protected |
TableFunctionIndividual(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
smadeira.ontologizer.GOFrontEnd go)
Creates a new table of functions from the given rowData
and columnNames
1st column - GO Term ID
2nd column - GO Term Name
3rd column - Number of Genes in Population Annotated with the Term
GO Term IDGO Term Name#Ann.
protected |
TableFunctionIndividual(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
smadeira.ontologizer.GOFrontEnd go,
float pValueThreshold)
Creates a new table of functions with terms and p-values data. |
protected |
TableFunctionIndividual(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
smadeira.ontologizer.GOFrontEnd go,
float highlySignificantPValueThreshold,
float significantPValueThreshold)
Creates a new table of functions with GO terms and p-values data. |
protected |
TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
smadeira.ontologizer.GOFrontEnd go)
Creates a new table of functions for the given
tableSorterModel . |
protected |
TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
smadeira.ontologizer.GOFrontEnd go,
float pValueThreshold)
Creates a new table of functions from the given
tableSorterModel . |
protected |
TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
smadeira.ontologizer.GOFrontEnd go,
float highlySignificantPValueThreshold,
float significantPValueThreshold)
Creates a new table of functions for the given tableSorterModel . |
Method Summary |
protected static java.lang.Object[][] |
constructRowData(smadeira.ontologizer.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 |
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 |
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 |
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 |
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 |
HIGHLY_SIGNIFICANT_COLOR
public static final java.awt.Color HIGHLY_SIGNIFICANT_COLOR
- Default color for highly significant terms.
SIGNIFICANT_COLOR
public static final java.awt.Color SIGNIFICANT_COLOR
- Default color for significant terms.
EVEN_ROWS_COLOR
public static final java.awt.Color EVEN_ROWS_COLOR
- Default color for even rows.
ODD_ROWS_COLOR
public static final java.awt.Color ODD_ROWS_COLOR
- Default color for odd rows.
TableFunctionIndividual
public TableFunctionIndividual(smadeira.biclustering.Bicluster bicluster,
smadeira.ontologizer.GeneSetResult goProperties,
smadeira.ontologizer.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
| ... | ... | ... | ... | ... | ...
|
- Parameters:
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
- Throws:
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 it- See Also:
constructRowData(GeneSetResult goProperties, boolean onlyTerms) ,
#TableFunctionGroup(Object[][] rowData, Object[] columnNames))
TableFunctionIndividual
public TableFunctionIndividual(smadeira.biclustering.IMatrix matrix,
smadeira.ontologizer.GOFrontEnd go)
throws java.lang.Exception
- Creates a new function table from the GO terms infotmation
in
matrix . It 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
GO Term ID | GO Term Name | #Ann. Pop. Genes |
|
---|
GO:0007275 | development | 37
| GO:0051704 | interaction... | 16
| ... | ... | ...
|
- Parameters:
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
- Throws:
java.lang.Exception - if GO terms information does not exist- See Also:
#TableFunctionIndividualTable(Object[][] rowData, Object[] columnNames) ,
constructRowData(GeneSetResult goProperties, boolean onlyTerms) ,
getActualColumnNames(boolean onlyTerms)
TableFunctionIndividual
public TableFunctionIndividual(smadeira.ontologizer.GeneSetResult goProperties,
smadeira.ontologizer.GOFrontEnd go,
java.lang.String[] genesNames,
float pValueThreshold)
throws java.lang.Exception
- Creates a new function table from the given GO terms.
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
| ... | ... | ... | ... | ... | ...
|
- Parameters:
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
- Throws:
InvalidNodeObjectTypeException - when the type of the bicluster
object is not valid
java.lang.Exception - if goProperties is empty- See Also:
#constructRowData(Bicluster bicluster) ,
#TableFunctionIndividual(Object[][] rowData, Object[] columnNames))
TableFunctionIndividual
public TableFunctionIndividual(smadeira.ontologizer.GeneSetResult goProperties,
smadeira.ontologizer.GOFrontEnd go,
java.lang.String[] genesNames)
throws java.lang.Exception
- Creates a new function table from the given GO terms.
It 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
GO Term ID | GO Term Name | #Ann. Pop. Genes |
|
---|
GO:0007275 | development | 37
| GO:0051704 | interaction... | 16
| ... | ... | ...
|
- Parameters:
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
- Throws:
java.lang.Exception - if goProperties is empty- See Also:
constructRowData(GeneSetResult goProperties, boolean onlyTerms) ,
getActualColumnNames(boolean onlyTerms) ,
#TableFunctionIndividual(Object[][] rowData, Object[] columnNames))
TableFunctionIndividual
protected TableFunctionIndividual(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
smadeira.ontologizer.GOFrontEnd go,
float pValueThreshold)
throws java.lang.Exception
- Creates a new table of functions with terms and p-values data.
