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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.TableFunctionIndividual
public class TableFunctionIndividual
Title: Function Table for an Individual Bicluster
Description: Contains data about function analysis performed on a given bicluster.
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 | |
---|---|
protected static class |
TableFunctionIndividual.FloatCellRenderer
Title: FloatCellRenderer : A renderer for cells which
contain float numbers. |
protected static class |
TableFunctionIndividual.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.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 |
---|
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
---|---|
static java.awt.Color |
EVEN_ROWS_COLOR
Default color for even rows. |
static java.awt.Color |
HIGHLY_SIGNIFICANT_COLOR
Default color for highly significant terms. |
static java.awt.Color |
ODD_ROWS_COLOR
Default color for odd rows. |
static java.awt.Color |
SIGNIFICANT_COLOR
Default color for significant terms. |
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 |
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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 | |
---|---|
|
TableFunctionIndividual(Bicluster bicluster,
GeneSetResult goProperties,
GOFrontEnd go,
float pValueThreshold,
java.awt.Component parent)
Creates a new table of functions from the data of a bicluster object. |
|
TableFunctionIndividual(GeneSetResult goProperties,
GOFrontEnd go,
java.lang.String[] genesNames)
Creates a new function table from the given GO terms. |
|
TableFunctionIndividual(GeneSetResult goProperties,
GOFrontEnd go,
java.lang.String[] genesNames,
float pValueThreshold)
Creates a new function table from the given GO terms. |
|
TableFunctionIndividual(IMatrix matrix,
GOFrontEnd go)
Creates a new function table from the GO terms infotmation in matrix . |
protected |
TableFunctionIndividual(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
GOFrontEnd go,
float highlySignificantPValueThreshold,
float significantPValueThreshold)
Creates a new table of functions with GO terms and p-values data. |
protected |
TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
GOFrontEnd go,
float pValueThreshold)
Creates a new table of functions from the given tableSorterModel . |
protected |
TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
GOFrontEnd go,
float highlySignificantPValueThreshold,
float significantPValueThreshold)
Creates a new table of functions for the given tableSorterModel . |
Method Summary | |
---|---|
protected static java.lang.Object[][] |
constructRowData(GeneSetResult goProperties,
boolean onlyTerms)
Constructs the row data matrix with data retrieved from the bicluster object. |
protected javax.swing.table.JTableHeader |
createDefaultTableHeader()
Overrides JTable 's createDefaultTableHeader
method. |
java.lang.String[] |
getActualColumnNames()
Returns the actual column names for this table. |
java.lang.String[] |
getActualCompleteColumnNames()
Returns the actual complete, not abbreviated column names for this table. |
static java.lang.String[] |
getColumnNames()
Returns this table abbreviated columns names. |
static java.lang.String[] |
getCompleteColumnNames()
Returns this table complete columns names. |
java.awt.Color |
getEvenRowsColor()
Returns the Color used to mark even rows that are not selected. |
java.awt.Color |
getHighlySignificantColor()
Returns the Color used to mark highly significant terms. |
void |
getHighlySignificantColor(java.awt.Color newHighlySignificantColor)
Sets a new color to mark highly significant terms. |
float |
getHighlySignificantPValueThreshold()
Returns the p-value threshold for highly significant gene ontology terms. |
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. |
float |
getSignificantPValueThreshold()
Returns the p-value threshold for significant gene ontology 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. |
void |
this_mouseClicked(java.awt.event.MouseEvent e)
Handles the event fired when the user clicks a row of this table. |
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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public static final java.awt.Color HIGHLY_SIGNIFICANT_COLOR
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 TableFunctionIndividual(Bicluster bicluster, GeneSetResult goProperties, GOFrontEnd go, float pValueThreshold, java.awt.Component parent) throws InvalidNodeObjectTypeException, java.lang.Exception
Creates a new table of functions from the data of a bicluster object.
