loci.ome.editor

Class MetadataPane

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

loci.ome.editor.MetadataPane

All Implemented Interfaces:

ActionListener, ImageObserver, MenuContainer, Serializable, Runnable, EventListener, Accessible

public class MetadataPane
extends JPanel
implements ActionListener, Runnable

A panel that displays OME-XML metadata. Most of the gui code is in here. If you want a panel instead of a window, instantiate this instead of MetadataEditor. Sadly you lose quite a bit of functionality such as the various views if you choose to directly instatiate.

Source code:

Trac, Gitweb

Author:

Christopher Peterson crpeterson2 at wisc.edu

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	MetadataPane.TablePanel Helper class to handle the various TablePanels that will be created to display the attributes of Elements that have no nested Elements
class	MetadataPane.TabPanel Helper class to make my life easier in the creation and use of tabs associates a given xml template element and also an optional OMEXMLNode with a JPanel that represents the content of a tab.

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

JPanel.AccessibleJPanel

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

JComponent.AccessibleJComponent

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
static Color	ADD_COLOR The color that signifies a button's operation is to add something.
protected Vector	addItems A list of external references to be added to the combobox cell editor.
protected boolean	addSave If true, the save button should be display in each TabPanel.
protected File	currentFile Holds the currently edited file, or null if none.
static ImageIcon	DATA_BULLET An icon that signifies metadata is present.
static Color	DELETE_COLOR The color that signifies a button's operation is to delete something.
protected boolean	editable Whether or not the user should be able to edit metadata.
protected String	fileID
boolean	hasChanged Signifies that the current file has changed from the last saved version.
BufferedImage[]	images
BufferedImage	img Holds the first image of a tiff file.
Hashtable	internalDefs Hashtable containing internal semantic type defs in current file.
protected OMEXMLMetadata	ms
static ImageIcon	NO_DATA_BULLET An icon that signifies no metadata is present.
protected File	originalTIFF Holds the original file if it is of TIFF format.
protected Vector	panelList A list of all TablePanel objects.
protected Vector	panelsWithID A list of TablePanel objects that have ID attributes.
protected boolean	raw Whether XML is being displayed in raw form.
protected JPanel	rawPanel Panel containing raw XML dump.
protected JTextArea	rawText Text area displaying raw XML.
protected BufferedImageReader	reader Holds the image reader used to open image or null if none used.
protected boolean	showIDs Whether or not to display ID attributes.
protected JTabbedPane	tabPane Pane containing XML tree.
protected Vector	tabPanelList A list of the TabPanels.
static Color	TEXT_COLOR The main text color of most things.
protected org.openmicroscopy.xml.OMENode	thisOmeNode Keeps track of the OMENode being operated on currently.
BufferedImage	thumb Holds the first image of a tiff file.
BufferedImage[]	thumbs
protected Hashtable	tiffDataStore
protected TemplateParser	tParse TemplateParser object.
protected static String[]	TREE_COLUMNS Defines the names of columns in the TablePanels.

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

Constructors

Constructor and Description
MetadataPane() Constructs default widget for displaying OME-XML metadata.
MetadataPane(File file) Constructs a pane to display the OME-XML metadata of a given file.
MetadataPane(File file, boolean save) Constructs a pane to display the OME-XML metadata of a given file and with the given save policy.
MetadataPane(File file, boolean save, boolean editMe) Constructs a pane to display the OME-XML metadata of a given file with the given save and editing policy.

