apollo.gui.detailviewers.sequencealigner.AAPanel
Class AAMultiSequenceAlignerPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel
                      apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel

All Implemented Interfaces:

AnnotationChangeListener, BaseScrollable, ControlledObjectI, FeatureSelectionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.beans.PropertyChangeListener, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

public class AAMultiSequenceAlignerPanel
extends MultiSequenceAlignerPanel

The main class for the Amino Acid view.

See Also:

Serialized Form

Nested Class Summary

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

Fields inherited from class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

colorIndex, colorList

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

AAMultiSequenceAlignerPanel(GuiCurationState curationState, Strand strand, ReadingFrame frame)
Constructor

Method Summary

boolean	annotationFilter(SeqFeatureI f) I don't think this is used in any way...
void	clearAnnotations() removes all the annotations from the annotation list and the annotation panel
void	clearResults() removes all of the results from the results list and the result panel
static java.util.Set<SeqFeatureI>	filterByFrame(java.util.Collection<SeqFeatureI> set, ReadingFrame frame)
void	flipOrientation() Flipping the orientation will not work, more work is needed to implement...
AbstractScrollablePanel	getAddressComponent() Gets the address bar (shows the base numbers you are looking at)
MultiComparator	getAnnotationComparator() Gets the comparator used to order annotations
MultiFilter	getAnnotationFilter() Gets the filter used to decide which annotations to display
MultiTierPanelHeaderTable	getAnnotationHeader() Gets the header for the annotation panel
javax.swing.JScrollPane	getAnnotationPane() Gets the JScrollPane which holds the Annotation Panel
MultiTierPanel	getAnnotationPanel() Gets the Annotation Panel
java.util.List<SeqFeatureI>	getAnnotations() Gets the list of annotations.
Controller	getController() Gets the Controller for the object
java.lang.Object	getControllerWindow() Shouldnt this return Window - would we ever want a non-window?
ReadingFrame	getFrame() Gets the frame that is currently being viewed
javax.swing.JMenu	getMenu() Gets the Menu object
Overview	getOverview() Gets the overview object for the panel
MultiTierPanel	getReferencePanel() Gets the reference panel (the one in between the annotation and result)
SequenceI	getReferenceSequence(Strand s, ReadingFrame rf) Creates a Sequence object which can be used as a reference for the given strand/frame pair
MultiComparator	getResultComparator() Gets the comparator used to order results
MultiFilter	getResultFilter() Gets the filter used to decide which results to display
MultiTierPanelHeaderTable	getResultHeader() Gets the header for the result panel
MultiTierPanel	getResultPanel() Gets the Result Panel
java.util.List<SeqFeatureI>	getResults() Gets the list of results.
javax.swing.JScrollBar	getScrollBar() Gets the main horizontal scrollbar for the window
Strand	getStrand() Gets the strand of the annotations currently being viewed
java.lang.String	getType() Gets the type (always AA)
int	getVisibleBase()
int	getVisibleBaseCount()
boolean	handleFeatureSelectionEvent(FeatureSelectionEvent evt)
void	init() Creates all of the components and lays everything out
static AAMultiSequenceAlignerPanel	makeAligner(GuiCurationState curationState, int strand, ReadingFrame frame) Factory method for creating Amino Acid Panels
boolean	needsAutoRemoval() If getControllerWindow is non null, and needsAutoRemoval is true then Controller will automatically remove the ControlledObjectI as a listener when its ControllerWindow is closing.
void	propertyChange(java.beans.PropertyChangeEvent evt)
void	reformat()
void	reformatReferenceHeader() updates the header for the reference panel
boolean	resultFilter(SeqFeatureI f) I don't think this is used in any way...
void	scrollToBase(int basePair)
void	setAnnotations(java.util.List<SeqFeatureI> annotations) Sets the annotations (no side effects)
void	setController(Controller controller) Sets the Controller for the object
void	setFrame(ReadingFrame frame)
void	setResults(java.util.List<SeqFeatureI> results) Sets the results (no side effects)
void	setStrand(Strand s) Sets the currently selected strand (no side effects)
static SequenceI	translateToAA(SequenceI SeqDNA, ReadingFrame frame)
void	validate()

Methods inherited from class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

addAnnotations, addEditRegion, addFeatureToPanel, addResults, canHandleSelection, cleanUp, filter, getAnnotations, getColorArray, getCurationState, getIndicatorColor, getMenuBar, getResults, getResults, getSelection, getThis, getTransOrOneLevelAnn, handleAnnotationChangeEvent, makeAligner, makeMenu, nextAnnotation, noExternalSelection, prevAnnotation, reformatAnnotationPanel, reformatReferencePanel, reformatResultPanel, setCurationState, setIndicatorColor, setNoExternalSelection, setSelection, sort, sortAnnotations, sortResults, switchAnnotations, switchResults, updateEditRegion, updateTitle

