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SUMMARY: JavaDoc of apollo.gui.genomemap.StrandedZoomableApolloPanel JAVADOC | Sourc code of apollo.gui.genomemap.StrandedZoomableApolloPanel SOURCE | Download apollo.gui.genomemap.StrandedZoomableApolloPanel DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

apollo.gui.genomemap
Class StrandedZoomableApolloPanel  view StrandedZoomableApolloPanel download StrandedZoomableApolloPanel.java

java.lang.Object
  extended byjava.awt.Component
      extended byjava.awt.Container
          extended byjavax.swing.JComponent
              extended byjavax.swing.JPanel
                  extended byapollo.gui.ControlledPanel
                      extended byapollo.gui.genomemap.StrandedZoomableApolloPanel
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.event.AdjustmentListener, apollo.gui.event.BaseFocusListener, apollo.gui.ControlledObjectI, apollo.gui.drawable.DrawableAnnotationConstants, java.util.EventListener, apollo.gui.event.FeatureSelectionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, apollo.gui.event.NamedFeatureSelectionListener, apollo.gui.event.OrientationListener, apollo.gui.event.RegionChangeListener, apollo.gui.event.ReverseComplementListener, apollo.gui.event.RubberbandListener, java.io.Serializable, apollo.gui.event.TypesChangedListener
public class StrandedZoomableApolloPanel
extends apollo.gui.ControlledPanel
implements java.awt.event.ActionListener, java.awt.event.AdjustmentListener, apollo.gui.event.BaseFocusListener, apollo.gui.ControlledObjectI, apollo.gui.drawable.DrawableAnnotationConstants, apollo.gui.event.FeatureSelectionListener, apollo.gui.event.NamedFeatureSelectionListener, apollo.gui.event.OrientationListener, apollo.gui.event.RegionChangeListener, apollo.gui.event.RubberbandListener, apollo.gui.event.TypesChangedListener, apollo.gui.event.ReverseComplementListener

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.

Nested Class Summary
private  class StrandedZoomableApolloPanel.HighlightDragListener
          Handles dragging of highlights.
private  class StrandedZoomableApolloPanel.HighlightWrapper
           
private  class StrandedZoomableApolloPanel.NavigatorManager
          NavigatorManager inner class, for navigating up and down chromosome Just wraps MovementPanel moveP, which is the gui for navigation
 
Nested classes inherited from class javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
 
Nested classes inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
 
Nested classes inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
(package private)  apollo.datamodel.StrandedFeatureSetI annots
           
