edu.iastate.metnet.metaomgraph
Class MetaOmTablePanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  edu.iastate.metnet.metaomgraph.MetaOmTablePanel

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener, javax.swing.event.ListSelectionListener

public class MetaOmTablePanel
extends javax.swing.JPanel
implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener, javax.swing.event.ChangeListener

A JPanel for displaying information related to a MetaOmProject, and accessing many of MetaOmGraph's functions. The panel contains a JTabbedPane with at least one tab. The first tab is the main project window for MetaOmGraph. It contains row names, gene lists, and buttons for all major MetaOmGraph operations. The second tab is optional, and only appears when the

Author:

Nick Ransom

See Also:

Serialized Form

Nested Class Summary

class

MetaOmTablePanel.ListNameComparator Comparator for comparing names of lists.

Nested classes/interfaces inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

static java.lang.String	ATGENESEARCH_COMMAND
static java.lang.String	DELETE_LIST_COMMAND
static java.lang.String	EDIT_LIST_COMMAND
static java.lang.String	GRAPH_FILTERED_COMMAND
static java.lang.String	GRAPH_LIST_COMMAND
static java.lang.String	GRAPH_SELECTED_COMMAND
static java.lang.String	LIST_FROM_FILTER_COMMAND
static java.lang.String	NEW_LIST_COMMAND
static java.lang.String	PEARSON_COMMAND
static java.lang.String	REMOVE_ALL_CORRELATIONS_COMMAND
static java.lang.String	REMOVE_CORRELATION_COMMAND
static java.lang.String	RENAME_LIST_COMMAND
static java.lang.String	REPORT_COMMAND
static java.lang.String	SAVE_CORRELATION_COMMAND
static java.lang.String	SPEARMAN_COMMAND
static java.lang.String	TAIR_COMMAND

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

MetaOmTablePanel(MetaOmProject project)
Constructs a MetaOmTablePanel from the given MetaOmProject.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e)
void	addExtInfoTab()
void	applyFilter(java.lang.String[] values, boolean caseSensitive)
void	applyFilter(java.lang.String value, boolean caseSensitive)
void	deleteSelectedList()
int[]	getAllTrueRows()
javax.swing.JList	getGeneLists()
CorrelationValue[]	getLastCorrelation()
javax.swing.JTable	getListDisplay()
int	getSelectedGeneIndex()
java.lang.String	getSelectedGeneName()
java.lang.String	getSelectedListName()
TableSorter	getSorter()
javax.swing.JTabbedPane	getTabbedPane()
javax.swing.JTable	getTable()
int	getTrueRow(int row)
int	getTrueSelectedRow()
int[]	getTrueSelectedRows()
void	graphFilteredList() Creates a plot for all the rows allowed by the current filter and displays it in a JInternalFrame.
void	graphSelectedList() Creates a plot for the selected list and displays it in a JInternalFrame.
void	graphSelectedRows() Creates a plot for the selected rows and displays it in a JInternalFrame.
boolean	keepLastCorrelation()
void	launchAtGeneSearch() Opens a browser to the AtGeneSearch results page for the selected rows.
void	launchTAIR() Opens a browser to the TAIR page for the selected rows.
void	makeReport() Generates a report for the selected row.
void	selectList(java.lang.String listName) Selects the given gene list, if it exists.
void	selectNode(java.lang.String findMe)
void	selectRows(java.util.Collection<java.lang.Integer> rows)
void	selectValues(java.lang.String[] values)
void	setExtInfoDividerPos(double pos)
void	setLastCorrelation(CorrelationValue[] lastCorrelation)
void	sizeColumnsToFit() Resizes the columns of the entry table to their initial length.
void	stateChanged(javax.swing.event.ChangeEvent event) Called when this table's MetaOmProject changes.
void	valueChanged(javax.swing.event.ListSelectionEvent event) Called when a new gene list is selected.

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, 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, 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, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, 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, doLayout, 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

GRAPH_LIST_COMMAND

public static final java.lang.String GRAPH_LIST_COMMAND

See Also:

Constant Field Values

GRAPH_SELECTED_COMMAND

public static final java.lang.String GRAPH_SELECTED_COMMAND

See Also:

Constant Field Values

GRAPH_FILTERED_COMMAND

public static final java.lang.String GRAPH_FILTERED_COMMAND

See Also:

Constant Field Values

REPORT_COMMAND

public static final java.lang.String REPORT_COMMAND

See Also:

Constant Field Values

ATGENESEARCH_COMMAND

public static final java.lang.String ATGENESEARCH_COMMAND

See Also:

Constant Field Values

TAIR_COMMAND

public static final java.lang.String TAIR_COMMAND

See Also:

Constant Field Values

LIST_FROM_FILTER_COMMAND

public static final java.lang.String LIST_FROM_FILTER_COMMAND

See Also:

Constant Field Values

DELETE_LIST_COMMAND

public static final java.lang.String DELETE_LIST_COMMAND

See Also:

Constant Field Values

NEW_LIST_COMMAND

public static final java.lang.String NEW_LIST_COMMAND

See Also:

Constant Field Values

EDIT_LIST_COMMAND

public static final java.lang.String EDIT_LIST_COMMAND

See Also:

Constant Field Values

RENAME_LIST_COMMAND

public static final java.lang.String RENAME_LIST_COMMAND

See Also:

Constant Field Values

PEARSON_COMMAND

public static final java.lang.String PEARSON_COMMAND

See Also:

Constant Field Values

SPEARMAN_COMMAND

public static final java.lang.String SPEARMAN_COMMAND

See Also:

Constant Field Values

SAVE_CORRELATION_COMMAND

public static final java.lang.String SAVE_CORRELATION_COMMAND

See Also:

Constant Field Values

REMOVE_CORRELATION_COMMAND

public static final java.lang.String REMOVE_CORRELATION_COMMAND

See Also:

Constant Field Values

REMOVE_ALL_CORRELATIONS_COMMAND

public static final java.lang.String REMOVE_ALL_CORRELATIONS_COMMAND

See Also:

Constant Field Values

Constructor Detail

MetaOmTablePanel

public MetaOmTablePanel(MetaOmProject project)

Constructs a MetaOmTablePanel from the given MetaOmProject.

Parameters:

project - the MetaOmProject to be displayed

Method Detail

stateChanged

public void stateChanged(javax.swing.event.ChangeEvent event)

Called when this table's MetaOmProject changes. Refreshes the gene lists and the entries table.

Specified by:

stateChanged in interface javax.swing.event.ChangeListener

Parameters:

event - a ChangeEvenet object

selectList

public void selectList(java.lang.String listName)

Selects the given gene list, if it exists.

Parameters:

listName - the name of the list to select

sizeColumnsToFit

public void sizeColumnsToFit()

Resizes the columns of the entry table to their initial length. Column widths will be a) wide enough to display the longest element in that column, b) wide enough to display the longest element in that column up to the first semicolon (if one exists), or c) 300 pixels. Whichever's smaller.

valueChanged

public void valueChanged(javax.swing.event.ListSelectionEvent event)

Called when a new gene list is selected. Loads the selected list's entries into the entries table.

Specified by:

valueChanged in interface javax.swing.event.ListSelectionListener

Parameters:

event - a ListSelectionEvent object

launchAtGeneSearch

public void launchAtGeneSearch()

Opens a browser to the AtGeneSearch results page for the selected rows. Displays an error if there are no gene IDs in the selected rows.

launchTAIR

public void launchTAIR()

Opens a browser to the TAIR page for the selected rows. Displays an error if there are no Locus IDs in the selected rows.

makeReport

public void makeReport()

Generates a report for the selected row. Currently, this can only be used to find columns in which the value of the row is greater than a given value.

graphSelectedRows

public void graphSelectedRows()

Creates a plot for the selected rows and displays it in a JInternalFrame. Only to be used with MetaOmGraph.

graphSelectedList

public void graphSelectedList()

Creates a plot for the selected list and displays it in a JInternalFrame. Only to be used with MetaOmGraph.

graphFilteredList

public void graphFilteredList()

Creates a plot for all the rows allowed by the current filter and displays it in a JInternalFrame. Only to be used with MetaOmGraph.

deleteSelectedList

public void deleteSelectedList()

getSelectedGeneName

public java.lang.String getSelectedGeneName()

getSelectedGeneIndex

public int getSelectedGeneIndex()

addExtInfoTab

public void addExtInfoTab()

selectNode

public void selectNode(java.lang.String findMe)

setExtInfoDividerPos

public void setExtInfoDividerPos(double pos)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

getTrueRow

public int getTrueRow(int row)

getAllTrueRows

public int[] getAllTrueRows()

getTrueSelectedRow

public int getTrueSelectedRow()

getTrueSelectedRows

public int[] getTrueSelectedRows()

getSorter

public TableSorter getSorter()

getTable

public javax.swing.JTable getTable()

selectRows

public void selectRows(java.util.Collection<java.lang.Integer> rows)

selectValues

public void selectValues(java.lang.String[] values)

applyFilter

public void applyFilter(java.lang.String[] values,
                        boolean caseSensitive)

applyFilter

public void applyFilter(java.lang.String value,
                        boolean caseSensitive)

getLastCorrelation

public CorrelationValue[] getLastCorrelation()

setLastCorrelation

public void setLastCorrelation(CorrelationValue[] lastCorrelation)

keepLastCorrelation

public boolean keepLastCorrelation()

getTabbedPane

public javax.swing.JTabbedPane getTabbedPane()

getSelectedListName

public java.lang.String getSelectedListName()

getListDisplay

public javax.swing.JTable getListDisplay()

Returns:

Returns the listDisplay.

getGeneLists

public javax.swing.JList getGeneLists()

Returns:

Returns the geneLists.