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, 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, paint, paintBorder, paintChildren, paintComponent, 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, setVisible, 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, 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, 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

Constructor Detail

AAMultiSequenceAlignerPanel

public AAMultiSequenceAlignerPanel(GuiCurationState curationState,
                                   Strand strand,
                                   ReadingFrame frame)

Constructor

Parameters:

curationState -

strand -

frame -

Method Detail

makeAligner

public static AAMultiSequenceAlignerPanel makeAligner(GuiCurationState curationState,
                                                      int strand,
                                                      ReadingFrame frame)

Factory method for creating Amino Acid Panels

Parameters:

curationState -

strand -

frame -

Returns:

getAnnotationPanel

public MultiTierPanel getAnnotationPanel()

Description copied from class: MultiSequenceAlignerPanel

Gets the Annotation Panel

Specified by:

getAnnotationPanel in class MultiSequenceAlignerPanel

getAnnotationPane

public javax.swing.JScrollPane getAnnotationPane()

Description copied from class: MultiSequenceAlignerPanel

Gets the JScrollPane which holds the Annotation Panel

Specified by:

getAnnotationPane in class MultiSequenceAlignerPanel

getResultPanel

public MultiTierPanel getResultPanel()

Description copied from class: MultiSequenceAlignerPanel

Gets the Result Panel

Specified by:

getResultPanel in class MultiSequenceAlignerPanel

getType

public java.lang.String getType()

Gets the type (always AA)

Specified by:

getType in class MultiSequenceAlignerPanel

getStrand

public Strand getStrand()

Description copied from class: MultiSequenceAlignerPanel

Gets the strand of the annotations currently being viewed

Specified by:

getStrand in class MultiSequenceAlignerPanel

getFrame

public ReadingFrame getFrame()

Description copied from class: MultiSequenceAlignerPanel

Gets the frame that is currently being viewed

Specified by:

getFrame in class MultiSequenceAlignerPanel

getMenu

public javax.swing.JMenu getMenu()

Description copied from class: MultiSequenceAlignerPanel

Gets the Menu object

Specified by:

getMenu in class MultiSequenceAlignerPanel

getAnnotations

public java.util.List<SeqFeatureI> getAnnotations()

Description copied from class: MultiSequenceAlignerPanel

Gets the list of annotations. This list is used to determine if an annotation is already added to the panel. TODO redesign use of annotations, probably a better way to do this.

Specified by:

getAnnotations in class MultiSequenceAlignerPanel

setAnnotations

public void setAnnotations(java.util.List<SeqFeatureI> annotations)

Description copied from class: MultiSequenceAlignerPanel

Sets the annotations (no side effects)

Specified by:

setAnnotations in class MultiSequenceAlignerPanel

getResults

public java.util.List<SeqFeatureI> getResults()

Description copied from class: MultiSequenceAlignerPanel

Gets the list of results. This list is used to determine if a result is already added to the panel. TODO redesign use of results, probably a better way to do this.

Specified by:

getResults in class MultiSequenceAlignerPanel

setResults

public void setResults(java.util.List<SeqFeatureI> results)

Description copied from class: MultiSequenceAlignerPanel

Sets the results (no side effects)

Specified by:

setResults in class MultiSequenceAlignerPanel

reformat

public void reformat()

init

public void init()

Description copied from class: MultiSequenceAlignerPanel

Creates all of the components and lays everything out

Specified by:

init in class MultiSequenceAlignerPanel

validate

public void validate()

Overrides:

validate in class java.awt.Container

handleFeatureSelectionEvent

public boolean handleFeatureSelectionEvent(FeatureSelectionEvent evt)

getController

public Controller getController()

Description copied from interface: ControlledObjectI

Gets the Controller for the object

getControllerWindow

public java.lang.Object getControllerWindow()

Description copied from interface: ControlledObjectI

Shouldnt this return Window - would we ever want a non-window?

needsAutoRemoval

public boolean needsAutoRemoval()

Description copied from interface: ControlledObjectI

If getControllerWindow is non null, and needsAutoRemoval is true then Controller will automatically remove the ControlledObjectI as a listener when its ControllerWindow is closing. If getControllerWindow is null needsAutoRemoval is meaningless. Rename this removeAsListenerOnWindowClose?

setController

public void setController(Controller controller)

