apollo.gui.genomemap
Class AnnotationView

java.lang.Object
  apollo.gui.genomemap.LinearView
      apollo.gui.genomemap.ManagedView
          apollo.gui.genomemap.TierView
              apollo.gui.genomemap.FeatureView
                  apollo.gui.genomemap.AnnotationView

All Implemented Interfaces:

AnnotationChangeListener, ControlledObjectI, TierManagerListener, DropTargetViewI, ManagedViewI, PickViewI, PopupViewI, SelectViewI, TierViewI, ViewI, java.awt.event.AdjustmentListener, java.io.Serializable, java.util.EventListener

public class AnnotationView
extends FeatureView
implements ControlledObjectI, DropTargetViewI, AnnotationChangeListener

A view to display annotations in

See Also:

Serialized Form

Field Summary

protected AnnotationEditor	editor The AnnotationEditor for performing edits in this view.
protected static org.apache.log4j.Logger	logger
protected ResultView	resultView The ResultView linked to this AnnotationView for edit purposes.
protected SiteView	siteView The SiteView linked to this AnnotationView for edit purposes.

Fields inherited from class apollo.gui.genomemap.FeatureView

dfset, drawables, pickSize

Fields inherited from class apollo.gui.genomemap.TierView

controller, dragSources, rightSide, selectionManager, vScroll, vscrollable

Fields inherited from class apollo.gui.genomemap.ManagedView

dropSpaceSize, leadSpaceSize, manager, visibleDrawables

Fields inherited from class apollo.gui.genomemap.LinearView

apollo_panel, backgroundColour, debug, foregroundColour, graphics, limitsSet, transformer, transparent, viewBounds, visibilityListeners, visible

Fields inherited from interface apollo.gui.genomemap.ViewI

LEFTSIDE, NONE, RIGHTSIDE

Constructor Summary

AnnotationView(javax.swing.JComponent component, java.lang.String name, SelectionManager selectionManager, GuiCurationState curationState)

Method Summary

boolean	allowsTierDrags() Whether this view allows tier dragging
void	annotDrag(DragViewI dragView, java.util.Vector annots, boolean doFlag, java.lang.StringBuffer action)
protected void	changeTierHeight(int change)
protected void	clear(boolean justFeatures)
protected javax.swing.JPopupMenu	createPopupMenu(ApolloPanelI ap, java.awt.event.MouseEvent evt) This is overridden by ResultView and AnnotView - make abstract?
AnnotationEditor	getAnnotationEditor()
EvidenceFinder	getEvidenceFinder() i think evidence finder is pase now that theres edge matching - rip out?
FeatureSetI	getGeneHolder() Returns the model(not drawable) of top of the model for the view.
ResultView	getResultView()
SiteView	getSiteView()
FeatureSetI	getTopModel() Returns the topmost model object of the result view, the FeatureSet that holds all of the tiers, (just dfset.getFeatureSet())
boolean	handleAnnotationChangeEvent(AnnotationChangeEvent evt)
boolean	handleTierManagerEvent(TierManagerEvent evt)
boolean	interpretDrop(DragViewI dragView, java.awt.event.MouseEvent evt)
boolean	interpretDrop(DragViewI dragView, java.awt.event.MouseEvent evt, boolean doFlag, java.lang.StringBuffer action) Returns true if drop is sucessful (?) If editing is disabled does nothing, returns false.
boolean	isEditingEnabled()
protected boolean	needsTextAvoidUpdate()
void	setController(Controller c) A ControlledObjectI method.
protected void	setCurationSet(CurationSet curation)
void	setDrawableSet(DrawableSetI fset) Expects a DrawableFeatureSet (which is a FeatureSetI)
void	setEditingEnabled(boolean enable) Setting to false disables editing.
void	setResultView(ResultView rv)
void	setSiteView(SiteView sv)

