apollo.gui.genomemap
Class SiteView

java.lang.Object
  apollo.gui.genomemap.LinearView
      apollo.gui.genomemap.ManagedView
          apollo.gui.genomemap.TierView
              apollo.gui.genomemap.SiteView

All Implemented Interfaces:

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

public class SiteView
extends TierView

A view to display sites (start and stop codons). Displays 3 stop tiers/Sites and 3 start tiers/Sites. Took out implementing of SelectViewI. SelectViewI is for handling external selections, but presently there is no way to externally select a codon, except that codons will select when transcripts are selected, but this is handled through handlefeatureSelection(it's easier that way)

See Also:

Serialized Form

Field Summary

protected CurationSet	curation
protected int	height
protected static org.apache.log4j.Logger	logger
protected ResultView	resultView For TranslationStartStopSelectionListener
protected Sites[]	sitesArray [0,1,2] start sites, [3,4,5] for stop sites (3 frames for each)
static char[]	startCodon
static int	startCodonHashCode

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

Constructor Summary

SiteView(javax.swing.JComponent ap, java.lang.String name, Controller controller, SelectionManager selectionManager)
component is ApolloPanel

Method Summary

void	_createSites(int[] visRange) visRange[] has 2 ints which are the start and stop in basepair of what is currently visible.
boolean	allowsTierDrags() Whether this view allows tier dragging
void	clearSelections() Clear all selections in all Sites
protected java.util.Vector	findDrawables(java.awt.Rectangle rect, boolean selected_only) Finds all the sites in rect and creates SiteCodon for them.
Selection	findFeaturesForSelection(java.awt.Rectangle rect, boolean selectParents) From PickViewI for selection, selectParents is ignored here
java.awt.Rectangle	getPreferredSize() Get the preferred size for the view
ResultView	getResultView()
Selection	getViewSelection(Selection selection) given the entirety of what is currently selected, remove anything that doesn't belong to this view and return the remaining selections.
boolean	handleTierManagerEvent(TierManagerEvent evt)
protected boolean	needsTextAvoidUpdate()
void	paintDrawables()
void	selectParents(Selection selection)
void	setCentre(int val) Set the centre position.
void	setCurationSet(CurationSet set)
void	setResultView(ResultView rv)
void	setVisible(boolean state) Set whether or not a view is visible
void	setZoomFactor(double fac) Set the ZoomFactor along the linear axis

Methods inherited from class apollo.gui.genomemap.TierView

addScrollBar, adjustmentValueChanged, beginTierDrag, changeTierHeight, clear, createDragView, decrementTierHeight, drawablesForDrag, endTierDrag, findDrawables, findDrawables, findFeatures, findFeatures, findFeatures, findFeaturesForSelection, findFeaturesForSelection, fireViewEvent, getController, getControllerWindow, getInvertedScrollbarValue, getLowestVisibleTier, getMaxScrollbarValue, getMinScrollbarValue, getScrollbarValue, getVisibleScrollbarValue, incrementTierHeight, interpretDrop, interpretDrop, isDownOrientation, isUpOrientation, isValidDragSource, moveScrollbarByWheelAmount, needsAutoRemoval, paintView, printScrollValues, putScrollAtStart, registerDragSource, setController, setLowestVisibleTier, setScrollbarValue, setScrollHack, setScrollSide, setScrollValues, setScrollVisibility, setSelectionManager, setTierManager, setVScrollable, setYOrientation, updateManagerHeight, updateTierDrag

Methods inherited from class apollo.gui.genomemap.ManagedView

getDropSpaceSize, getLeadSpaceSize, getTierManager, getVisibleDrawables, getYRange, setBounds, setDropSpaceSize, setLeadSpaceSize, setTierManager, setXOrientation

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, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface apollo.gui.genomemap.TierViewI

getVisibleDrawables

Methods inherited from interface apollo.gui.genomemap.ManagedViewI

getTierManager, setTierManager

Field Detail

logger

protected static final org.apache.log4j.Logger logger

startCodon

public static final char[] startCodon

startCodonHashCode

public static final int startCodonHashCode

height

protected int height

sitesArray

protected Sites[] sitesArray

[0,1,2] start sites, [3,4,5] for stop sites (3 frames for each)

curation

protected CurationSet curation

resultView

protected ResultView resultView

For TranslationStartStopSelectionListener

Constructor Detail

SiteView

public SiteView(javax.swing.JComponent ap,
                java.lang.String name,
                Controller controller,
                SelectionManager selectionManager)

component is ApolloPanel

Method Detail

setCurationSet

public void setCurationSet(CurationSet set)

paintDrawables

public void paintDrawables()

Overrides:

paintDrawables in class ManagedView

setVisible

public void setVisible(boolean state)

Description copied from interface: ViewI

Set whether or not a view is visible

Specified by:

setVisible in interface ViewI

Overrides:

setVisible in class TierView

setCentre

public void setCentre(int val)

Description copied from interface: ViewI

Set the centre position.

Specified by:

setCentre in interface ViewI

Overrides:

setCentre in class LinearView

needsTextAvoidUpdate

protected boolean needsTextAvoidUpdate()

setZoomFactor

public void setZoomFactor(double fac)

Description copied from interface: ViewI

Set the ZoomFactor along the linear axis

Specified by:

setZoomFactor in interface ViewI

Overrides:

setZoomFactor in class LinearView

_createSites

public void _createSites(int[] visRange)

visRange[] has 2 ints which are the start and stop in basepair of what is currently visible. Changed _createSites to modify directly sitesArray rather than returning a newly made Sites array. It now clears out the positions on the old Sites and resuses them. This was needed to preserve the selection state.

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

getPreferredSize

public java.awt.Rectangle getPreferredSize()

Description copied from interface: ViewI

Get the preferred size for the view

Specified by:

getPreferredSize in interface ViewI

Overrides:

getPreferredSize in class LinearView

setResultView

public void setResultView(ResultView rv)

getResultView

public ResultView getResultView()

handleTierManagerEvent

public boolean handleTierManagerEvent(TierManagerEvent evt)

Specified by:

handleTierManagerEvent in interface TierManagerListener

Overrides:

handleTierManagerEvent in class TierView

findFeaturesForSelection

public Selection findFeaturesForSelection(java.awt.Rectangle rect,
                                          boolean selectParents)

From PickViewI for selection, selectParents is ignored here

Specified by:

findFeaturesForSelection in class TierView

findDrawables

protected java.util.Vector findDrawables(java.awt.Rectangle rect,
                                         boolean selected_only)

Finds all the sites in rect and creates SiteCodon for them. Returns vector of SiteCodons The SiteCodons are not drawn. Sites are notified when a SiteCodon is selected.

Specified by:

findDrawables in class TierView

clearSelections

public void clearSelections()

Clear all selections in all Sites

selectParents

public void selectParents(Selection selection)

getViewSelection

public Selection getViewSelection(Selection selection)

Description copied from class: TierView

given the entirety of what is currently selected, remove anything that doesn't belong to this view and return the remaining selections. This used to be handled in the Selection class, but it didn't quite work, because the 'source'=='where it was originally selected' which, may or may not be, the same as this view.

Specified by:

getViewSelection in interface TierViewI

Specified by:

getViewSelection in class TierView