biggests.tables
Class TableValuesWithMissingValues

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JTable
                  extended by biggests.tables.TableValues
                      extended by biggests.tables.TableValuesWithMissingValues
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener, javax.swing.Scrollable

public class TableValuesWithMissingValues
extends TableValues

Title: Table of values with missing values

Description:

Defines a table of values with the following data:
- header -> conditions' names (more widely, Strings)
- first column -> genes' names (more widely, Strings)
- all other columns' cells -> gene expression values (more widely, float values)

This is a simple table that shows the raw values that are assigned when using one of the constructors and implements sorting functionality on the columns, i.e., allows the reordering of the rows, sorting them by the values of a specific column in ascending or descending order.

Specific for data with missing values, that is, some erroneus values that are not part of the original data and are marked by some float value.

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.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class biggests.tables.TableValues
TableValues.FloatCellRenderer, TableValues.NumberCellRenderer
 
Nested classes/interfaces inherited from class javax.swing.JTable
javax.swing.JTable.AccessibleJTable, javax.swing.JTable.PrintMode
 
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
(package private)  float missingValue
          The value used to fill missing values.
 
Fields inherited from class biggests.tables.TableValues
goFrontEnd, parent
 
Fields inherited from class javax.swing.JTable
AUTO_RESIZE_ALL_COLUMNS, AUTO_RESIZE_LAST_COLUMN, AUTO_RESIZE_NEXT_COLUMN, AUTO_RESIZE_OFF, AUTO_RESIZE_SUBSEQUENT_COLUMNS, autoCreateColumnsFromModel, autoResizeMode, cellEditor, cellSelectionEnabled, columnModel, dataModel, defaultEditorsByColumnClass, defaultRenderersByColumnClass, editingColumn, editingRow, editorComp, gridColor, preferredViewportSize, rowHeight, rowMargin, rowSelectionAllowed, selectionBackground, selectionForeground, selectionModel, showHorizontalLines, showVerticalLines, tableHeader
 
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
TableValuesWithMissingValues(IMatrix expressionMatrix)
          Creates a new values table from the data of an expression matrix with missing values.
TableValuesWithMissingValues(IMatrix expressionMatrix, GOFrontEnd go, java.awt.Component parent)
          Creates a new values table from the data of an expression matrix with missing values.
 
Method Summary
 java.lang.String getToolTipText(java.awt.event.MouseEvent event)
          Overrides TableValues's getToolTipText method in order to allow the renderer's tips to be used if they have text set.
 java.awt.Component prepareRenderer(javax.swing.table.TableCellRenderer renderer, int row, int column)
          Overrides TableValues's prepareRenderer method.
 
Methods inherited from class biggests.tables.TableValues
constructColumnNames, constructRowData, createDefaultTableHeader, this_mouseClicked
 
Methods inherited from class javax.swing.JTable
addColumn, addColumnSelectionInterval, addNotify, addRowSelectionInterval, changeSelection, clearSelection, columnAdded, columnAtPoint, columnMarginChanged, columnMoved, columnRemoved, columnSelectionChanged, configureEnclosingScrollPane, convertColumnIndexToModel, convertColumnIndexToView, createDefaultColumnModel, createDefaultColumnsFromModel, createDefaultDataModel, createDefaultEditors, createDefaultRenderers, createDefaultSelectionModel, createScrollPaneForTable, doLayout, editCellAt, editCellAt, editingCanceled, editingStopped, getAccessibleContext, getAutoCreateColumnsFromModel, getAutoResizeMode, getCellEditor, getCellEditor, getCellRect, getCellRenderer, getCellSelectionEnabled, getColumn, getColumnClass, getColumnCount, getColumnModel, getColumnName, getColumnSelectionAllowed, getDefaultEditor, getDefaultRenderer, getDragEnabled, getEditingColumn, getEditingRow, getEditorComponent, getGridColor, getIntercellSpacing, getModel, getPreferredScrollableViewportSize, getPrintable, getRowCount, getRowHeight, getRowHeight, getRowMargin, getRowSelectionAllowed, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getSelectedColumn, getSelectedColumnCount, getSelectedColumns, getSelectedRow, getSelectedRowCount, getSelectedRows, getSelectionBackground, getSelectionForeground, getSelectionModel, getShowHorizontalLines, getShowVerticalLines, getSurrendersFocusOnKeystroke, getTableHeader, getUI, getUIClassID, getValueAt, initializeLocalVars, isCellEditable, isCellSelected, isColumnSelected, isEditing, isRowSelected, moveColumn, paramString, prepareEditor, print, print, print, print, processKeyBinding, removeColumn, removeColumnSelectionInterval, removeEditor, removeNotify, removeRowSelectionInterval, resizeAndRepaint, rowAtPoint, selectAll, setAutoCreateColumnsFromModel, setAutoResizeMode, setCellEditor, setCellSelectionEnabled, setColumnModel, setColumnSelectionAllowed, setColumnSelectionInterval, setDefaultEditor, setDefaultRenderer, setDragEnabled, setEditingColumn, setEditingRow, setGridColor, setIntercellSpacing, setModel, setPreferredScrollableViewportSize, setRowHeight, setRowHeight, setRowMargin, setRowSelectionAllowed, setRowSelectionInterval, setSelectionBackground, setSelectionForeground, setSelectionMode, setSelectionModel, setShowGrid, setShowHorizontalLines, setShowVerticalLines, setSurrendersFocusOnKeystroke, setTableHeader, setUI, setValueAt, sizeColumnsToFit, sizeColumnsToFit, tableChanged, unconfigureEnclosingScrollPane, updateUI, valueChanged
 
