phenote.gui
Class TermInfo2

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.bbop.framework.AbstractGUIComponent
                      phenote.gui.TermInfo2

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, org.bbop.framework.GUIComponent

public class TermInfo2
extends org.bbop.framework.AbstractGUIComponent

This is the second implementation of the Term Info window to provide read-only information about ontology terms for the user.

This constructs the toolbar as well as the information panels.

This uses the StackedBox and JXCollapsablePane classes.

Things to fix:

• make more generic...so that components can be moved around, right now they are in a set order
• make sure text doesn't go off the panel to the right. esp important for the term name and definition, as they seem to be having problems
• fancy things might include remembering state between sessions
• should be able to close a panel, and never display if not interested perhaps regain it again through a right-click menu or something. could be something for the 'configure this panel' when we move to john's gui stuff
• The whole termInfo panel should probably be an array of panels, or at least they should be kept track of that way. that will reduce the size of the code a bit and will make it easier when it comes time for customization to be able to swap panels around, so that particular panels won't be married to a particular position.

Author:

Nicole Washington

See Also:

Serialized Form

Nested Class Summary

(package private) class	TermInfo2.HTMLEditorKit2
static class	TermInfo2.TermInfo2Config

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

protected java.util.Map<org.obo.datamodel.OBOObject,java.lang.Integer>	cachedAnnotationCountByClass
protected java.util.Map<org.obo.datamodel.OBOObject,java.lang.Float>	cachedAnnotationInformationContentByClass
protected boolean	includeExternalDatabaseAnnotations
protected boolean	includeImplicitAnnotations

Fields inherited from class org.bbop.framework.AbstractGUIComponent

title

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

TermInfo2()
Create the panel

TermInfo2(boolean useOBOSessionManager)

TermInfo2(SelectionManager selManager)

Method Summary

(package private) int	getAnnotationCountByClass(org.obo.datamodel.OBOObject oboClass)
(package private) float	getAnnotationInformationContentByClass(org.obo.datamodel.OBOObject oboClass)
(package private) java.util.Collection<org.obo.annotation.datamodel.Annotation>	getAnnotationsByClass(org.obo.datamodel.OBOObject oboClass)
org.bbop.framework.ComponentConfiguration	getConfiguration()
org.bbop.framework.ConfigurationPanel	getConfigurationPanel()
void	getCurrentAnnotations()
int	getNaviIndex()
java.lang.String	getObjHref(org.obo.datamodel.LinkedObject obj)
org.bbop.swing.HyperlinkLabel	getObjHrefLabel(org.obo.datamodel.LinkedObject obj)
boolean	getShowEmptyPanelsFlag()
static java.lang.String	getTermFromNaviHistory(int position)
java.util.List<java.lang.String>	getTermInfoNaviHistory()
(package private) java.lang.String	getTermNameText()
UseTermListener	getUseTermListener() just gets useTermListener from terminfotoolbar, which back & forward action use, which actually probably isnt right as back & forward might be hitting terms with different use term listeners but good enough for now
static TermInfo2	inst()
boolean	isIncludeExternalDatabaseAnnotations()
boolean	isIncludeImplicitAnnotations()
void	naviRefresh(java.lang.String action)
void	setComponentTitleFromOBOObject(org.obo.datamodel.OBOObject oboClass) Puts the currently browsed term name into the component title
void	setConfiguration(org.bbop.framework.ComponentConfiguration config)
void	setIncludeExternalDatabaseAnnotations(boolean includeExternalDatabaseAnnotations)
void	setIncludeImplicitAnnotations(boolean includeImplicitAnnotations)
void	setNaviIndex(int index)
void	setShowEmptyPanelsFlag(boolean flag)
(package private) void	simulateHyperlinkEvent(javax.swing.event.HyperlinkEvent e) for testing

Methods inherited from class org.bbop.framework.AbstractGUIComponent

cleanup, getComponent, getID, getTitle, init, isXMLSettable, setTitle, setXML, teardownWhenHidden

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, 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, 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

