charite.christo.metannogen
Class MetannogenTree

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JTree
                  charite.christo.ChJTree
                      charite.christo.metannogen.MetannogenTree

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, EventListener, Accessible, TreeSelectionListener, Scrollable, TreeModel

public class MetannogenTree
extends ChJTree
implements TreeModel

HELP Several browsable trees are available in different tabs of the tabbed pane:

• Tabs for networks like KEGG and the Palsson-Human-Network
• Tab for objects matching a keyword search
• Tab for clicked objects
• Tab for datasets
• Tab for datasets ordered by pathway

Multiple selection of tree nodes follows the conventions of Windows and X-Windows and requires the Shift key and the Ctrl key.

Finished Networks

Metannogen allows to load and browse finished networks like Kegg or the Palsson-Human-Network. The immutable network data is shown as a hierarchical trees with expandable nodes: Pathway, reaction, EC-class, metabolites.

JCOMPONENT:MetannogenTree#docuTree()!

Datasets

The datasets are listed in two trees located in adjacent tabs:

1. Datasets: Datasets are in flat lists: Several branches are available:
   • TREENODE:MetannogenStatics#NODE_DATASETS: This branch contains all datasets edited and modified by the user.
   • TREENODE:MetannogenStatics#NODE_DATASETS_KILL: This branch contains all datasets that have been deleted during the current session. Deleted datasets can be rescued with the menu-item "Duplicate focused dataset" in the dataset-menu or by clicking the ICON:IC_KILL button. All deleted datasets are finally lost after the session.
   • TREENODE:MetannogenStatics#NODE_ORPHAN_DATASETS: This branch contains all datasets that are not assigned to a reaction because the ID does not match to any reaction.
   • TREENODE:MetannogenStatics#NODE_TRANSPORTER_DATASETS: This branch contains all datasets with more that one compartment.
2. By PW: Datasets are ordered by pathway. Only those datasets are included where a pathway is defined in the Pathway-text-field.

Tool buttons of the object tree

• LABEL:"Search Data": The search buttons allows free text search in all objects. Several search strings can be combined using boolean operators. All matching objects are shown in the tab "Matching".
• ICON:IC_MAIN: The selected objects are shown in a graphical KEGG map.

Bugs: Sometimes the tree is not displaying any more. Workaround: "Redraw"-button.

See Also:

Serialized Form

Nested Class Summary

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

JTree.DropLocation, JTree.DynamicUtilTreeNode

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

JComponent.AccessibleJComponent

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

Component.BaselineResizeBehavior

Field Summary

Reference

WEAK_REF

Fields inherited from class javax.swing.JTree

ANCHOR_SELECTION_PATH_PROPERTY, CELL_EDITOR_PROPERTY, CELL_RENDERER_PROPERTY, EDITABLE_PROPERTY, EXPANDS_SELECTED_PATHS_PROPERTY, INVOKES_STOP_CELL_EDITING_PROPERTY, LARGE_MODEL_PROPERTY, LEAD_SELECTION_PATH_PROPERTY, ROOT_VISIBLE_PROPERTY, ROW_HEIGHT_PROPERTY, SCROLLS_ON_EXPAND_PROPERTY, SELECTION_MODEL_PROPERTY, SHOWS_ROOT_HANDLES_PROPERTY, TOGGLE_CLICK_COUNT_PROPERTY, TREE_MODEL_PROPERTY, VISIBLE_ROW_COUNT_PROPERTY

Fields inherited from class javax.swing.JComponent

TOOL_TIP_TEXT_KEY, 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

MetannogenTree(Object root)

Method Summary

void	addTreeModelListener(TreeModelListener li)
static JComponent	docuTree()
static MetannogenTree[]	getAllTrees()
Object	getChild(Object parent, int i)
int	getChildCount(Object parent)
int	getIndexOfChild(Object parent, Object child)
Object	getRoot()
boolean	isLeaf(Object o)
void	paintComponent(Graphics g)
void	processEvent(AWTEvent ev)
void	removeTreeModelListener(TreeModelListener li)
static void	repaintAll()
void	updateIfRootChanged(char what)
static void	updateIfRootChangedAll(char what)
void	updateTree()
void	updateUI()
void	valueForPathChanged(TreePath tp, Object o)