Methods inherited from class javax.swing.JComponent
addAncestorListener, 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, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, 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, 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

missingValue

float missingValue
The value used to fill missing values.

Constructor Detail

TableValuesWithMissingValues

public TableValuesWithMissingValues(IMatrix expressionMatrix,
                                    GOFrontEnd go,
                                    java.awt.Component parent)
                             throws InvalidNodeObjectTypeException,
                                    java.lang.Exception
Creates a new values table from the data of an expression matrix with missing values. A table of values contains the following data:
- header -> conditions' names
- first column -> genes' names
- all other column's cells -> gene expression float values
This table also displays the terms annotated with each gene (when a specific table's row is clicked by the user).

Parameters:
expressionMatrix - the ExpressionMatrix with missing values from which the table of values is created
go - the GOFrontEnd
parent - the GUI's parent Component
Throws:
InvalidNodeObjectTypeException - when the type of the node object is not valid (normally this is not a problem, since an object of type ExpressionMatrix is considered to be a valid type for a node object
java.lang.Exception
See Also:
#TableValuesWithMissingValues(Object[][] rowData, Object[] columnNames)), TableValues.constructRowData(NodeObjectInterface nodeObject), TableValues.constructColumnNames(NodeObjectInterface nodeObject)

TableValuesWithMissingValues

public TableValuesWithMissingValues(IMatrix expressionMatrix)
                             throws InvalidNodeObjectTypeException,
                                    java.lang.Exception
Creates a new values table from the data of an expression matrix with missing values. A table of values contains the following data:
- header -> conditions' names
- first column -> genes' names
- all other column's cells -> gene expression float values

Parameters:
expressionMatrix - the ExpressionMatrix with missing values from which the table of values is created
Throws:
InvalidNodeObjectTypeException - when the type of the node object is not valid (normally this is not a problem, since an object of type ExpressionMatrix is considered to be a valid type for a node object
java.lang.Exception
See Also:
#TableValuesWithMissingValues(Object[][] rowData, Object[] columnNames)), TableValues.constructRowData(NodeObjectInterface nodeObject), TableValues.constructColumnNames(NodeObjectInterface nodeObject)
Method Detail

prepareRenderer

public java.awt.Component prepareRenderer(javax.swing.table.TableCellRenderer renderer,
                                          int row,
                                          int column)
Overrides TableValues's prepareRenderer method. Prepares the renderer by querying the data model for the value and selection state of the cell at row, column. Returns the component (may be a Component or a JComponent) under the event location.

Overrides:
prepareRenderer in class TableValues
Parameters:
renderer - the TableCellRenderer to prepare
row - the row of the cell to render, where 0 is the first row
column - the column of the cell to render, where 0 is the first column
Returns:
the Component under the event location
See Also:
TableValues.prepareRenderer(TableCellRenderer renderer, int row, int column)

getToolTipText

public java.lang.String getToolTipText(java.awt.event.MouseEvent event)
Overrides TableValues's getToolTipText method in order to allow the renderer's tips to be used if they have text set.

Overrides:
getToolTipText in class TableValues
Parameters:
event - MouseEvent the event that triggered the tool tip display
Returns:
String the message set as tool tip for the pointed table cell
See Also:
JTable.getToolTipText(MouseEvent event)