A B C D E F G H I J L M N O P Q R S T U V W X

A

AbstractMdeBean - class edu.ucsb.nceas.metaedit.AbstractMdeBean.
 
AbstractMdeBean() - Constructor for class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
AccessionNumber - class edu.ucsb.nceas.morpho.datapackage.AccessionNumber.
Class that implements Accession Number utility functions for morpho
AccessionNumber(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.datapackage.AccessionNumber
 
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.metaedit.Options
Processes events generated when the user clicks the dialog buttons.
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
Handle any events passed to the class.
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.metaedit.NewDialog
Handle events for this dialog.
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.metaedit.Inputer
Handle events passed to this dialog window.
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
Handle OK button events.
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.EntityGUI
Handles actions from all components in the Container
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
Handles actions from all components in the Container
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShell
Handles actions from all components in the Container
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard
handles the actions from the menus if this package wizard is run in stand alone mode.
addCellEditorListener(CellEditorListener) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
addCellEditorListener(CellEditorListener) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
addChild(QueryGroup) - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
Add a child QueryGroup to this QueryGroup
addChild(QueryTerm) - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
Add a child QueryTerm to this QueryGroup
addChild(String, int, String, String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Add a child node to the specified parent
addChildNode(BasicNode) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Add a child node to this node
addConnectionListener(ConnectionListener) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to register a listener for changes in the Connection status.
addMenu(String, Integer) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to register a menu that the plugin wants created, but that currently has no items.
addMenu(String, Integer, Action[]) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to register a menu and its associated Actions.
AddMetadataWizard - class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard.
A graphical window for adding new files to a package
AddMetadataWizard(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
Construct a dialog and set the framework
AddMetadataWizard(ClientFramework, boolean, DataPackage) - Constructor for class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
Construct the dialog
addNotify() - Method in class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 
addNotify() - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
addNotify() - Method in class edu.ucsb.nceas.morpho.editor.edit_plugin
Notifies this component that it has been added to a container This method should be called by Container.add, and not by user code directly.
addNotify() - Method in class edu.ucsb.nceas.morpho.editor.EditorController
Notifies this component that it has been added to a container This method should be called by Container.add, and not by user code directly.
addNotify() - Method in class edu.ucsb.nceas.morpho.framework.SplashFrame
Override addNotify -- vis cafe does this, but why?
addNotify() - Method in class edu.ucsb.nceas.morpho.framework.ConnectionFrame
Adjust the window size
addNotify() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Notifies this component that it has been added to a container This method should be called by Container.add, and not by user code directly.
addNotify() - Method in class edu.ucsb.nceas.morpho.query.QueryDialog
Used by visual cafe -- but why?
addSchema(String, String, String, String, String) - Method in class edu.ucsb.nceas.metaedit.Options
Adds a document type to the list and the schema hash table
addService(Class, ServiceProvider) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to register a particular service that the plugin can perform.
addToolbarActions(Action[]) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to register a toolbar Action.
addTriple(Triple) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
Add a single triple to this collection
addTriplesToTriplesFile(TripleCollection, DataPackage, ClientFramework) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
method to add a collection of triples to a triples file.
addWindow(JFrame) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to register a Window that the plugin has created.
appendElement(Element, Element) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
appendElement(Element, Element) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
AttrEditFrame - class edu.ucsb.nceas.metaedit.AttrEditFrame.
A TableModelListener is implemented in the data model below.
AttrEditFrame.AttrJTableModel - class edu.ucsb.nceas.metaedit.AttrEditFrame.AttrJTableModel.
 
AttrEditFrame.CustomCellEditor - class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.
 
AttrEditFrame.CustomCellEditor.JComboBoxWithListeners - class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners.
 
AttrEditFrame.CustomCellEditor(AttrEditFrame, JTextField) - Constructor for class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor
 
AttrEditFrame.DataElement - class edu.ucsb.nceas.metaedit.AttrEditFrame.DataElement.
 
AttrEditFrame.DataElement1 - class edu.ucsb.nceas.metaedit.AttrEditFrame.DataElement1.
 
AttrEditFrame.DataElementNAME_TOKEN_GROUP - class edu.ucsb.nceas.metaedit.AttrEditFrame.DataElementNAME_TOKEN_GROUP.
 
AttrEditFrame() - Constructor for class edu.ucsb.nceas.metaedit.AttrEditFrame
Construct a new ElementChoice dialog in the containing frame.
AttributeEditDialog - class edu.ucsb.nceas.morpho.editor.AttributeEditDialog.
This is a simple dialog which allows the viewing/editing of the attributes of an XML element as stored in the DocFrame JTree XML editor.
AttributeEditDialog() - Constructor for class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 
AttributeEditDialog(Frame) - Constructor for class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 
AttributeEditDialog(Frame, String, DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
dialog is given a DefaultMutableTreeNode (nd) with the attribute data to be displayed
AttributeEditDialog(String) - Constructor for class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 