Description copied from interface: ControlledObjectI

Sets the Controller for the object

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent evt)

getVisibleBase

public int getVisibleBase()

getVisibleBaseCount

public int getVisibleBaseCount()

scrollToBase

public void scrollToBase(int basePair)

translateToAA

public static SequenceI translateToAA(SequenceI SeqDNA,
                                      ReadingFrame frame)

setFrame

public void setFrame(ReadingFrame frame)

filterByFrame

public static java.util.Set<SeqFeatureI> filterByFrame(java.util.Collection<SeqFeatureI> set,
                                                       ReadingFrame frame)

reformatReferenceHeader

public void reformatReferenceHeader()

Description copied from class: MultiSequenceAlignerPanel

updates the header for the reference panel

Specified by:

reformatReferenceHeader in class MultiSequenceAlignerPanel

flipOrientation

public void flipOrientation()

Description copied from class: MultiSequenceAlignerPanel

Flipping the orientation will not work, more work is needed to implement...

Overrides:

flipOrientation in class MultiSequenceAlignerPanel

getOverview

public Overview getOverview()

Description copied from class: MultiSequenceAlignerPanel

Gets the overview object for the panel

Specified by:

getOverview in class MultiSequenceAlignerPanel

Returns:

getReferencePanel

public MultiTierPanel getReferencePanel()

Description copied from class: MultiSequenceAlignerPanel

Gets the reference panel (the one in between the annotation and result)

Specified by:

getReferencePanel in class MultiSequenceAlignerPanel

getScrollBar

public javax.swing.JScrollBar getScrollBar()

Description copied from class: MultiSequenceAlignerPanel

Gets the main horizontal scrollbar for the window

Specified by:

getScrollBar in class MultiSequenceAlignerPanel

Returns:

setStrand

public void setStrand(Strand s)

Description copied from class: MultiSequenceAlignerPanel

Sets the currently selected strand (no side effects)

Specified by:

setStrand in class MultiSequenceAlignerPanel

getAnnotationHeader

public MultiTierPanelHeaderTable getAnnotationHeader()

Description copied from class: MultiSequenceAlignerPanel

Gets the header for the annotation panel

Specified by:

getAnnotationHeader in class MultiSequenceAlignerPanel

getResultHeader

public MultiTierPanelHeaderTable getResultHeader()

Description copied from class: MultiSequenceAlignerPanel

Gets the header for the result panel

Specified by:

getResultHeader in class MultiSequenceAlignerPanel

getReferenceSequence

public SequenceI getReferenceSequence(Strand s,
                                      ReadingFrame rf)

Description copied from class: MultiSequenceAlignerPanel

Creates a Sequence object which can be used as a reference for the given strand/frame pair

Specified by:

getReferenceSequence in class MultiSequenceAlignerPanel

Parameters:

s - the strand

rf - the frame

Returns:

a reference sequence

annotationFilter

public boolean annotationFilter(SeqFeatureI f)

Description copied from class: MultiSequenceAlignerPanel

I don't think this is used in any way... should probably remove

Specified by:

annotationFilter in class MultiSequenceAlignerPanel

resultFilter

public boolean resultFilter(SeqFeatureI f)

Description copied from class: MultiSequenceAlignerPanel

I don't think this is used in any way... should probably remove

Specified by:

resultFilter in class MultiSequenceAlignerPanel

getAnnotationComparator

public MultiComparator getAnnotationComparator()

Description copied from class: MultiSequenceAlignerPanel

Gets the comparator used to order annotations

Specified by:

getAnnotationComparator in class MultiSequenceAlignerPanel

getResultComparator

public MultiComparator getResultComparator()

Description copied from class: MultiSequenceAlignerPanel

Gets the comparator used to order results

Specified by:

getResultComparator in class MultiSequenceAlignerPanel

clearResults

public void clearResults()

Description copied from class: MultiSequenceAlignerPanel

removes all of the results from the results list and the result panel

Specified by:

clearResults in class MultiSequenceAlignerPanel

getAnnotationFilter

public MultiFilter getAnnotationFilter()

Description copied from class: MultiSequenceAlignerPanel

Gets the filter used to decide which annotations to display

Specified by:

getAnnotationFilter in class MultiSequenceAlignerPanel

getResultFilter

public MultiFilter getResultFilter()

Description copied from class: MultiSequenceAlignerPanel

Gets the filter used to decide which results to display

Specified by:

getResultFilter in class MultiSequenceAlignerPanel

clearAnnotations

public void clearAnnotations()

Description copied from class: MultiSequenceAlignerPanel

removes all the annotations from the annotation list and the annotation panel

Specified by:

clearAnnotations in class MultiSequenceAlignerPanel

getAddressComponent

public AbstractScrollablePanel getAddressComponent()

Description copied from class: MultiSequenceAlignerPanel

Gets the address bar (shows the base numbers you are looking at)

Specified by:

getAddressComponent in class MultiSequenceAlignerPanel

Returns: