Package org.biojava.bio.gui

Class FeatureTree

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JTree

org.biojava.bio.gui.FeatureTree

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible, Scrollable

public class FeatureTree
extends JTree

FeatureTree is GUI tree to display the features and annotations of the sequences in a SequenceDB Nested Features are displayed as expandable leaves.

Copyright: Copyright (c) 2002

Company: AgResearch

Version:

1.0

Author:

Mark Schreiber

See Also:

Serialized Form

Nested Class Summary

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

JTree.AccessibleJTree, JTree.DropLocation, JTree.DynamicUtilTreeNode, JTree.EmptySelectionModel, JTree.TreeModelHandler, JTree.TreeSelectionRedirector

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

JComponent.AccessibleJComponent

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields inherited from class javax.swing.JTree

ANCHOR_SELECTION_PATH_PROPERTY, CELL_EDITOR_PROPERTY, CELL_RENDERER_PROPERTY, cellEditor, cellRenderer, editable, EDITABLE_PROPERTY, EXPANDS_SELECTED_PATHS_PROPERTY, INVOKES_STOP_CELL_EDITING_PROPERTY, invokesStopCellEditing, LARGE_MODEL_PROPERTY, largeModel, LEAD_SELECTION_PATH_PROPERTY, ROOT_VISIBLE_PROPERTY, rootVisible, ROW_HEIGHT_PROPERTY, rowHeight, SCROLLS_ON_EXPAND_PROPERTY, scrollsOnExpand, SELECTION_MODEL_PROPERTY, selectionModel, selectionRedirector, SHOWS_ROOT_HANDLES_PROPERTY, showsRootHandles, TOGGLE_CLICK_COUNT_PROPERTY, toggleClickCount, TREE_MODEL_PROPERTY, treeModel, treeModelListener, VISIBLE_ROW_COUNT_PROPERTY, visibleRowCount

Fields inherited from class javax.swing.JComponent

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

accessibleContext, 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

Constructors

Constructor	Description
FeatureTree()	Create a new FeatureTree

Method Summary

Modifier and Type	Method	Description
String	convertValueToText(Object value, boolean selected, boolean expanded, boolean leaf, int row, boolean hasFocus)	Labels Sequence objects with their name, Annotations with the tag Annotations, Features with the tag Features and other objects with the toString value.
void	setSequenceDB(SequenceDB db)	Use this method to provide the sequences for the tree to work with.

Methods inherited from class javax.swing.JTree

addSelectionInterval, addSelectionPath, addSelectionPaths, addSelectionRow, addSelectionRows, addTreeExpansionListener, addTreeSelectionListener, addTreeWillExpandListener, cancelEditing, clearSelection, clearToggledPaths, collapsePath, collapseRow, createTreeModel, createTreeModelListener, expandPath, expandRow, fireTreeCollapsed, fireTreeExpanded, fireTreeWillCollapse, fireTreeWillExpand, fireValueChanged, getAccessibleContext, getAnchorSelectionPath, getCellEditor, getCellRenderer, getClosestPathForLocation, getClosestRowForLocation, getDefaultTreeModel, getDescendantToggledPaths, getDragEnabled, getDropLocation, getDropMode, getEditingPath, getExpandedDescendants, getExpandsSelectedPaths, getInvokesStopCellEditing, getLastSelectedPathComponent, getLeadSelectionPath, getLeadSelectionRow, getMaxSelectionRow, getMinSelectionRow, getModel, getNextMatch, getPathBetweenRows, getPathBounds, getPathForLocation, getPathForRow, getPreferredScrollableViewportSize, getRowBounds, getRowCount, getRowForLocation, getRowForPath, getRowHeight, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getScrollsOnExpand, getSelectionCount, getSelectionModel, getSelectionPath, getSelectionPaths, getSelectionRows, getShowsRootHandles, getToggleClickCount, getToolTipText, getTreeExpansionListeners, getTreeSelectionListeners, getTreeWillExpandListeners, getUI, getUIClassID, getVisibleRowCount, hasBeenExpanded, isCollapsed, isCollapsed, isEditable, isEditing, isExpanded, isExpanded, isFixedRowHeight, isLargeModel, isPathEditable, isPathSelected, isRootVisible, isRowSelected, isSelectionEmpty, isVisible, makeVisible, paramString, removeDescendantSelectedPaths, removeDescendantToggledPaths, removeSelectionInterval, removeSelectionPath, removeSelectionPaths, removeSelectionRow, removeSelectionRows, removeTreeExpansionListener, removeTreeSelectionListener, removeTreeWillExpandListener, scrollPathToVisible, scrollRowToVisible, setAnchorSelectionPath, setCellEditor, setCellRenderer, setDragEnabled, setDropMode, setEditable, setExpandedState, setExpandsSelectedPaths, setInvokesStopCellEditing, setLargeModel, setLeadSelectionPath, setModel, setRootVisible, setRowHeight, setScrollsOnExpand, setSelectionInterval, setSelectionModel, setSelectionPath, setSelectionPaths, setSelectionRow, setSelectionRows, setShowsRootHandles, setToggleClickCount, setUI, setVisibleRowCount, startEditingAtPath, stopEditing, treeDidChange, 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, getBaseline, getBaselineResizeBehavior, 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, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, 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, 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, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, 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, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, 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

Constructor Detail

FeatureTree

public FeatureTree()

Create a new FeatureTree

Method Detail

setSequenceDB

public void setSequenceDB(SequenceDB db)
                   throws BioException

Use this method to provide the sequences for the tree to work with.

Parameters:

db - A database of Sequences to display

Throws:

BioException - if information cannot be retrieved from db

convertValueToText

public String convertValueToText(Object value,
                                 boolean selected,
                                 boolean expanded,
                                 boolean leaf,
                                 int row,
                                 boolean hasFocus)

Labels Sequence objects with their name, Annotations with the tag Annotations, Features with the tag Features and other objects with the toString value.

Overrides:

convertValueToText in class JTree