A table of functions for a bicluster contains the following
information:
1st column - GO Term ID
2nd column - GO Term Name
3rd column - Number of Genes in Population Annotated with the Term
4th column - Number of Genes in Set Annotated with the Term
5th column - Hypergeometric P-Value
6th column - Bonferroni Corrected Hypergeometric P-Value
GO Term ID | GO Term Name | #Ann. Pop. Genes | #Ann. Set Genes | P-Value | Corrected P.Value |
---|---|---|---|---|---|
GO:0007275 | development | 37 | 2 | 0.0093.. | 1.0 |
GO:0051704 | interaction... | 16 | 1 | 0.0831.. | 1.0 |
... | ... | ... | ... | ... | ... |
bicluster
- the Bicluster
from which the
function table is createdgoProperties
- the GeneSetResult
for the given
bicluster
go
- GOFrontEnd the GO frontend to the gene ontology for this
table's population of genespValueThreshold
- the significancy threshold float
p-value to
color significant terms (GO terms are significant if their
Bonferroni corrected hypergeometric p-value is below
pValueThreshold
parent
- the GUI's parent Component
InvalidNodeObjectTypeException
- when the type of the bicluster
object is not valid
java.lang.Exception
- if bicluster
has no gene set result
with GO terms associated with itconstructRowData(GeneSetResult goProperties, boolean onlyTerms)
,
#TableFunctionGroup(Object[][] rowData, Object[] columnNames))
public TableFunctionIndividual(IMatrix matrix, GOFrontEnd go) throws java.lang.Exception
matrix
. It contains the following information:GO Term ID | GO Term Name | #Ann. Pop. Genes | |
---|---|---|---|
GO:0007275 | development | 37 | |
GO:0051704 | interaction... | 16 | |
... | ... | ... |
matrix
- the IMatrix
which contains the GO
terms to present in the tablego
- GOFrontEnd the GO frontend to the gene ontology for this
table's population of genes
java.lang.Exception
- if GO terms information does not exist#TableFunctionIndividualTable(Object[][] rowData, Object[] columnNames)
,
constructRowData(GeneSetResult goProperties, boolean onlyTerms)
,
getActualColumnNames(boolean onlyTerms)
public TableFunctionIndividual(GeneSetResult goProperties, GOFrontEnd go, java.lang.String[] genesNames, float pValueThreshold) throws java.lang.Exception
GO Term ID | GO Term Name | #Ann. Pop. Genes | #Ann. Set Genes | P-Value | Corrected P.Value |
---|---|---|---|---|---|
GO:0007275 | development | 37 | 2 | 0.0093.. | 1.0 |
GO:0051704 | interaction... | 16 | 1 | 0.0831.. | 1.0 |
... | ... | ... | ... | ... | ... |
goProperties
- the GeneSetResult
which contains the
GO terms annotated for the genesgo
- GOFrontEnd the GO frontend to the gene ontology for this
table's population of genesgenesNames
- String[]
the names of the genes in gene setpValueThreshold
- the significancy threshold float
p-value to
color significant terms (GO terms are significant if their
Bonferroni corrected hypergeometric p-value is below
pValueThreshold
InvalidNodeObjectTypeException
- when the type of the bicluster
object is not valid
java.lang.Exception
- if goProperties
is empty#constructRowData(Bicluster bicluster)
,
#TableFunctionIndividual(Object[][] rowData, Object[] columnNames))
public TableFunctionIndividual(GeneSetResult goProperties, GOFrontEnd go, java.lang.String[] genesNames) throws java.lang.Exception
GO Term ID | GO Term Name | #Ann. Pop. Genes | |
---|---|---|---|
GO:0007275 | development | 37 | |
GO:0051704 | interaction... | 16 | |
... | ... | ... |
goProperties
- the GeneSetResult
which contains the
GO terms annotated for the genesgo
- GOFrontEnd the GO frontend to the gene ontology for this
table's population of genesgenesNames
- String[]
the names of the genes in gene set
java.lang.Exception
- if goProperties
is emptyconstructRowData(GeneSetResult goProperties, boolean onlyTerms)
,
getActualColumnNames(boolean onlyTerms)
,
#TableFunctionIndividual(Object[][] rowData, Object[] columnNames))
protected TableFunctionIndividual(java.lang.Object[][] rowData, java.lang.Object[] columnNames, GOFrontEnd go, float highlySignificantPValueThreshold, float significantPValueThreshold) throws java.lang.Exception
pValueThreshold
are colored differently.
