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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JTable
biggests.tables.TableValues
biggests.tables.TableSymbols
public class TableSymbols
Title: Table of Symbols
Description:
Defines a table of symbols 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 symbols
(more widely, char
acters)
A table of symbols has a vertical text header and each of its cells is colored according to the symbol that holds in it.
This table implements sorting functionality on the columns, i.e., allows the reordering of the rows, sorting them by a specific column cells' values in ascending or descending order.
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 biggests.tables.TableValues |
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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 |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
---|---|
protected char[] |
alphabet
The alphabet with all discretization symbols used in the discretization technique that gave rise to the set of discrete values that may appear in this symbols table. |
protected java.awt.Color[] |
colors
The set of colors. |
Fields inherited from class biggests.tables.TableValues |
---|
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 | |
---|---|
|
TableSymbols(NodeObjectInterface nodeObject)
Creates a new table of symbols with data from the the given node object's matrix. |
|
TableSymbols(NodeObjectInterface nodeObject,
GOFrontEnd go,
java.awt.Component parent)
Creates a new table of symbols with data from the the given node object's matrix. |
protected |
TableSymbols(java.lang.Object[][] rowData,
java.lang.Object[] columnNames)
Creates a new table of symbols with data from the the given node object's matrix. |
Method Summary | |
---|---|
protected static java.lang.Object[] |
constructColumnNames(NodeObjectInterface nodeObject)
Constructs the column names' array with symbolic data retrieved from the node object's symbolic matrix. |
protected static java.lang.Object[][] |
constructRowData(NodeObjectInterface nodeObject)
Constructs the row data matrix with symbolic data retrieved from the node object's symbolic matrix. |
void |
exportToImage()
Exports this table to an image file. |
char[] |
getAlphabet()
Returns the alphabet with all discretization symbols used in the discretization technique that gave rise to the set of discrete values that may appear in this symbols table. |
java.awt.Color[] |
getColors()
Returns the set of colors used to color each of the table's cells. |
protected void |
initializeColors()
Initializes the array of colors to be used by prepareRenderer to color cells, when the table has to be displayed. |
java.awt.Component |
prepareRenderer(javax.swing.table.TableCellRenderer renderer,
int row,
int column)
Overrides TableValues 's prepareRenderer method. |
void |
this_mouseClicked(java.awt.event.MouseEvent e)
Handles a mouse click in this table of colors. |
Methods inherited from class biggests.tables.TableValues |
---|
createDefaultTableHeader, getToolTipText |
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 |
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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 |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected char[] alphabet
protected java.awt.Color[] colors
Constructor Detail |
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public TableSymbols(NodeObjectInterface nodeObject, GOFrontEnd go, java.awt.Component parent) throws InvalidNodeObjectTypeException
nodeObject
- the NodeObjectInterface
from which the
colored table will be createdgo
- the GOFrontEnd
parent
- the GUI's parent Component
InvalidNodeObjectTypeException
- when the type of the node
object is not validTableSymbols(Object[][] rowData, Object[] columnNames)
,
constructRowData(NodeObjectInterface nodeObject)
,
constructColumnNames(NodeObjectInterface nodeObject)
public TableSymbols(NodeObjectInterface nodeObject) throws InvalidNodeObjectTypeException
nodeObject
- the NodeObjectInterface
from which the
colored table will be created
InvalidNodeObjectTypeException
- when the type of the node
object is not validTableSymbols(Object[][] rowData, Object[] columnNames)
,
constructRowData(NodeObjectInterface nodeObject)
,
constructColumnNames(NodeObjectInterface nodeObject)
protected TableSymbols(java.lang.Object[][] rowData, java.lang.Object[] columnNames)
TableSymbols
rowData
- the Object[][]
array with the data to fill
the rows of the tablecolumnNames
- the Object[][]
array with the data to
fill the header of the table
InvalidNodeObjectTypeException
- when the type of the node
object is not validTableValues#TableValues(TableSorter tableSorterModel)
,
DefaultTableModel.DefaultTableModel(Object[][] rowData, Object[] columnNames)
Method Detail |
---|
protected void initializeColors()
Color
in colors[i]
is the color that will fill the background
of the cells that contain the char symbol in alphabet[i]
.
public java.awt.Component prepareRenderer(javax.swing.table.TableCellRenderer renderer, int row, int column)
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.
prepareRenderer
in class TableValues
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 locationTableValues.prepareRenderer(TableCellRenderer renderer, int row, int column)
protected static java.lang.Object[][] constructRowData(NodeObjectInterface nodeObject) throws InvalidNodeObjectTypeException
The final structure of the row data is:
- the first column corresponds to the names of the genes
- the other cells of the matrix contain char values, which are the gene
expression symbols under certain conditions
protected
: it's intended to be used only by the
TableSymbols
constructor and
constructors of TableSymbols
's
subclasses.
static
: because object this
cannot be
referrenced by the constructor before it is
actually created.
Valid node object classes are:
DiscretizedExpressionMatrix
CCC_Bicluster
E_CCC_Bicluster
nodeObject
- the NodeObjectInterface
which provides the
data needed to create the row data matrix
Object[][]
row data matrix, ready to be used by
TableValues
's constructor
InvalidNodeObjectTypeException
- when the type of the node object is not validprotected static java.lang.Object[] constructColumnNames(NodeObjectInterface nodeObject) throws InvalidNodeObjectTypeException
The final structure of the column names' array is:
- the first cell contains the gene column name
- the remaining cells contain the condition names.
protected
: it's intended to be used only by the
TableValues
's constructor and
TableValues
subclasses'
constructors.
static
: because object this
cannot be
referrenced by the constructor before it is
actually created.
Valid node object classes are:
DiscretizedExpressionMatrix
CCC_Bicluster
E_CCC_Bicluster
nodeObject
- the NodeObjectInterface
which provides the
data needed to create the column names' array
Object[]
array with the column names
InvalidNodeObjectTypeException
- when the type of the node object is not validpublic void exportToImage()
public char[] getAlphabet()
char[]
the set of symbols of discretizationpublic java.awt.Color[] getColors()
Color[]
the set of Color
s that
correspond to the respective symbols of the alphabetpublic void this_mouseClicked(java.awt.event.MouseEvent e)
TableValues
this_mouseClicked
method to display the terms
annotated with the gene in the clicked row of the table.
If the click is in the mouse's right button, shows 'Export to image'
popup menu.
this_mouseClicked
in class TableValues
e
- the MouseEvent
fired when the user clicks this table
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