPanel

getSelectionManager

public SelectionManager getSelectionManager()

handleRubberbandEvent

public boolean handleRubberbandEvent(RubberbandEvent evt)

Specified by:

handleRubberbandEvent in interface RubberbandListener

handleDataLoadEvent

public boolean handleDataLoadEvent(DataLoadEvent evt)

Specified by:

handleDataLoadEvent in interface DataLoadListener

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent evt)

Action event listener

Specified by:

actionPerformed in interface java.awt.event.ActionListener

setShiftForLockedZooming

public void setShiftForLockedZooming(boolean state)

resetViews

public void resetViews()

setZoomFactor

public void setZoomFactor(double factor)

Specified by:

setZoomFactor in interface ApolloPanelHolderI

setTextAvoidance

public void setTextAvoidance(boolean state)

setStatusBar

public void setStatusBar(StatusBar sb)

Specified by:

setStatusBar in interface ApolloPanelHolderI

setEdgeMatching

public void setEdgeMatching(boolean state)

getTransformer

public Transformer getTransformer()

haveSequence

public boolean haveSequence()

clearData

public void clearData()

Specified by:

clearData in interface ApolloPanelHolderI

getOrganismLabel

public javax.swing.JLabel getOrganismLabel()

A label that's stamped with a curation set's organism name and range whenever I'm informed of a new curation set.

repaint

public void repaint()

Overrides:

repaint in class java.awt.Component

handleZoomEvent

public boolean handleZoomEvent(ZoomEvent event)

Specified by:

handleZoomEvent in interface ZoomListener

getComponent

public java.awt.Component getComponent()

Specified by:

getComponent in interface ApolloPanelHolderI

setAnnotationViewsVisible

public void setAnnotationViewsVisible(boolean state)

areAnnotationViewsVisible

public boolean areAnnotationViewsVisible()

getViewForFeature

public ResultView getViewForFeature(SeqFeatureI sf)

setResultViewsVisible

public void setResultViewsVisible(boolean state)

areResultViewsVisible

public boolean areResultViewsVisible()

setScaleViewVisible

public void setScaleViewVisible(boolean state)

isScaleViewVisible

public boolean isScaleViewVisible()

setSiteViewVisibleOnZoom

public void setSiteViewVisibleOnZoom(boolean state)

If state is false hide site view, even if zoomed in. If state true show sites only if at proper zoom level.

getSiteViewVisibleOnZoom

public boolean getSiteViewVisibleOnZoom()

This does not return whther the sites are actually visible but whether they are capable of being visible. Returns false if not visible at any zoom level, return true if visible when zoomed in. In either state sites are not visible when zoomed out.

setScrollingPropagated

public void setScrollingPropagated(boolean value)

isScrollingPropagated

public boolean isScrollingPropagated()

isShowingEdgeMatches

public boolean isShowingEdgeMatches()

saveLayout

public void saveLayout(misc.JIniFile iniFile,
                       java.lang.String section)

applyVisibilityFromLayout

public void applyVisibilityFromLayout(misc.JIniFile iniFile,
                                      java.lang.String section)

applyLayout

public void applyLayout(misc.JIniFile iniFile,
                        java.lang.String section,
                        boolean updateBaseLocation)

removeAllGraphs

public void removeAllGraphs()

removeGraph

public void removeGraph(GraphView graph)