(package private)  ApolloPanel apolloPanel
           
private  int baseWindowStart
           
private  int baseWindowWidth
           
(package private)  apollo.gui.Controller controller
           
(package private)  apollo.datamodel.CurationSet curationSet
           
 AnnotationView forwardAnnotView
           
(package private)  LaidoutViewContainer forwardContainerView
           
(package private)  ResultView forwardResultView
           
(package private)  boolean forwardSitesVisible
           
(package private)  SiteView forwardSiteView
           
(package private)  PickSplitterView forwardSplitterView
           
(package private)  boolean forwardVisible
           
(package private)  apollo.datamodel.StrandedFeatureSetI fset
           
(package private)  GraphView graphView
           
(package private)  GuideLine guide
           
private  boolean haveSequence
           
(package private)  java.util.Vector highlightRegions
           
(package private)  javax.swing.JScrollBar hScroll
           
(package private)  boolean HSCROLLABLE
           
private  boolean loadInProgress
           
(package private)  MovementPanel moveP
           
(package private)  java.lang.String name
           
(package private)  boolean NAVIGABLE
           
(package private)  StrandedZoomableApolloPanel.NavigatorManager navManager
           
private  javax.swing.JLabel organismLabel
           
(package private)  javax.swing.JPanel panel2
           
(package private)  javax.swing.JButton reset
           
private  RevCompListener revCompListener
           
 AnnotationView reverseAnnotView
           
(package private)  boolean reverseComplement
           
(package private)  LaidoutViewContainer reverseContainerView
           
(package private)  ResultView reverseResultView
           
(package private)  boolean reverseSitesVisible
           
(package private)  SiteView reverseSiteView
           
(package private)  PickSplitterView reverseSplitterView
           
(package private)  boolean reverseVisible
           
(package private)  ScaleView scaleView
           
private  apollo.gui.SelectionManager selectionManager
           
(package private)  boolean settingScroller
           
(package private)  apollo.gui.StatusBar statusBar
           
(package private)  PickSplitterView strandSplitter
           
private  StrandVisibilityListener strandVisibilityListener
           
(package private)  boolean useScrollHack
           
(package private)  double xscale
           
(package private)  boolean ZOOMABLE
           
(package private)  javax.swing.JButton zoomin
           
(package private)  javax.swing.JButton zoomin2
           
(package private)  javax.swing.JLabel zoomLabel
           
(package private)  javax.swing.JButton zoomout
           
(package private)  javax.swing.JButton zoomout2
           
(package private)  java.lang.String ZOOMPOSITION
           
(package private)  javax.swing.JScrollBar zscroll
           
 
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.Container
 
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(boolean hscrollable, boolean zoomable, boolean navigable, apollo.gui.Controller c)
           
StrandedZoomableApolloPanel(boolean hscrollable, boolean zoomable, boolean navigable, java.lang.String zoomPosition, apollo.gui.Controller c)
           
StrandedZoomableApolloPanel(boolean hscrollable, boolean zoomable, apollo.gui.Controller c)
           
StrandedZoomableApolloPanel(boolean hscrollable, boolean zoomable, java.lang.String zoompos, apollo.gui.Controller c)
           
 
Method Summary
private  int _positionToScroll(int posVal)
           
private  int _scrollToPosition(int scrollVal)
           
 void actionPerformed(java.awt.event.ActionEvent evt)
          Action event listener
private  void addAllViews()
          This sets up the constraints for all the views.
 void addHighlightRegion(apollo.gui.BaseScrollable scroller, java.awt.Color color, boolean reverse)
           
 void adjustmentValueChanged(java.awt.event.AdjustmentEvent e)
          This method is called when an adjustable value changes.
 java.awt.Rectangle calculateHighlightRect(StrandedZoomableApolloPanel.HighlightWrapper hw)
           
private  boolean canShowSites(boolean viewIsVisible)
           
private  boolean canShowSites(boolean viewIsVisible, apollo.datamodel.CurationSet set)
           
 void changeYOrientation()
           
 void clearData()
           
 void expandAllTiers(boolean state)
           
private  void fireBaseFocusEvent(int position)
           
 apollo.datamodel.FeatureSetI getAnnotations()
           
 AnnotationView getAnnotView(int strand)
           
 ApolloPanel getApolloPanel()
           
 int getCentreBase()
           
 apollo.gui.Controller getController()
          Gets the Controller for the object
 apollo.datamodel.CurationSet getCurationSet()
           
 apollo.datamodel.FeatureSetI getForwardAnnotations()
           
 apollo.datamodel.FeatureSetI getForwardResults()
           
 GraphView getGraphView()
           
 boolean getGraphVisibility()
          true if GraphView is visible
 javax.swing.Action getNavigationAction()
           
 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.
 apollo.datamodel.FeatureSetI getResults()
           
 RevCompListener getRevCompListener()
           
 apollo.datamodel.FeatureSetI getReverseAnnotations()
           
 apollo.datamodel.FeatureSetI getReverseResults()
           
 ViewI getScaleView()
           
 apollo.gui.SelectionManager getSelectionManager()
           