Method Summary

Methods

Modifier and Type	Method and Description
void	actionPerformed(ActionEvent e) Handle the "QuickSave" button actions.
String	addTiffData(String xml, File file)
void	askCompanionInstead(File file)
boolean	checkOMETiff(File file)
protected static ImageIcon	createImageIcon(String path, String description) Returns an ImageIcon, or null if the path was invalid.
Document	getDoc() Retrieves the current document object describing the whole OMEXMLNode tree.
static int	getKey(int i) Converts a number into the KeyEvent for that number.
org.openmicroscopy.xml.OMENode	getRoot() Get the OMENode currently being edited.
boolean	getState() Tells whether or not the XML has changed due to user manipulation.
static Vector	getTreePathList(Element e) Returns a vector of Strings representing the XMLNames of the template's ancestors in ascending order in the list.
static String	getTreePathName(Element e) Get a path name for an element in the template.
static String	getTreePathName(Element el, OMEXMLNode on) Get a path name for a given OMEXMLNode found in the current file being edited based on the template.
static boolean	isInCustom(String tagName) Tests if the given tagname should be placed under a CustomAttributesNode.
static OMEXMLNode	makeNode(String unknownName, OMEXMLNode parent) Return a new node of type specified by unknownName with the specified parent.
void	merge()
void	renderTab(MetadataPane.TabPanel tp) Fleshes out the GUI of a given TabPanel, adding TablePanels appropriately.
void	reRender() resets all gui to reflect changes to the node tree
void	run() Shows or hides the proper subpanes.
void	saveCompanionFile(File file)
void	saveFile(File file) Save to the given file.
void	saveTiffFile(File file)
void	saveTiffFile(File file, String outId)
boolean	setOMEXML(File file) Sets the displayed OME-XML metadata to correspond to the given OME-XML or OME-TIFF file.
protected void	setOMEXML(org.openmicroscopy.xml.OMENode ome) Sets the displayed OME-XML metadata.
void	setupTabs() Sets up the JTabbedPane based on a template, assumes that no OMEXML file is being compared to the template, so no data will be displayed.
void	setupTabs(org.openmicroscopy.xml.OMENode ome) sets up the JTabbedPane given an OMENode from an OMEXML file.
void	stateChanged(boolean change) Sets whether or not the XML has changed due to user manipulation.
void	storeTiffData(File file)
void	tabChange(int i) changes the selected tab to tab of index i
boolean	testThirdParty(File file)

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, 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, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, 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, 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, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

TREE_COLUMNS

protected static final String[] TREE_COLUMNS

Defines the names of columns in the TablePanels.

DATA_BULLET

public static final ImageIcon DATA_BULLET

An icon that signifies metadata is present.

NO_DATA_BULLET

public static final ImageIcon NO_DATA_BULLET

An icon that signifies no metadata is present.

ADD_COLOR

public static final Color ADD_COLOR

The color that signifies a button's operation is to add something.

DELETE_COLOR

public static final Color DELETE_COLOR

The color that signifies a button's operation is to delete something.

TEXT_COLOR

public static final Color TEXT_COLOR

The main text color of most things.

tabPane

protected JTabbedPane tabPane

Pane containing XML tree.

tParse

protected TemplateParser tParse

TemplateParser object.

thisOmeNode

protected org.openmicroscopy.xml.OMENode thisOmeNode

Keeps track of the OMENode being operated on currently.

panelList

protected Vector panelList

A list of all TablePanel objects.

panelsWithID

protected Vector panelsWithID

A list of TablePanel objects that have ID attributes.

addItems

protected Vector addItems

A list of external references to be added to the combobox cell editor.

tabPanelList

protected Vector tabPanelList

A list of the TabPanels.

internalDefs

public Hashtable internalDefs

Hashtable containing internal semantic type defs in current file.

hasChanged

public boolean hasChanged

Signifies that the current file has changed from the last saved version.

addSave

protected boolean addSave

If true, the save button should be display in each TabPanel.

editable

protected boolean editable

Whether or not the user should be able to edit metadata.

showIDs

protected boolean showIDs

Whether or not to display ID attributes. By default, is false.

originalTIFF

protected File originalTIFF

Holds the original file if it is of TIFF format.

currentFile

protected File currentFile

Holds the currently edited file, or null if none.

img

public BufferedImage img

Holds the first image of a tiff file.

thumb

public BufferedImage thumb

Holds the first image of a tiff file.

images

public BufferedImage[] images

thumbs

public BufferedImage[] thumbs

reader

protected BufferedImageReader reader

Holds the image reader used to open image or null if none used.

fileID

protected String fileID

tiffDataStore

protected Hashtable tiffDataStore

ms

protected OMEXMLMetadata ms

rawPanel

protected JPanel rawPanel

Panel containing raw XML dump.

rawText

protected JTextArea rawText

Text area displaying raw XML.

raw

protected boolean raw

Whether XML is being displayed in raw form.

Constructor Detail

MetadataPane

public MetadataPane()

Constructs default widget for displaying OME-XML metadata.

MetadataPane

public MetadataPane(File file)

Constructs a pane to display the OME-XML metadata of a given file.

Parameters:

file - The file to be initially displayed.

MetadataPane

public MetadataPane(File file,
            boolean save)

Constructs a pane to display the OME-XML metadata of a given file and with the given save policy.

