biggests.tables
Class TableFunctionIndividual

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JTable
                  extended by biggests.tables.TableFunctionIndividual
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.RowSorterListener, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener, javax.swing.Scrollable

public class TableFunctionIndividual
extends javax.swing.JTable

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.

See Also:
Serialized Form

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
javax.swing.JTable.AccessibleJTable, javax.swing.JTable.DropLocation, 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.BaselineResizeBehavior, 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
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
 
Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
  TableFunctionIndividual(smadeira.biclustering.Bicluster bicluster, smadeira.ontologizer.GeneSetResult goProperties, smadeira.ontologizer.GOFrontEnd go, float pValueThreshold, java.awt.Component parent)
           Creates a new table of functions from the data of a bicluster object.
  TableFunctionIndividual(smadeira.ontologizer.GeneSetResult goProperties, smadeira.ontologizer.GOFrontEnd go, java.lang.String[] genesNames)
          Creates a new function table from the given GO terms.
  TableFunctionIndividual(smadeira.ontologizer.GeneSetResult goProperties, smadeira.ontologizer.GOFrontEnd go, java.lang.String[] genesNames, float pValueThreshold)
          Creates a new function table from the given GO terms.
  TableFunctionIndividual(smadeira.biclustering.IMatrix matrix, smadeira.ontologizer.GOFrontEnd go)
          Creates a new function table from the GO terms infotmation in matrix.
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
 

Field Detail

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.

Constructor Detail

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 IDGO Term Name#Ann. Pop. Genes#Ann. Set GenesP-Value Corrected P.Value
GO:0007275 development3720.0093..1.0
GO:0051704interaction...1610.0831..1.0
..................

Parameters:
bicluster - the Bicluster from which the function table is created
goProperties - the GeneSetResult for the given bicluster
go - GOFrontEnd the GO frontend to the gene ontology for this table's population of genes
pValueThreshold - 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 IDGO Term Name#Ann. Pop. Genes
GO:0007275 development37
GO:0051704interaction...16
.........

Parameters:
matrix - the IMatrix which contains the GO terms to present in the table
go - 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 IDGO Term Name#Ann. Pop. Genes#Ann. Set GenesP-Value Corrected P.Value
GO:0007275 development3720.0093..1.0
GO:0051704interaction...1610.0831..1.0
..................

Parameters:
goProperties - the GeneSetResult which contains the GO terms annotated for the genes
go - GOFrontEnd the GO frontend to the gene ontology for this table's population of genes
genesNames - String[] the names of the genes in gene set
pValueThreshold - 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 IDGO Term Name#Ann. Pop. Genes
GO:0007275 development37
GO:0051704interaction...16
.........

Parameters:
goProperties - the GeneSetResult which contains the GO terms annotated for the genes
go - GOFrontEnd the GO frontend to the gene ontology for this table's population of genes
genesNames - 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 IDGO Term Name#Ann. Pop. Genes#Ann. Set GenesP-Value Corrected P.Value
GO:0007275 development3720.0093..1.0
GO:0051704interaction...1610.0831..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 genes
pValueThreshold - 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 IDGO Term Name#Ann. Pop. Genes#Ann. Set GenesP-Value Corrected P.Value
GO:0007275 development3720.0093..1.0
GO:0051704interaction...1610.0831..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 genes
highlySignificantPValueThreshold - 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 IDGO Term Name#Ann. Pop. Genes
GO:0007275 development37
GO:0051704interaction...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 IDGO Term Name#Ann. Pop. Genes#Ann. Set GenesP-Value Corrected P.Value
GO:0007275 development3720.0093..1.0
GO:0051704interaction...1610.0831..1.0
..................

Parameters:
tableSorterModel - the TableSorterFunctionIndividual model for the table
go - GOFrontEnd the GO frontend to the gene ontology for this table's population of genes
pValueThreshold - 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 IDGO Term Name#Ann. Pop. Genes#Ann. Set GenesP-Value Corrected P.Value
GO:0007275 development3720.0093..1.0
GO:0051704interaction...1610.0831..1.0
..................

Parameters:
tableSorterModel - the TableSorterFunctionIndividual model for the table
go - GOFrontEnd the GO frontend to the gene ontology for this table's population of genes
highlySignificantPValueThreshold - 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 IDGO Term Name#Ann. Pop. Genes
GO:0007275 development37
GO:0051704interaction...16
.........

Parameters:
tableSorterModel - TableSorterFunctionIndividual the model to build the table from
go - GOFrontEnd the GO frontend to the gene ontology for this table's population of genes
Method Detail

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 prepare
row - the row of the cell to render, where 0 is the first row
column - 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 terms
onlyTerms - 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