 StrandVisibilityListener getStrandVisibilityListener()
           
 apollo.gui.Transformer getTransformer()
           
private  double getZoomFactor()
           
 boolean handleBaseFocusEvent(apollo.gui.event.BaseFocusEvent evt)
           
 boolean handleFeatureSelectionEvent(apollo.gui.event.FeatureSelectionEvent evt)
          Just returns false - should this even be a FeatureSelectionListener?
 boolean handleNamedFeatureSelectionEvent(apollo.gui.event.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(apollo.gui.event.OrientationEvent evt)
           
 boolean handleRegionChangeEvent(apollo.gui.event.RegionChangeEvent evt)
           
 boolean handleReverseComplementEvent(apollo.gui.event.ReverseComplementEvent evt)
           
 boolean handleRubberbandEvent(apollo.gui.event.RubberbandEvent evt)
           
 boolean handleTiersChangedEvent(apollo.gui.event.TypesChangedEvent evt)
           
 boolean haveSequence()
           
 boolean isReverseComplement()
           
private  void jbInit()
           
private  apollo.gui.drawable.DrawableAnnotatedFeatureSet makeDrawableAnnotatedSet(apollo.datamodel.FeatureSetI fset)
           
private  apollo.gui.drawable.DrawableFeatureSet makeDrawableSet(apollo.datamodel.FeatureSetI fset)
           
private  void notifyRevCompListener()
           
private  void notifyStrandVisibility(boolean isForward)
           
 void paint(java.awt.Graphics g)
          Paint the component.
 void paintComponent(java.awt.Graphics g)
          Paint the component's body.
private  void printScrollValues()
           
private  void printViewLimits(java.lang.String where)
           
 void putVerticalScrollbarsAtStart()
          This sets all the views scrollbars at start position.
private  void removeAllViews()
           
 void removeHighlightRegion(apollo.gui.BaseScrollable scroller)
           
 void repaint()
          Repaint this entire component.
 void repaintHighlights()
           
 void resetViews()
           
 void scrollToSelection()
           
 boolean selectFeaturesByName(java.lang.String name)
          Searches features for name and selects all that are found, does nothing if none are found.
 void setAllTiersVisible(boolean state)
           
private  void setAnnotations(apollo.datamodel.StrandedFeatureSetI annots)
           
 void setCentreBase(int location)
           
 void setController(apollo.gui.Controller controller)
          Sets the Controller for the object
 void setCurationSet(apollo.datamodel.CurationSet set)
           
 void setEdgeMatching(boolean state)
           
private  void setFeatureSet(apollo.datamodel.CurationSet cset)
           
 void setForwardVisible(boolean state)
           
 void setGraphVisibility(boolean state)
           
 void setGuideLine(boolean state)
           
 void setLoadInProgress(boolean inProgress)
           
 void setRealRemove(boolean state)
           
 void setRevCompListener(RevCompListener l)
           
 void setReverseComplement(boolean state)
           
 void setReverseVisible(boolean state)
           
 void setScrollValues()
           
private  void setSelectedStrandVisible()
          If selection in a strand thats not visible, make strand visible
 void setSelectionManager(apollo.gui.SelectionManager sm)
           
 void setStatusBar(apollo.gui.StatusBar sb)
           
 void setStrandVisibilityListener(StrandVisibilityListener l)
          For now only one listener, if need more then one listener in future make this addStrandVisibilyListener and add to vector
private  void setStrandVisible(AnnotationView av, ResultView rv, int strand, boolean state)
           
 void setTextAvoidance(boolean state)
           
 void setViewColours()
           
 void setVisible(boolean state)
          setVisible calls setTextAvoidance(true).
private  void setZoomFactor(double factor)
           
private  void setZoomFactor(double factor, boolean force)
          boolean force means force in the new factor and dont test it against the limits.
private  void updateSiteVisibility(boolean force)
           
 void zoomToSelection()
           
 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, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, 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, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, 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, unregisterKeyboardAction, update
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, 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, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, 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, 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, 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, transferFocusBackward, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface apollo.gui.ControlledObjectI
getControllerWindow, needsAutoRemoval
 