Parameters:

file - The file to be initially displayed.

save - Whether saving should be allowed.

MetadataPane

public MetadataPane(File file,
            boolean save,
            boolean editMe)

Constructs a pane to display the OME-XML metadata of a given file with the given save and editing policy.

Parameters:

file - the file to open initially

save - whether or not to display the save button

editMe - whether or not the user should be able to edit metadata

Method Detail

getDoc

public Document getDoc()

Retrieves the current document object describing the whole OMEXMLNode tree.

getState

public boolean getState()

Tells whether or not the XML has changed due to user manipulation.

stateChanged

public void stateChanged(boolean change)

Sets whether or not the XML has changed due to user manipulation.

Parameters:

change - Has the XML changed?

getRoot

public org.openmicroscopy.xml.OMENode getRoot()

Get the OMENode currently being edited.

testThirdParty

public boolean testThirdParty(File file)

askCompanionInstead

public void askCompanionInstead(File file)

saveFile

public void saveFile(File file)

Save to the given file.

saveCompanionFile

public void saveCompanionFile(File file)

saveTiffFile

public void saveTiffFile(File file)

saveTiffFile

public void saveTiffFile(File file,
                String outId)

merge

public void merge()

storeTiffData

public void storeTiffData(File file)

addTiffData

public String addTiffData(String xml,
                 File file)

checkOMETiff

public boolean checkOMETiff(File file)

setOMEXML

public boolean setOMEXML(File file)

Sets the displayed OME-XML metadata to correspond to the given OME-XML or OME-TIFF file.

Returns:

true if the operation was successful

setOMEXML

protected void setOMEXML(org.openmicroscopy.xml.OMENode ome)

Sets the displayed OME-XML metadata.

setupTabs

public void setupTabs()

Sets up the JTabbedPane based on a template, assumes that no OMEXML file is being compared to the template, so no data will be displayed. should be used to initialize the application and to create new OMEXML documents based on the template

setupTabs

public void setupTabs(org.openmicroscopy.xml.OMENode ome)

sets up the JTabbedPane given an OMENode from an OMEXML file. the template will set which parts of the file are displayed.

renderTab

public void renderTab(MetadataPane.TabPanel tp)

Fleshes out the GUI of a given TabPanel, adding TablePanels appropriately.

tabChange

public void tabChange(int i)

changes the selected tab to tab of index i

reRender

public void reRender()

resets all gui to reflect changes to the node tree

run

public void run()

Shows or hides the proper subpanes.

Specified by:

run in interface Runnable

actionPerformed

public void actionPerformed(ActionEvent e)

Handle the "QuickSave" button actions.

Specified by:

actionPerformed in interface ActionListener

createImageIcon

protected static ImageIcon createImageIcon(String path,
                        String description)

Returns an ImageIcon, or null if the path was invalid.

getTreePathName

public static String getTreePathName(Element e)

Get a path name for an element in the template.

getTreePathName

public static String getTreePathName(Element el,
                     OMEXMLNode on)

Get a path name for a given OMEXMLNode found in the current file being edited based on the template. Only by calling this method will duplicate OMEXMLNodes be accounted for, e.g. this method adds Project (1) or Project (2) to signify multiple elements.

Parameters:

el - The template element that corresponds to this OMEXMLNode.

on - The OMEXMLNode that we want the path name for.

Returns:

A string representing the OMEXMLNode's path name.

isInCustom

public static boolean isInCustom(String tagName)

Tests if the given tagname should be placed under a CustomAttributesNode.

makeNode

public static OMEXMLNode makeNode(String unknownName,
                  OMEXMLNode parent)

Return a new node of type specified by unknownName with the specified parent. N.B. The Parent can either be the direct parent or the ancestor that has the CustomAttributesNode that is the real parent.

Parameters:

unknownName - The name this new OMEXMLNode should have.

parent - The parent of the new OMEXMLNode. NEVER pass in a CustomAttributesNode, but rather the parent of that CANode.

getTreePathList

public static Vector getTreePathList(Element e)

Returns a vector of Strings representing the XMLNames of the template's ancestors in ascending order in the list.

Parameters:

e - The template element we want the path list for.

Returns:

A vector holding the tagnames of all parent elements.

getKey

public static int getKey(int i)

Converts a number into the KeyEvent for that number.