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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JTable
biggests.tables.TableFunctionGroup
public class TableFunctionGroup
Title: Table of Functions for a Group of Biclusters
Description: Defines a table for displaying data of function
analysis performed on a given a group of biclusters.
It contains the following information:
1st column - Bicluster ID
2nd column - Number of Genes
3rd column - Number of Conditions
4th column - Best p-value
5th column - Best corrected p-value
6th column - Number of significant functions
7th column - Number of highly significant functions
8th column - P-value user's threshold
9th column - Number of significant functions (user's threshold)
Note: if the bicluster group is a post-processed one, an an extra
column is added at the beggining, holding the post-processed
bicluster id.
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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protected static class |
TableFunctionGroup.FloatCellRenderer
Title: FloatCellRenderer : A renderer for cells which
contain float numbers. |
protected static class |
TableFunctionGroup.NumberCellRenderer
Title: NumberCellRenderer : A renderer for cells which
contain numbers. |
Nested classes/interfaces inherited from class javax.swing.JTable |
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javax.swing.JTable.AccessibleJTable, javax.swing.JTable.DropLocation, javax.swing.JTable.PrintMode |
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.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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static java.awt.Color |
EVEN_ROWS_COLOR
Default color to user in even rows (when they are not selected). |
static java.awt.Color |
ODD_ROWS_COLOR
Default color to user in odd rows (when they are not selected). |
static java.awt.Color |
SIGNIFICANT_COLOR
Default color to mark rows that contain biclusters with significant terms. |
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 |
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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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|
TableFunctionGroup(smadeira.biclustering.Biclustering biclustering,
java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary,
boolean postProcessed)
Creates a new function table from the data of a biclusters group object. |
protected |
TableFunctionGroup(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
boolean postProcessed)
Creates a new function table from the data of a biclusters group object. |
protected |
TableFunctionGroup(TableSorterFunctionGroup tableSorterModel)
Creates a new function table from the data of a biclusters group object. |
Method Summary | |
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static java.lang.String[] |
columnNames(boolean postProcessed)
Returns the abbreviated names for the columns of this functions table. |
static java.lang.String[] |
completeColumnNames(boolean postProcessed)
Returns the complete names of the columns of this functions table. |
protected static java.lang.Object[][] |
constructRowData(smadeira.biclustering.Biclustering biclustering,
java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary,
boolean postProcessed)
Constructs the row data matrix with data retrieved from the biclustering object. |
protected javax.swing.table.JTableHeader |
createDefaultTableHeader()
Overrides JTable 's createDefaultTableHeader
method. |
java.awt.Color |
getEvenRowsColor()
Returns the Color used to mark even rows that are not selected. |
java.awt.Color |
getOddRowsColor()
Returns the Color used to mark odd rows that are not selected. |
java.awt.Color |
getSignificantColor()
Returns the Color used to mark significant terms. |
java.lang.String |
getToolTipText(java.awt.event.MouseEvent event)
Overrides JTable '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 JTable 's prepareRenderer method. |
void |
setEvenRowsColor(java.awt.Color newEvenRowsColor)
Sets a new color to mark even rows that are not selected. |
void |
setOddRowsColor(java.awt.Color newOddRowsColor)
Sets a new color to mark odd rows that are not selected. |
void |
setSignificantColor(java.awt.Color newSignificantColor)
Sets a new color to mark significant terms. |
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, convertRowIndexToModel, convertRowIndexToView, createDefaultColumnModel, createDefaultColumnsFromModel, createDefaultDataModel, createDefaultEditors, createDefaultRenderers, createDefaultSelectionModel, createScrollPaneForTable, doLayout, editCellAt, editCellAt, editingCanceled, editingStopped, getAccessibleContext, getAutoCreateColumnsFromModel, getAutoCreateRowSorter, getAutoResizeMode, getCellEditor, getCellEditor, getCellRect, getCellRenderer, getCellSelectionEnabled, getColumn, getColumnClass, getColumnCount, getColumnModel, getColumnName, getColumnSelectionAllowed, getDefaultEditor, getDefaultRenderer, getDragEnabled, getDropLocation, getDropMode, getEditingColumn, getEditingRow, getEditorComponent, getFillsViewportHeight, getGridColor, getIntercellSpacing, getModel, getPreferredScrollableViewportSize, getPrintable, getRowCount, getRowHeight, getRowHeight, getRowMargin, getRowSelectionAllowed, getRowSorter, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getSelectedColumn, getSelectedColumnCount, getSelectedColumns, getSelectedRow, getSelectedRowCount, getSelectedRows, getSelectionBackground, getSelectionForeground, getSelectionModel, getShowHorizontalLines, getShowVerticalLines, getSurrendersFocusOnKeystroke, getTableHeader, getUI, getUIClassID, getUpdateSelectionOnSort, getValueAt, initializeLocalVars, isCellEditable, isCellSelected, isColumnSelected, isEditing, isRowSelected, moveColumn, paramString, prepareEditor, print, print, print, print, print, processKeyBinding, removeColumn, removeColumnSelectionInterval, removeEditor, removeNotify, removeRowSelectionInterval, resizeAndRepaint, rowAtPoint, selectAll, setAutoCreateColumnsFromModel, setAutoCreateRowSorter, setAutoResizeMode, setCellEditor, setCellSelectionEnabled, setColumnModel, setColumnSelectionAllowed, setColumnSelectionInterval, setDefaultEditor, setDefaultRenderer, setDragEnabled, setDropMode, setEditingColumn, setEditingRow, setFillsViewportHeight, setGridColor, setIntercellSpacing, setModel, setPreferredScrollableViewportSize, setRowHeight, setRowHeight, setRowMargin, setRowSelectionAllowed, setRowSelectionInterval, setRowSorter, setSelectionBackground, setSelectionForeground, setSelectionMode, setSelectionModel, setShowGrid, setShowHorizontalLines, setShowVerticalLines, setSurrendersFocusOnKeystroke, setTableHeader, setUI, setUpdateSelectionOnSort, setValueAt, sizeColumnsToFit, sizeColumnsToFit, sorterChanged, 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, getBaseline, getBaselineResizeBehavior, 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, isPaintingForPrint, 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 |
