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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JTree
biggests.tree.DatasetTree
public class DatasetTree
Title: Dataset Tree
Description: The dynamic tree which contains the gene expression datasets, matrices and biclusters. Allows one to add specific nodes to it.
Copyright: Copyright (C) 2007 Joana Gonçalves This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JTree |
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javax.swing.JTree.AccessibleJTree, javax.swing.JTree.DynamicUtilTreeNode, javax.swing.JTree.EmptySelectionModel, javax.swing.JTree.TreeModelHandler, javax.swing.JTree.TreeSelectionRedirector |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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static long |
serialVersionUID
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Fields inherited from class javax.swing.JTree |
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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 |
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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 |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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DatasetTree()
Constructs a dataset tree with a single (mutable) tree node (called "Datasets"). |
Method Summary | |
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javax.swing.tree.TreePath |
addLoadedDataset(NodeInfo originalNodeInfo)
Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset. |
void |
addLoadedDataset(NodeInfo originalNodeInfo,
boolean setNewPath)
Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset. |
javax.swing.tree.TreePath |
addNewNode(NodeInfo nodeInfo,
javax.swing.tree.TreePath selectionPath)
Adds a new node to the datasets tree, associated with a node information object. |
void |
addNewNode(NodeInfo nodeInfo,
javax.swing.tree.TreePath selectionPath,
boolean setNewPath)
Adds a new node to the datasets tree, associated with a node information object. |
NodeInfo |
findBiclusterNodeByIDinSetOfBiclustersNodes(java.util.Enumeration setOfBiclustersNodes,
int id)
Looks for a NodeInfo object of a bicluster or
post-processed bicluster object with a specific id . |
int |
generateNewDatasetId()
Generates a dataset id for a new Dataset object. |
int |
generateNewNodeInfoId(int nodeObjectType,
javax.swing.tree.TreePath selectionPath,
boolean update)
Returns the next id for a new NodeInfo object to be
created in the dataset of the given selected path. |
javax.swing.tree.DefaultMutableTreeNode |
getRoot()
Returns the root node of the dataset tree. |
void |
reload()
Reloads the tree model, so all (new) nodes get visible. |
Methods inherited from class javax.swing.JTree |
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addSelectionInterval, addSelectionPath, addSelectionPaths, addSelectionRow, addSelectionRows, addTreeExpansionListener, addTreeSelectionListener, addTreeWillExpandListener, cancelEditing, clearSelection, clearToggledPaths, collapsePath, collapseRow, convertValueToText, createTreeModel, createTreeModelListener, expandPath, expandRow, fireTreeCollapsed, fireTreeExpanded, fireTreeWillCollapse, fireTreeWillExpand, fireValueChanged, getAccessibleContext, getAnchorSelectionPath, getCellEditor, getCellRenderer, getClosestPathForLocation, getClosestRowForLocation, getDefaultTreeModel, getDescendantToggledPaths, getDragEnabled, 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, 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 |
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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, 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 |
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final long serialVersionUID
Constructor Detail |
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public DatasetTree()
Method Detail |
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public javax.swing.tree.TreePath addLoadedDataset(NodeInfo originalNodeInfo) throws InvalidNodeObjectTypeException
showPathOfNewNode
is set to true.NodeInfo.ORIGINAL
originalNodeInfo
- the NodeInfo
object of the new dataset
TreePath
of the new node
InvalidNodeObjectTypeException
- if the type of the node object is not validpublic javax.swing.tree.TreePath addNewNode(NodeInfo nodeInfo, javax.swing.tree.TreePath selectionPath) throws InvalidNodeObjectTypeException
showPathOfNewNode
is set to true.NodeInfo.PREPROCESSED
NodeInfo.DISCRETIZED
NodeInfo.BICLUSTER_GROUP
NodeInfo.POSTPROCESSED_GROUP
nodeInfo
- NodeInfo the node information object associated with the tree nodeselectionPath
- TreePath the tree selection path
TreePath
of the new node
InvalidNodeObjectTypeException
- when the type of the node object is not validpublic void addLoadedDataset(NodeInfo originalNodeInfo, boolean setNewPath) throws InvalidNodeObjectTypeException
NodeInfo.ORIGINAL
originalNodeInfo
- the NodeInfo
object of the new datasetsetNewPath
- the boolean
which indicates if new
node's path is to display in the treeInvalidNodeObjectTypeException
- when the type of the
NodeInfo
is not validaddLoadedDataset(NodeInfo originalNodeInfo)
public void addNewNode(NodeInfo nodeInfo, javax.swing.tree.TreePath selectionPath, boolean setNewPath) throws InvalidNodeObjectTypeException
NodeInfo.PREPROCESSED
NodeInfo.DISCRETIZED
NodeInfo.BICLUSTER_GROUP
NodeInfo.POSTPROCESSED_GROUP
nodeInfo
- NodeInfo the node information object associated with the tree nodeselectionPath
- TreePath the tree selection pathsetNewPath
- the boolean
which indicates if new
node's path is to display in the treeInvalidNodeObjectTypeException
- when the type of the node object is not validaddNewNode(NodeInfo nodeInfo, TreePath selectionPath)
public void reload()
public javax.swing.tree.DefaultMutableTreeNode getRoot()
public int generateNewNodeInfoId(int nodeObjectType, javax.swing.tree.TreePath selectionPath, boolean update) throws InvalidNodeObjectTypeException
NodeInfo
object to be
created in the dataset of the given selected path. The next id depends on:
nodeObjectType
- int the type of the node object (so we know in which
group of node information objects we have to look for the next id):NodeInfo.PREPROCESSED
NodeInfo.DISCRETIZED
NodeInfo.BICLUSTER_GROUP
NodeInfo.POSTPROCESSED_GROUP
selectionPath
- TreePath the selected pathupdate
- boolean
true
to update the
number of nodes created in the tree for this
nodeObjectType
so far; false
if one only wants to know which id is next, without
inserting a new node in the tree
NodeInfo
object
- Throws:
InvalidNodeObjectTypeException
- if the type of the node object is not valid
public int generateNewDatasetId()
Dataset
object.
public NodeInfo findBiclusterNodeByIDinSetOfBiclustersNodes(java.util.Enumeration setOfBiclustersNodes, int id)
NodeInfo
object of a bicluster or
post-processed bicluster object with a specific id
.
Returns the corresponding NodeInfo
object if search
succeeds and null otherwise.
setOfBiclustersNodes
- Enumeration
with the set of
bicluster nodes where to look for the bicluster node information
object with the given id
; each element of the
setOfBiclustersNodes
has type
DefaultMutableTreeNode
and contains a NodeInfo
object which, in turn, contains a bicluster or post-processed
bicluster objectid
- the int
of the bicluster to search for
id
; null if bicluster was not found
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