GO Term ID | GO Term Name | #Ann. Pop. Genes | #Ann. Set Genes | P-Value | Corrected P.Value |
---|---|---|---|---|---|
GO:0007275 | development | 37 | 2 | 0.0093.. | 1.0 |
GO:0051704 | interaction... | 16 | 1 | 0.0831.. | 1.0 |
... | ... | ... | ... | ... | ... |
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)go
- GOFrontEnd the GO frontend to the gene ontology for this
table's population of geneshighlySignificantPValueThreshold
- float
the maximum
Bonferroni corrected hypergeometric p-value to color highly
significant GO terms; GO terms are highly significant if
their Bonferroni corrected hypergeometric p-value is in
[0, highlySignificantPValueThreshold[significantPValueThreshold
- float
the maximum
p-value to color significant GO terms; GO terms are significant
if their Bonferroni corrected hypergeometric p-value is in
[highlySignificantPValueThreshold, significantPValueThreshold[
java.lang.Exception
#TableFunctionIndividual(TableSorterFunctionIndividual
tableSorterModel, float highlySignificantPValueThreshold,
float significantPValueThreshold)
,
applicationgui.utils.TableSorter#TableSorter(TableModel tableModel)
,
DefaultTableModel.DefaultTableModel(Object[][]
rowData, Object[] columnNames)
protected TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel, GOFrontEnd go, float pValueThreshold) throws java.lang.Exception
tableSorterModel
.
The table contains the following information:GO Term ID | GO Term Name | #Ann. Pop. Genes | #Ann. Set Genes | P-Value | Corrected P.Value |
---|---|---|---|---|---|
GO:0007275 | development | 37 | 2 | 0.0093.. | 1.0 |
GO:0051704 | interaction... | 16 | 1 | 0.0831.. | 1.0 |
... | ... | ... | ... | ... | ... |
tableSorterModel
- the TableSorterFunctionIndividual
model for the tablego
- GOFrontEnd the GO frontend to the gene ontology for this
table's population of genespValueThreshold
- the significancy threshold float
p-value to color significant terms (GO terms are significant
if their Bonferroni corrected hypergeometric p-value is below
pValueThreshold
java.lang.Exception
JTable.JTable(TableModel dm)
protected TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel, GOFrontEnd go, float highlySignificantPValueThreshold, float significantPValueThreshold) throws java.lang.Exception
tableSorterModel
.
The table contains the following information:GO Term ID | GO Term Name | #Ann. Pop. Genes | #Ann. Set Genes | P-Value | Corrected P.Value |
---|---|---|---|---|---|
GO:0007275 | development | 37 | 2 | 0.0093.. | 1.0 |
GO:0051704 | interaction... | 16 | 1 | 0.0831.. | 1.0 |
... | ... | ... | ... | ... | ... |
tableSorterModel
- the TableSorterFunctionIndividual
model for the tablego
- GOFrontEnd the GO frontend to the gene ontology for this
table's population of geneshighlySignificantPValueThreshold
- float
the maximum
Bonferroni corrected hypergeometric p-value to color highly
significant GO terms; GO terms are highly significant if
their Bonferroni corrected hypergeometric p-value is in
[0, highlySignificantPValueThreshold[significantPValueThreshold
- float
the maximum
p-value to color significant GO terms; GO terms are significant
if their Bonferroni corrected hypergeometric p-value is in
[highlySignificantPValueThreshold, significantPValueThreshold[
java.lang.Exception
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(GeneSetResult goProperties, boolean onlyTerms) throws java.lang.Exception
The final structure of the row data is:
1st column - GO Term ID
2nd column - GO Term Name
3rd column - Number of Genes in Population Annotated with this Term
4th column - Number of Genes in Bicluster Annotated with this Term
5th column - Hypergeometric P-Value
6th column - Bonferroni Corrected Hypergeometric P-Value
protected
: it's intended to be used only by the
TableFunctionIndividual
's constructor and
constructors of TableFunctionIndividual
's
subclasses.
static
: because object this
cannot be
referenced by the constructor before it is
actually created.
goProperties
- the GeneSetResult
which contains
the annotated GO termsonlyTerms
- boolean
true
if the table
should have only term information, no p-values;
false
otherwise
Object[][]
row data matrix, ready to be used by
TableFunctionIndividual
's constructor
java.lang.Exception
- if gene set result is emptypublic float getHighlySignificantPValueThreshold()
public float getSignificantPValueThreshold()
public java.awt.Color getHighlySignificantColor()
Color
used to mark highly significant terms.
public 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 static java.lang.String[] getColumnNames()
String[]
set of abbreviated columns namespublic static java.lang.String[] getCompleteColumnNames()
String[]
set of complete columns namespublic java.lang.String[] getActualColumnNames()
public java.lang.String[] getActualCompleteColumnNames()
public void getHighlySignificantColor(java.awt.Color newHighlySignificantColor)
newHighlySignificantColor
- Color
to mark
highly significant termspublic 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 selectedpublic void this_mouseClicked(java.awt.event.MouseEvent e)
e
- MouseEvent
the event fired when the user
clicks a row of this table
|
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