Field Detail |
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public static final java.awt.Color SIGNIFICANT_COLOR
public static final java.awt.Color EVEN_ROWS_COLOR
public static final java.awt.Color ODD_ROWS_COLOR
Constructor Detail |
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public TableFunctionGroup(smadeira.biclustering.Biclustering biclustering, java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary, boolean postProcessed) throws InvalidNodeObjectTypeException
biclustering
- the Biclustering
from which the
function table is createdbiologicalRelevanceSummary
- the Hashtable
which
contains the biological relevance summaries for all
biclusters' group biclusterspostProcessed
- boolean
true
if
biclustering
is a post-processed biclusters
group object
InvalidNodeObjectTypeException
- when the type of the biclustering
object is not valid#constructRowData(Biclustering biclustering)
,
#TableFunctionGroup(Object[][] rowData, Object[] columnNames))
protected TableFunctionGroup(java.lang.Object[][] rowData, java.lang.Object[] columnNames, boolean postProcessed)
rowData
- the Object[][]
row data (for all table
cells except the ones from the table header)columnNames
- the Object[]
column names (for
the table header)postProcessed
- boolean
true
if
biclustering
is a post-processed biclusters
group objectTableFunctionGroup(TableSorterFunctionGroup tableSorterModel)
,
applicationgui.utils.TableSorter#TableSorter(TableModel tableModel)
,
DefaultTableModel.DefaultTableModel(Object[][] rowData, Object[] columnNames)
protected TableFunctionGroup(TableSorterFunctionGroup tableSorterModel)
tableSorterModel
- the TableSorter
model for the tableJTable.JTable(TableModel dm)
Method Detail |
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public java.awt.Component prepareRenderer(javax.swing.table.TableCellRenderer renderer, int row, int column)
JTable
'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 javax.swing.JTable
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 locationJTable.prepareRenderer(TableCellRenderer renderer, int row, int column)
public java.lang.String getToolTipText(java.awt.event.MouseEvent event)
JTable
's getToolTipText
method
in order to allow the renderer's tips to be used if they have text set.
getToolTipText
in class javax.swing.JTable
event
- MouseEvent the event that triggered the tool tip display
JTable.getToolTipText(MouseEvent event)
protected javax.swing.table.JTableHeader createDefaultTableHeader()
JTable
's createDefaultTableHeader
method.
createDefaultTableHeader
in class javax.swing.JTable
TableHeaderFunction
, i.e, a specific table
header for a table of functionsJTable.columnModel
,
JTable.createDefaultTableHeader()
,
applicationgui.utils.TableHeader#TableHeader(TableColumnModel cm)
protected static java.lang.Object[][] constructRowData(smadeira.biclustering.Biclustering biclustering, java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary, boolean postProcessed) throws InvalidNodeObjectTypeException
The final structure of the row data is:
for GROUPS OF BICLUSTERS
1st column - Bicluster ID
2nd column - Number of Genes
3rd column - Number of Conditions
4th column - Best p-value
5th column - Best corrected p-value
6th column - Number of significant functions
7th column - Number of highly significant functions
8th column - P-value user's threshold
9th column - Number of significant functions (user's threshold)
for POST-PROCESSED GROUPS OF BICLUSTERS
1st column - Post-Processed ID
2nd column - Bicluster ID
3rd column - Number of Genes
4th column - Number of Conditions
5th column - Best p-value
6th column - Best corrected p-value
7th column - Number of significant functions
8th column - Number of highly significant functions
9th column - P-value user's threshold
10th column - Number of significant functions (user's threshold)
biclustering
- the Biclustering
object which provides the
data needed to create the row data matrixbiologicalRelevanceSummary
- Hashtable
contains
the summary of function analysis results for all the
biclusters in the group of biclusters (biclustering
)postProcessed
- boolean
true
if
biclustering
is a post-processed biclusters
group object
Object[][]
row data matrix, ready to be used by
TableFunctionGroup
's constructor
InvalidNodeObjectTypeException
- when the type of the biclustering object is not validpublic static java.lang.String[] columnNames(boolean postProcessed)
postProcessed
- boolean
true
if
biclustering
is a post-processed biclusters
group object
String[]
set of abbreviated columns namespublic static java.lang.String[] completeColumnNames(boolean postProcessed)
postProcessed
- boolean
true
if
biclustering
is a post-processed biclusters
group object
String[]
set of complete columns namespublic java.awt.Color getSignificantColor()
Color
used to mark significant terms.
public java.awt.Color getEvenRowsColor()
Color
used to mark even rows that are not selected.
public java.awt.Color getOddRowsColor()
Color
used to mark odd rows that are not selected.
public void setSignificantColor(java.awt.Color newSignificantColor)
newSignificantColor
- Color
to mark
significant termspublic void setEvenRowsColor(java.awt.Color newEvenRowsColor)
newEvenRowsColor
- Color
to mark even
rows that are not selectedpublic void setOddRowsColor(java.awt.Color newOddRowsColor)
newOddRowsColor
- Color
to mark odd
rows that are not selected
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