Methods inherited from class charite.christo.ChJTree

getToolTipText, valueChanged

Methods inherited from class javax.swing.JTree

addSelectionInterval, addSelectionPath, addSelectionPaths, addSelectionRow, addSelectionRows, addTreeExpansionListener, addTreeSelectionListener, addTreeWillExpandListener, cancelEditing, clearSelection, collapsePath, collapseRow, convertValueToText, expandPath, expandRow, fireTreeCollapsed, fireTreeExpanded, fireTreeWillCollapse, fireTreeWillExpand, getAccessibleContext, getAnchorSelectionPath, getCellEditor, getCellRenderer, getClosestPathForLocation, getClosestRowForLocation, getDragEnabled, getDropLocation, getDropMode, getEditingPath, getExpandedDescendants, getExpandsSelectedPaths, getInvokesStopCellEditing, getLastSelectedPathComponent, getLeadSelectionPath, getLeadSelectionRow, getMaxSelectionRow, getMinSelectionRow, getModel, getNextMatch, getPathBounds, getPathForLocation, getPathForRow, getPreferredScrollableViewportSize, getRowBounds, getRowCount, getRowForLocation, getRowForPath, getRowHeight, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getScrollsOnExpand, getSelectionCount, getSelectionModel, getSelectionPath, getSelectionPaths, getSelectionRows, getShowsRootHandles, getToggleClickCount, getTreeExpansionListeners, getTreeSelectionListeners, getTreeWillExpandListeners, getUI, getUIClassID, getVisibleRowCount, hasBeenExpanded, isCollapsed, isCollapsed, isEditable, isEditing, isExpanded, isExpanded, isFixedRowHeight, isLargeModel, isPathEditable, isPathSelected, isRootVisible, isRowSelected, isSelectionEmpty, isVisible, makeVisible, removeSelectionInterval, removeSelectionPath, removeSelectionPaths, removeSelectionRow, removeSelectionRows, removeTreeExpansionListener, removeTreeSelectionListener, removeTreeWillExpandListener, scrollPathToVisible, scrollRowToVisible, setAnchorSelectionPath, setCellEditor, setCellRenderer, setDragEnabled, setDropMode, setEditable, setExpandsSelectedPaths, setInvokesStopCellEditing, setLargeModel, setLeadSelectionPath, setModel, setRootVisible, setRowHeight, setScrollsOnExpand, setSelectionInterval, setSelectionModel, setSelectionPath, setSelectionPaths, setSelectionRow, setSelectionRows, setShowsRootHandles, setToggleClickCount, setUI, setVisibleRowCount, startEditingAtPath, stopEditing, treeDidChange

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, 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, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, 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, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, 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, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, enableInputMethods, 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, 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

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

Field Detail

WEAK_REF

public final Reference WEAK_REF

Constructor Detail

MetannogenTree

public MetannogenTree(Object root)

Method Detail

valueForPathChanged

public void valueForPathChanged(TreePath tp,
                                Object o)

Specified by:

valueForPathChanged in interface TreeModel

getIndexOfChild

public int getIndexOfChild(Object parent,
                           Object child)

Specified by:

getIndexOfChild in interface TreeModel

getChild

public Object getChild(Object parent,
                       int i)

Specified by:

getChild in interface TreeModel

removeTreeModelListener

public void removeTreeModelListener(TreeModelListener li)

Specified by:

removeTreeModelListener in interface TreeModel

addTreeModelListener

public void addTreeModelListener(TreeModelListener li)

Specified by:

addTreeModelListener in interface TreeModel

isLeaf

public boolean isLeaf(Object o)

Specified by:

isLeaf in interface TreeModel

getChildCount

public int getChildCount(Object parent)

Specified by:

getChildCount in interface TreeModel

getRoot

public Object getRoot()

Specified by:

getRoot in interface TreeModel

processEvent

public void processEvent(AWTEvent ev)

Overrides:

processEvent in class ChJTree

updateTree

public void updateTree()

updateUI

public void updateUI()

Overrides:

updateUI in class JTree

paintComponent

public void paintComponent(Graphics g)

Overrides:

paintComponent in class ChJTree

docuTree

public static JComponent docuTree()

getAllTrees

public static MetannogenTree[] getAllTrees()

repaintAll

public static void repaintAll()

updateIfRootChangedAll

public static void updateIfRootChangedAll(char what)

updateIfRootChanged

public void updateIfRootChanged(char what)