It 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 Bicluster Annotated with the Term
5th column - Hypergeometric P-Value
6th column - Bonferroni Corrected Hypergeometric P-Value
GO terms with hypergeometric p-value lower than 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
| ... | ... | ... | ... | ... | ...
|
- Parameters:
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 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
- Throws:
java.lang.Exception - See Also:
#TableFunctionIndividual(TableSorterFunctionIndividual
tableSorterModel, float pValueThreshold) ,
applicationgui.utils.TableSorter#TableSorter(TableModel tableModel) ,
DefaultTableModel.DefaultTableModel(Object[][]
rowData, Object[] columnNames)
TableFunctionIndividual
protected TableFunctionIndividual(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
smadeira.ontologizer.GOFrontEnd go,
float highlySignificantPValueThreshold,
float significantPValueThreshold)
throws java.lang.Exception
- Creates a new table of functions with GO terms and p-values data.
It 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 Bicluster Annotated with the Term
5th column - Hypergeometric P-Value
6th column - Bonferroni Corrected Hypergeometric P-Value
GO terms with hypergeometric p-value lower than 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
| ... | ... | ... | ... | ... | ...
|
- Parameters:
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[
- Throws:
java.lang.Exception - See Also:
#TableFunctionIndividual(TableSorterFunctionIndividual
tableSorterModel, float highlySignificantPValueThreshold,
float significantPValueThreshold) ,
applicationgui.utils.TableSorter#TableSorter(TableModel tableModel) ,
DefaultTableModel.DefaultTableModel(Object[][]
rowData, Object[] columnNames)
TableFunctionIndividual
protected TableFunctionIndividual(java.lang.Object[][] rowData,
java.lang.Object[] columnNames,
smadeira.ontologizer.GOFrontEnd go)
- Creates a new table of functions from the given
rowData
and columnNames
1st column - GO Term ID
2nd column - GO Term Name
3rd column - Number of Genes in Population Annotated with the Term
GO Term ID | GO Term Name | #Ann. Pop. Genes
|
---|
GO:0007275 | development | 37
| GO:0051704 | interaction... | 16
| ... | ... | ...
|
- Parameters:
rowData - Object[][]columnNames - Object[]go - GOFrontEnd the GO frontend to the gene ontology for this
table's population of genes- See Also:
applicationgui.utils.TableSorter#TableSorter(TableModel tableModel) ,
DefaultTableModel.DefaultTableModel(Object[][]
rowData, Object[] columnNames)
TableFunctionIndividual
protected TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
smadeira.ontologizer.GOFrontEnd go,
float pValueThreshold)
throws java.lang.Exception
- Creates a new table of functions from the given
tableSorterModel .
The table contains the following information:
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 Set Annotated with this 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
| ... | ... | ... | ... | ... | ...
|
- Parameters:
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
- Throws:
java.lang.Exception - See Also:
JTable.JTable(TableModel dm)
TableFunctionIndividual
protected TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
smadeira.ontologizer.GOFrontEnd go,
float highlySignificantPValueThreshold,
float significantPValueThreshold)
throws java.lang.Exception
- Creates a new table of functions for the given
tableSorterModel .
The table contains the following information:
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 Set Annotated with this 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
| ... | ... | ... | ... | ... | ...
|
- Parameters:
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[
- Throws:
java.lang.Exception
TableFunctionIndividual
protected TableFunctionIndividual(TableSorterFunctionIndividual tableSorterModel,
smadeira.ontologizer.GOFrontEnd go)
- Creates a new table of functions for the given
tableSorterModel .
The table contains the following information:
1st column - GO Term ID
2nd column - GO Term Name
3rd column - Number of Genes in Population Annotated with this Term
GO Term ID | GO Term Name | #Ann. Pop. Genes
|
---|
GO:0007275 | development | 37
| GO:0051704 | interaction... | 16
| ... | ... | ...
|
- Parameters:
tableSorterModel - TableSorterFunctionIndividual
the model to build the table fromgo - GOFrontEnd the GO frontend to the gene ontology for this
table's population of genes
prepareRenderer
public java.awt.Component prepareRenderer(javax.swing.table.TableCellRenderer renderer,
int row,
int column)
- Overrides
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.
- Overrides:
prepareRenderer in class javax.swing.JTable
- Parameters:
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
- Returns:
- the
Component under the event location - See Also:
JTable.prepareRenderer(TableCellRenderer renderer, int row, int column)
getToolTipText
public 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.
- Overrides:
getToolTipText in class javax.swing.JTable
- Parameters:
event - MouseEvent the event that triggered the tool tip display
- Returns:
- String the message set as tool tip for the pointed table cell
- See Also:
JTable.getToolTipText(MouseEvent event)
createDefaultTableHeader
protected javax.swing.table.JTableHeader createDefaultTableHeader()
- Overrides
JTable 's createDefaultTableHeader
method.
