cytoscape.data.annotation
Class OntologyMapperDialog

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Dialog
                  javax.swing.JDialog
                      cytoscape.data.annotation.OntologyMapperDialog

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants

public class OntologyMapperDialog
extends JDialog

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JDialog

JDialog.AccessibleJDialog

Nested classes/interfaces inherited from class java.awt.Dialog

Dialog.AccessibleAWTDialog

Nested classes/interfaces inherited from class java.awt.Window

Window.AccessibleAWTWindow

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

protected BioDataServer	dataServer
protected String	defaultSpecies
static String	GO_BIOLOGICAL_PROCESS
static String	GO_CELLULAR_COMPONENT
static String	GO_MOLECULAR_FUNCTION

Fields inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

OntologyMapperDialog()

OntologyMapperDialog(Frame parent, boolean modal)
Creates new form OntologyMapperDialog

Method Summary

Set	addAllAnnotationToNodes(AnnotationDescription aDesc, String annotationName)
Set	addAnnotationToNodes(AnnotationDescription aDesc, int level, String annotationNameAtLevel)
protected void	appendToSelectionTree(String currentAnnotationCategory, Set uniqueAnnotationValues, AnnotationDescription aDesc)
protected void	buildOntologyTree()
protected JTree	createAvailableAnnotationsTree()
protected JTree	createNodeSelectionTree()
protected void	createTreeNodes(DefaultMutableTreeNode root, AnnotationDescription[] descriptions)

Methods inherited from class javax.swing.JDialog

addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Dialog

addNotify, getTitle, hide, isModal, isResizable, isUndecorated, setModal, setResizable, setTitle, setUndecorated, show

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, finalize, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

GO_MOLECULAR_FUNCTION

public static final String GO_MOLECULAR_FUNCTION

See Also:

Constant Field Values

GO_BIOLOGICAL_PROCESS

public static final String GO_BIOLOGICAL_PROCESS

See Also:

Constant Field Values

GO_CELLULAR_COMPONENT

public static final String GO_CELLULAR_COMPONENT

See Also:

Constant Field Values

dataServer

protected BioDataServer dataServer

defaultSpecies

protected String defaultSpecies

Constructor Detail

OntologyMapperDialog

public OntologyMapperDialog()

OntologyMapperDialog

public OntologyMapperDialog(Frame parent,
                            boolean modal)

Creates new form OntologyMapperDialog

Method Detail

appendToSelectionTree

protected void appendToSelectionTree(String currentAnnotationCategory,
                                     Set uniqueAnnotationValues,
                                     AnnotationDescription aDesc)

createAvailableAnnotationsTree

protected JTree createAvailableAnnotationsTree()

createTreeNodes

protected void createTreeNodes(DefaultMutableTreeNode root,
                               AnnotationDescription[] descriptions)

buildOntologyTree

protected void buildOntologyTree()

createNodeSelectionTree

protected JTree createNodeSelectionTree()

addAnnotationToNodes

public Set addAnnotationToNodes(AnnotationDescription aDesc,
                                int level,
                                String annotationNameAtLevel)

addAllAnnotationToNodes

public Set addAllAnnotationToNodes(AnnotationDescription aDesc,
                                   String annotationName)