Field Detail

cachedAnnotationInformationContentByClass

protected java.util.Map<org.obo.datamodel.OBOObject,java.lang.Float> cachedAnnotationInformationContentByClass

cachedAnnotationCountByClass

protected java.util.Map<org.obo.datamodel.OBOObject,java.lang.Integer> cachedAnnotationCountByClass

includeImplicitAnnotations

protected boolean includeImplicitAnnotations

includeExternalDatabaseAnnotations

protected boolean includeExternalDatabaseAnnotations

Constructor Detail

TermInfo2

public TermInfo2()

Create the panel

TermInfo2

public TermInfo2(SelectionManager selManager)

TermInfo2

public TermInfo2(boolean useOBOSessionManager)

Parameters:

useOBOSessionManager - When true, the TermInfo panel uses the global SessionManager to get the OBO session for looking up term IDs. This allows the panel to be used when the CharFieldManager is not in use.

Method Detail

isIncludeImplicitAnnotations

public boolean isIncludeImplicitAnnotations()

setIncludeImplicitAnnotations

public void setIncludeImplicitAnnotations(boolean includeImplicitAnnotations)

isIncludeExternalDatabaseAnnotations

public boolean isIncludeExternalDatabaseAnnotations()

setIncludeExternalDatabaseAnnotations

public void setIncludeExternalDatabaseAnnotations(boolean includeExternalDatabaseAnnotations)

getConfigurationPanel

public org.bbop.framework.ConfigurationPanel getConfigurationPanel()

Specified by:

getConfigurationPanel in interface org.bbop.framework.GUIComponent

Overrides:

getConfigurationPanel in class org.bbop.framework.AbstractGUIComponent

getConfiguration

public org.bbop.framework.ComponentConfiguration getConfiguration()

Specified by:

getConfiguration in interface org.bbop.framework.GUIComponent

Overrides:

getConfiguration in class org.bbop.framework.AbstractGUIComponent

setConfiguration

public void setConfiguration(org.bbop.framework.ComponentConfiguration config)

Specified by:

setConfiguration in interface org.bbop.framework.GUIComponent

Overrides:

setConfiguration in class org.bbop.framework.AbstractGUIComponent

inst

public static TermInfo2 inst()

setComponentTitleFromOBOObject

public void setComponentTitleFromOBOObject(org.obo.datamodel.OBOObject oboClass)

Puts the currently browsed term name into the component title

Parameters:

oboClass - the term being browsed

getUseTermListener

public UseTermListener getUseTermListener()

just gets useTermListener from terminfotoolbar, which back & forward action use, which actually probably isnt right as back & forward might be hitting terms with different use term listeners but good enough for now

getTermFromNaviHistory

public static java.lang.String getTermFromNaviHistory(int position)

naviRefresh

public void naviRefresh(java.lang.String action)

getTermNameText

java.lang.String getTermNameText()

getObjHref

public java.lang.String getObjHref(org.obo.datamodel.LinkedObject obj)

getObjHrefLabel

public org.bbop.swing.HyperlinkLabel getObjHrefLabel(org.obo.datamodel.LinkedObject obj)

getAnnotationInformationContentByClass

float getAnnotationInformationContentByClass(org.obo.datamodel.OBOObject oboClass)

getAnnotationCountByClass

int getAnnotationCountByClass(org.obo.datamodel.OBOObject oboClass)

getAnnotationsByClass

java.util.Collection<org.obo.annotation.datamodel.Annotation> getAnnotationsByClass(org.obo.datamodel.OBOObject oboClass)

getCurrentAnnotations

public void getCurrentAnnotations()

simulateHyperlinkEvent

void simulateHyperlinkEvent(javax.swing.event.HyperlinkEvent e)

for testing

getTermInfoNaviHistory

public java.util.List<java.lang.String> getTermInfoNaviHistory()

getNaviIndex

public int getNaviIndex()

setNaviIndex

public void setNaviIndex(int index)

setShowEmptyPanelsFlag

public void setShowEmptyPanelsFlag(boolean flag)

getShowEmptyPanelsFlag

public boolean getShowEmptyPanelsFlag()