Creates the default table header for a values' table, that is, a header
with specific text tool tips for this kind of table.
- Overrides:
createDefaultTableHeader in class javax.swing.JTable
- Returns:
- an instance of
TableHeaderFunction , i.e, a specific table
header for a table of functions - See Also:
JTable.columnModel ,
JTable.createDefaultTableHeader() ,
applicationgui.utils.TableHeader#TableHeader(TableColumnModel cm)
constructRowData
protected static java.lang.Object[][] constructRowData(smadeira.ontologizer.GeneSetResult goProperties,
boolean onlyTerms)
throws java.lang.Exception
- Constructs the row data matrix with data retrieved from the bicluster
object.
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.
- Parameters:
goProperties - the GeneSetResult which contains
the annotated GO termsonlyTerms - boolean true if the table
should have only term information, no p-values;
false otherwise
- Returns:
- the
Object[][] row data matrix, ready to be used by
TableFunctionIndividual 's constructor
- Throws:
java.lang.Exception - if gene set result is empty
getHighlySignificantPValueThreshold
public float getHighlySignificantPValueThreshold()
- Returns the p-value threshold for highly significant gene ontology terms.
- Returns:
- float the p-value threshold for significant gene ontology terms
getSignificantPValueThreshold
public float getSignificantPValueThreshold()
- Returns the p-value threshold for significant gene ontology terms.
- Returns:
- float the p-value threshold for significant gene ontology terms
getHighlySignificantColor
public java.awt.Color getHighlySignificantColor()
- Returns the
Color used to mark highly significant terms.
- Returns:
- Color used to mark highly significant terms
getSignificantColor
public java.awt.Color getSignificantColor()
- Returns the
Color used to mark significant terms.
- Returns:
- Color used to mark significant terms
getEvenRowsColor
public java.awt.Color getEvenRowsColor()
- Returns the
Color used to mark even rows that are not selected.
- Returns:
- Color used to mark even rows that are not selected
getOddRowsColor
public java.awt.Color getOddRowsColor()
- Returns the
Color used to mark odd rows that are not selected.
- Returns:
- Color used to mark odd rows that are not selected
getColumnNames
public static java.lang.String[] getColumnNames()
- Returns this table abbreviated columns names.
- Returns:
- the table
String[] set of abbreviated columns names
getCompleteColumnNames
public static java.lang.String[] getCompleteColumnNames()
- Returns this table complete columns names.
- Returns:
- the table
String[] set of complete columns names
getActualColumnNames
public java.lang.String[] getActualColumnNames()
- Returns the actual column names for this table. If this table
displays only terms information (no p-values), columns names
will be three (GO Term ID, GO Term Name, Number of Genes
in Population Annotated with the Term), otherwise will be six
(GO Term ID, GO Term Name, Number of Genes in Population
Annotated with the Term, Number of Genes in Set Annotated
with the Term, Hypergeometric P-Value, Bonferroni Corrected
Hypergeometric P-Value).
- Returns:
- String[] the actual columns names for this table
getActualCompleteColumnNames
public java.lang.String[] getActualCompleteColumnNames()
- Returns the actual complete, not abbreviated column names
for this table. If this table displays only terms information
(no p-values), columns names will be three (GO Term ID, GO Term
Name, Number of Genes in Population Annotated with the Term),
otherwise will be six (GO Term ID, GO Term Name, Number of
Genes in Population Annotated with the Term, Number of Genes in
Set Annotated with the Term, Hypergeometric P-Value, Bonferroni
Corrected Hypergeometric P-Value).
- Returns:
- String[] the actual columns names for this table
getHighlySignificantColor
public void getHighlySignificantColor(java.awt.Color newHighlySignificantColor)
- Sets a new color to mark highly significant terms.
- Parameters:
newHighlySignificantColor - Color to mark
highly significant terms
setSignificantColor
public void setSignificantColor(java.awt.Color newSignificantColor)
- Sets a new color to mark significant terms.
- Parameters:
newSignificantColor - Color to mark
significant terms
setEvenRowsColor
public void setEvenRowsColor(java.awt.Color newEvenRowsColor)
- Sets a new color to mark even rows that are not selected.
- Parameters:
newEvenRowsColor - Color to mark even
rows that are not selected
setOddRowsColor
public void setOddRowsColor(java.awt.Color newOddRowsColor)
- Sets a new color to mark odd rows that are not selected.
- Parameters:
newOddRowsColor - Color to mark odd
rows that are not selected
this_mouseClicked
public void this_mouseClicked(java.awt.event.MouseEvent e)
- Handles the event fired when the user clicks a row of this table.
Shows a popup window with the annotated genes for the clicked term.
- Parameters:
e - MouseEvent the event fired when the user
clicks a row of this table
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