Methods inherited from class apollo.gui.genomemap.FeatureView

beginTierDrag, clear, clearEdges, clearFeatures, clearHighlights, drawDragRectangle, endTierDrag, finalize, findDrawables, findFeaturesForSelection, getDrawableSet, getPreferredSize, getTierYCentre, getViewSelection, paintView, putScrollAtStart, select, setBounds, setCentre, setMatchingEdges, setTextAvoidance, setXOrientation, setZoomFactor, showPopupMenu, updateTierDrag, verticalScrollToSelection, verticalScrollToSelection

Methods inherited from class apollo.gui.genomemap.TierView

addScrollBar, adjustmentValueChanged, createDragView, decrementTierHeight, drawablesForDrag, findDrawables, findDrawables, findFeatures, findFeatures, findFeatures, findFeaturesForSelection, findFeaturesForSelection, fireViewEvent, getController, getControllerWindow, getInvertedScrollbarValue, getLowestVisibleTier, getMaxScrollbarValue, getMinScrollbarValue, getScrollbarValue, getVisibleScrollbarValue, incrementTierHeight, isDownOrientation, isUpOrientation, isValidDragSource, moveScrollbarByWheelAmount, needsAutoRemoval, printScrollValues, registerDragSource, setLowestVisibleTier, setScrollbarValue, setScrollHack, setScrollSide, setScrollValues, setScrollVisibility, setSelectionManager, setTierManager, setVisible, setVScrollable, setYOrientation, updateManagerHeight

Methods inherited from class apollo.gui.genomemap.ManagedView

getDropSpaceSize, getLeadSpaceSize, getTierManager, getVisibleDrawables, getYRange, paintDrawables, setDropSpaceSize, setLeadSpaceSize, setTierManager

Methods inherited from class apollo.gui.genomemap.LinearView

addViewListener, addVisibilityListener, areLimitsSet, fireViewEvent, getBackgroundColour, getBounds, getCentre, getComponent, getDrawBounds, getForegroundColour, getGraphics, getLimits, getMaximum, getMinimum, getName, getSelectionRectangle, getStrand, getTransform, getVisibleRange, init, isInvalid, isTransparent, isVisible, setBackgroundColour, setComponent, setDebug, setDrawBounds, setForegroundColour, setGraphics, setInvalidity, setLimits, setLimitsSet, setMaximum, setMinimum, setName, setStrand, setTransform, setTransparent, setVisible

Methods inherited from class java.lang.Object

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

Methods inherited from interface apollo.gui.ControlledObjectI

getController, getControllerWindow, needsAutoRemoval

Methods inherited from interface apollo.gui.genomemap.DropTargetViewI

isValidDragSource, registerDragSource

Methods inherited from interface apollo.gui.genomemap.TierViewI

createDragView, decrementTierHeight, getLowestVisibleTier, getVisibleDrawables, incrementTierHeight, setLowestVisibleTier

Methods inherited from interface apollo.gui.genomemap.ManagedViewI

getTierManager, setTierManager

Methods inherited from interface apollo.gui.genomemap.ViewI

addViewListener, areLimitsSet, getBounds, getCentre, getComponent, getLimits, getMaximum, getMinimum, getName, getTransform, getVisibleRange, isInvalid, isTransparent, isVisible, setComponent, setGraphics, setInvalidity, setLimits, setLimitsSet, setMaximum, setMinimum, setName, setTransparent, setVisible

Field Detail

logger

protected static final org.apache.log4j.Logger logger

resultView

protected ResultView resultView

The ResultView linked to this AnnotationView for edit purposes.

siteView

protected SiteView siteView

The SiteView linked to this AnnotationView for edit purposes.

editor

protected AnnotationEditor editor

The AnnotationEditor for performing edits in this view.

