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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JTable
biggests.tables.TableValues
biggests.tables.TableColors
biggests.tables.TableColorsWithMissingValues
public class TableColorsWithMissingValues
Title: Table of colors with missing values
Description:
Defines a table of colors with the following data:
- header -> conditions' names (more widely, String
s)
- first column -> genes' names (more widely, String
s)
- all other columns' cells -> gene expression values
(more widely, float
values)
A table of colors has a vertical text header and each of its cells is colored according to the float value it holds.
The cells which value is situated in the interval:
[minValue,
meanValue
[ are colored green (different shades of green,
according to the exact value)
{meanValue
} are
colored black
]meanValue
, maxValue] are colored
red (different shades of red, according to the exact value)
cells of
missing values are colored yellow
This table also displays the terms annotated with each gene (when a specific row of the table is clicked by the user).
This kind of table implements sorting functionality on the columns, i.e., allows the reordering of the rows, sorting them by the values of the cells of a given 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. Missing values are colored with a different color from that of the other values.
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 |
---|
Nested classes/interfaces inherited from class biggests.tables.TableValues |
---|
TableValues.FloatCellRenderer, TableValues.NumberCellRenderer |
Nested classes/interfaces inherited from class javax.swing.JTable |
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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 |
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Fields inherited from class biggests.tables.TableColors |
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divider, meanValue |
Fields inherited from class biggests.tables.TableValues |
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goFrontEnd, goProperties, 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 | |
---|---|
TableColorsWithMissingValues(AbstractExpressionMatrix expressionMatrix)
Creates a new colored table with data from the given expression matrix with missing values. |
|
TableColorsWithMissingValues(AbstractExpressionMatrix expressionMatrix,
GOFrontEnd go,
java.awt.Component parent)
Creates a new colored table with data from the given expression matrix with missing values. |
Method Summary | |
---|---|
float |
getMissingValue()
Returns the value used to mark cells which correspond to missing values on the original gene expression data. |
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 TableColors 's prepareRenderer method. |
Methods inherited from class biggests.tables.TableColors |
---|
exportToImage, getDivider, getMeanValue, this_mouseClicked |
Methods inherited from class biggests.tables.TableValues |
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constructColumnNames, constructRowData, createDefaultTableHeader |
Methods inherited from class javax.swing.JTable |
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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 |
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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 |
Constructor Detail |
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public TableColorsWithMissingValues(AbstractExpressionMatrix expressionMatrix, GOFrontEnd go, java.awt.Component parent) throws InvalidNodeObjectTypeException
expressionMatrix
- the AbstractExpressionMatrix
with missing values from which the colored
table will be createdgo
- the GOFrontEnd
parent
- the GUI's parent Component
InvalidNodeObjectTypeException
- if expressionMatrix
is not of a valid object type#TableColorsWithMissingValues(Object[][] rowData, Object[]
columnNames)
,
TableValues.constructRowData(NodeObjectInterface nodeObject)
,
TableValues.constructColumnNames(NodeObjectInterface nodeObject)
public TableColorsWithMissingValues(AbstractExpressionMatrix expressionMatrix) throws InvalidNodeObjectTypeException
expressionMatrix
- the ExpressionMatrix
with missing
values from which the colored table will be created
InvalidNodeObjectTypeException
- if expressionMatrix
is not of a valid object type#TableColorsWithMissingValues(Object[][] rowData, Object[]
columnNames)
,
TableValues.constructRowData(NodeObjectInterface nodeObject)
,
TableValues.constructColumnNames(NodeObjectInterface nodeObject)
Method Detail |
---|
public java.awt.Component prepareRenderer(javax.swing.table.TableCellRenderer renderer, int row, int column)
TableColors
'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.
prepareRenderer
in class TableColors
renderer
- the TableCellRenderer
to preparerow
- the row of the cell to render, where 0 is the first rowcolumn
- the column of the cell to render,
where 0 is the first column
Component
under the event locationTableColors.prepareRenderer(TableCellRenderer renderer, int row, int column)
public java.lang.String getToolTipText(java.awt.event.MouseEvent event)
TableValues
's getToolTipText
method
in order to allow the renderer's tips to be used if they have text set.
getToolTipText
in class TableValues
event
- MouseEvent the event that triggered the tool tip display
JTable.getToolTipText(MouseEvent event)
public float getMissingValue()
float
that marks missing values
|
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