Field Detail

panel2

javax.swing.JPanel panel2

apolloPanel

ApolloPanel apolloPanel

moveP

MovementPanel moveP

navManager

StrandedZoomableApolloPanel.NavigatorManager navManager

hScroll

javax.swing.JScrollBar hScroll

zscroll

javax.swing.JScrollBar zscroll

zoomin

javax.swing.JButton zoomin

zoomout

javax.swing.JButton zoomout

zoomin2

javax.swing.JButton zoomin2

zoomout2

javax.swing.JButton zoomout2

reset

javax.swing.JButton reset

statusBar

apollo.gui.StatusBar statusBar

HSCROLLABLE

boolean HSCROLLABLE

ZOOMABLE

boolean ZOOMABLE

ZOOMPOSITION

java.lang.String ZOOMPOSITION

NAVIGABLE

boolean NAVIGABLE

name

java.lang.String name

forwardVisible

boolean forwardVisible

reverseVisible

boolean reverseVisible

forwardSitesVisible

boolean forwardSitesVisible

reverseSitesVisible

boolean reverseSitesVisible

reverseComplement

boolean reverseComplement

forwardResultView

ResultView forwardResultView

reverseResultView

ResultView reverseResultView

forwardAnnotView

public AnnotationView forwardAnnotView

reverseAnnotView

public AnnotationView reverseAnnotView

forwardSplitterView

PickSplitterView forwardSplitterView

reverseSplitterView

PickSplitterView reverseSplitterView

forwardContainerView

LaidoutViewContainer forwardContainerView

reverseContainerView

LaidoutViewContainer reverseContainerView

strandSplitter

PickSplitterView strandSplitter

scaleView

ScaleView scaleView

forwardSiteView

SiteView forwardSiteView

reverseSiteView

SiteView reverseSiteView

fset

apollo.datamodel.StrandedFeatureSetI fset

annots

apollo.datamodel.StrandedFeatureSetI annots

controller

apollo.gui.Controller controller

selectionManager

private apollo.gui.SelectionManager selectionManager

xscale

double xscale

settingScroller

boolean settingScroller

zoomLabel

javax.swing.JLabel zoomLabel

highlightRegions

java.util.Vector highlightRegions

guide

GuideLine guide

graphView

GraphView graphView

curationSet

apollo.datamodel.CurationSet curationSet

haveSequence

private boolean haveSequence

loadInProgress

private boolean loadInProgress

strandVisibilityListener

private StrandVisibilityListener strandVisibilityListener

revCompListener

private RevCompListener revCompListener

organismLabel

private javax.swing.JLabel organismLabel

useScrollHack

boolean useScrollHack

baseWindowStart

private int baseWindowStart

baseWindowWidth

private int baseWindowWidth
Constructor Detail

StrandedZoomableApolloPanel

public StrandedZoomableApolloPanel(boolean hscrollable,
                                   boolean zoomable,
                                   apollo.gui.Controller c)

StrandedZoomableApolloPanel

public StrandedZoomableApolloPanel(boolean hscrollable,
                                   boolean zoomable,
                                   boolean navigable,
                                   apollo.gui.Controller c)

StrandedZoomableApolloPanel

public StrandedZoomableApolloPanel(boolean hscrollable,
                                   boolean zoomable,
                                   java.lang.String zoompos,
                                   apollo.gui.Controller c)

StrandedZoomableApolloPanel

public StrandedZoomableApolloPanel(boolean hscrollable,
                                   boolean zoomable,
                                   boolean navigable,
                                   java.lang.String zoomPosition,
                                   apollo.gui.Controller c)
Method Detail

setGraphVisibility

public void setGraphVisibility(boolean state)

setGuideLine

public void setGuideLine(boolean state)

getCurationSet

public apollo.datamodel.CurationSet getCurationSet()

setCurationSet

public void setCurationSet(apollo.datamodel.CurationSet set)

setAllTiersVisible

public void setAllTiersVisible(boolean state)

printViewLimits

private void printViewLimits(java.lang.String where)

getNavigationAction

public javax.swing.Action getNavigationAction()

getForwardResults

public apollo.datamodel.FeatureSetI getForwardResults()

getReverseResults

public apollo.datamodel.FeatureSetI getReverseResults()

setFeatureSet

private void setFeatureSet(apollo.datamodel.CurationSet cset)

setVisible

public void setVisible(boolean state)
setVisible calls setTextAvoidance(true). Its 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.

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.

getApolloPanel

public ApolloPanel getApolloPanel()

makeDrawableSet

private