Constructor Detail

AnnotationView

public AnnotationView(javax.swing.JComponent component,
                      java.lang.String name,
                      SelectionManager selectionManager,
                      GuiCurationState curationState)

Method Detail

getGeneHolder

public FeatureSetI getGeneHolder()

Returns the model(not drawable) of top of the model for the view. This is the holder of all the Genes. This is analogous to ResultViews getTopModel except that it returns a AnnotatedFeatureSetI. (Should there be a AnnotHolderI with getGenes, getTransposons...?)

getTopModel

public FeatureSetI getTopModel()

Description copied from class: FeatureView

Returns the topmost model object of the result view, the FeatureSet that holds all of the tiers, (just dfset.getFeatureSet())

Overrides:

getTopModel in class FeatureView

setDrawableSet

public void setDrawableSet(DrawableSetI fset)

Description copied from class: FeatureView

Expects a DrawableFeatureSet (which is a FeatureSetI)

Overrides:

setDrawableSet in class FeatureView

handleTierManagerEvent

public boolean handleTierManagerEvent(TierManagerEvent evt)

Specified by:

handleTierManagerEvent in interface TierManagerListener

Overrides:

handleTierManagerEvent in class TierView

allowsTierDrags

public boolean allowsTierDrags()

Description copied from interface: TierViewI

Whether this view allows tier dragging

Specified by:

allowsTierDrags in interface TierViewI

Overrides:

allowsTierDrags in class TierView

annotDrag

public void annotDrag(DragViewI dragView,
                      java.util.Vector annots,
                      boolean doFlag,
                      java.lang.StringBuffer action)

setEditingEnabled

public void setEditingEnabled(boolean enable)

Setting to false disables editing. At the moment this just disables dropping of exons, as other disabling of editing is done by getting rid of the associated menu items. This is presumptious though and really all editing functionality should be disabled, not sure how much of an ordeal that is and how necasary that is at this point.

isEditingEnabled

public boolean isEditingEnabled()

interpretDrop

public boolean interpretDrop(DragViewI dragView,
                             java.awt.event.MouseEvent evt)

Specified by:

interpretDrop in interface DropTargetViewI

Overrides:

interpretDrop in class TierView

getAnnotationEditor

public AnnotationEditor getAnnotationEditor()

interpretDrop

public boolean interpretDrop(DragViewI dragView,
                             java.awt.event.MouseEvent evt,
                             boolean doFlag,
                             java.lang.StringBuffer action)

Returns true if drop is sucessful (?) If editing is disabled does nothing, returns false. From DropTargetViewI

Specified by:

interpretDrop in interface DropTargetViewI

Overrides:

interpretDrop in class TierView

handleAnnotationChangeEvent

public boolean handleAnnotationChangeEvent(AnnotationChangeEvent evt)

Specified by:

handleAnnotationChangeEvent in interface AnnotationChangeListener

setResultView

public void setResultView(ResultView rv)

getEvidenceFinder

public EvidenceFinder getEvidenceFinder()

i think evidence finder is pase now that theres edge matching - rip out?

getResultView

public ResultView getResultView()

setSiteView

public void setSiteView(SiteView sv)

getSiteView

public SiteView getSiteView()

changeTierHeight

protected void changeTierHeight(int change)

Overrides:

changeTierHeight in class TierView

needsTextAvoidUpdate

protected boolean needsTextAvoidUpdate()

Overrides:

needsTextAvoidUpdate in class FeatureView

createPopupMenu

protected javax.swing.JPopupMenu createPopupMenu(ApolloPanelI ap,
                                                 java.awt.event.MouseEvent evt)

Description copied from class: FeatureView

This is overridden by ResultView and AnnotView - make abstract?

Specified by:

createPopupMenu in class FeatureView

clear

protected void clear(boolean justFeatures)

Overrides:

clear in class FeatureView

setCurationSet

protected void setCurationSet(CurationSet curation)

setController

public void setController(Controller c)

A ControlledObjectI method. This also resets the controller on the editor.

Specified by:

setController in interface ControlledObjectI

Overrides:

setController in class TierView