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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JTable
biggests.tables.TableValues
biggests.tables.TableSymbols
biggests.tables.TableSymbolsWithMissingValues
public class TableSymbolsWithMissingValues
Title: Table of Symbols with Missing Values
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 tha values 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 char
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.
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 |
---|
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary |
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Fields inherited from class biggests.tables.TableSymbols |
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alphabet, colors |
Fields inherited from class biggests.tables.TableValues |
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goFrontEnd, goProperties, parent |
Fields inherited from class javax.swing.JTable |
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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 |
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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 | |
---|---|
TableSymbolsWithMissingValues(DiscretizedExpressionMatrix discreteMatrix)
Creates a new table of symbols with data from the the given discretized expression matrix. |
|
TableSymbolsWithMissingValues(DiscretizedExpressionMatrix discreteMatrix,
GOFrontEnd go,
java.awt.Component parent)
Creates a new table of symbols with data from the the given discretized expression matrix. |
Method Summary | |
---|---|
protected static java.lang.Object[] |
constructColumnNames(DiscretizedExpressionMatrix discreteMatrix)
Constructs the column names' array with symbolic data retrieved from the given discretized expression matrix. |
protected static java.lang.Object[][] |
constructRowData(DiscretizedExpressionMatrix discreteMatrix)
Constructs the row data matrix with symbolic data retrieved from the node object's symbolic matrix. |
java.awt.Component |
prepareRenderer(javax.swing.table.TableCellRenderer renderer,
int row,
int column)
Overrides TableValues 's prepareRenderer method. |
Methods inherited from class biggests.tables.TableSymbols |
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constructColumnNames, constructRowData, exportToImage, getAlphabet, getColors, initializeColors, this_mouseClicked |
Methods inherited from class biggests.tables.TableValues |
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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 |
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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 TableSymbolsWithMissingValues(DiscretizedExpressionMatrix discreteMatrix, GOFrontEnd go, java.awt.Component parent) throws InvalidNodeObjectTypeException
discreteMatrix
- the DiscretizedExpressionMatrix
from which the colored table will be createdgo
- the GOFrontEnd
parent
- the GUI's parent Component
InvalidNodeObjectTypeException
- if the type of the node
object is not valid#TableSymbols(Object[][] rowData, Object[] columnNames)
,
TableSymbols.constructRowData(NodeObjectInterface nodeObject)
,
TableSymbols.constructColumnNames(NodeObjectInterface nodeObject)
public TableSymbolsWithMissingValues(DiscretizedExpressionMatrix discreteMatrix) throws InvalidNodeObjectTypeException
discreteMatrix
- the DiscretizedExpressionMatrix
from which the colored table will be created
InvalidNodeObjectTypeException
- when the type of the node
object is not valid#TableSymbols(Object[][] rowData, Object[] columnNames)
,
TableSymbols.constructRowData(NodeObjectInterface nodeObject)
,
TableSymbols.constructColumnNames(NodeObjectInterface nodeObject)
Method Detail |
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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 TableSymbols
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(DiscretizedExpressionMatrix discreteMatrix) 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
discreteMatrix
- the DiscretizedExpressionMatrix
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(DiscretizedExpressionMatrix discreteMatrix) 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.
discreteMatrix
- the DiscretizedExpressionMatrix
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 valid
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