B

BasicNode - class edu.ucsb.nceas.morpho.query.BasicNode.
A Class that represents an XML node and its contents
BasicNode() - Constructor for class edu.ucsb.nceas.morpho.query.BasicNode
Construct a Basic Node
BasicNode(long, String, long, int) - Constructor for class edu.ucsb.nceas.morpho.query.BasicNode
Construct a Basic Node
BasicNode(String) - Constructor for class edu.ucsb.nceas.morpho.query.BasicNode
Construct a Basic Node
BasicNode(String, long, int) - Constructor for class edu.ucsb.nceas.morpho.query.BasicNode
Construct a Basic Node
BOTH - Static variable in class edu.ucsb.nceas.morpho.datapackage.DataPackage
used to signify that this package is stored on metacat and locally.
breadthFirstEnumeration() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
buildMinimalLegalTree(ElementFactory.TreeElement, String) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
buildTree(DefaultMutableTreeNode) - Method in class edu.ucsb.nceas.morpho.editor.DTDTree
 

C

CacheAccessException - exception edu.ucsb.nceas.morpho.framework.CacheAccessException.
This exception is thrown when a service request is made of an object and that object can not properly handle the request, either because it is not designed to handle it, or there was an error in trying to handle it.
CacheAccessException(String) - Constructor for class edu.ucsb.nceas.morpho.framework.CacheAccessException
 
cachedir - Variable in class edu.ucsb.nceas.morpho.framework.DataStore
 
cancelAttrTable() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
cancelCellEditing() - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
cancelCellEditing() - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
cellEditorInit() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor
 
characters(char[], int, int) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
characters(char[], int, int) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleParser
 
characters(char[], int, int) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
 
characters(char[], int, int) - Method in class edu.ucsb.nceas.morpho.query.Query
callback method used by the SAX Parser when the text sequences of an xml stream are detected.
characters(char[], int, int) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
SAX handler callback that is called for character content of an element when parsing an XML document.
checkForService(Class) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to determine if a particular service has been registered and is available.
children() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
clearAppendablesList() - Method in class edu.ucsb.nceas.metaedit.ElementChoice
 
clearAttrTable() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
Clear the attribute table so it is blank.
ClientFramework - class edu.ucsb.nceas.morpho.framework.ClientFramework.
The ClientFramework is the main entry point for the Morpho application.
ClientFramework(ConfigXML) - Constructor for class edu.ucsb.nceas.morpho.framework.ClientFramework
Creates a new instance of ClientFramework
ClientFramework(String, ConfigXML) - Constructor for class edu.ucsb.nceas.morpho.framework.ClientFramework
Creates a new instance of ClientFramework with the given title.
componentHidden(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
 
componentHidden(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.Inputer
 
componentMoved(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
 
componentMoved(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.Inputer
 
componentResized(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Reset the preferred size of the element choice frame whenever the user resizes the frame.
componentResized(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.Inputer
Reset the preferred size of the text input/edit frame whenever the user resizes the frame.
componentShown(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
 
componentShown(ComponentEvent) - Method in class edu.ucsb.nceas.metaedit.Inputer
 
ConfigXML - class edu.ucsb.nceas.morpho.framework.ConfigXML.
This class is designed to store configuration information in an XML file.
ConfigXML(String) - Constructor for class edu.ucsb.nceas.morpho.framework.ConfigXML
String passed to the creator is the XML config file name
connectionChanged(boolean) - Method in interface edu.ucsb.nceas.morpho.framework.ConnectionListener
This method is called if there is a change in the connection status.
connectionChanged(boolean) - Method in class edu.ucsb.nceas.morpho.query.QueryPlugin
Implement the ConnectionListener interface so we know when to refresh queries.
ConnectionFrame - class edu.ucsb.nceas.morpho.framework.ConnectionFrame.
A graphical window for obtaining login information from the user and logging into Metacat
ConnectionFrame(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.framework.ConnectionFrame
Construct a frame and set the framework
ConnectionFrame(ClientFramework, boolean) - Constructor for class edu.ucsb.nceas.morpho.framework.ConnectionFrame
Construct the frame
ConnectionListener - interface edu.ucsb.nceas.morpho.framework.ConnectionListener.
Any object that is interested in the status of the morpho framework connection should implement this interface and register with the framework to be notified of changes, including changes to the username and connection status.
ConnectTest - class edu.ucsb.nceas.morpho.framework.tests.ConnectTest.
A JUnit test for testing the connection capabilities of the framework.
ConnectTest(String) - Constructor for class edu.ucsb.nceas.morpho.framework.tests.ConnectTest
Constructor to build the test
container - Variable in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
containsExtendedSQL() - Method in class edu.ucsb.nceas.morpho.query.Query
Returns true if the parsed query contains and extended xml query (i.e.
containsTriple(Triple) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
returns true if the collection contains triple, false otherwise
ContentEditFrame - class edu.ucsb.nceas.metaedit.ContentEditFrame.
Internal window frame for editing XML document content
ContentEditFrame() - Constructor for class edu.ucsb.nceas.metaedit.ContentEditFrame
Construct a new internal PreviewFrame window and set its dimension and location.
copy(File, File) - Static method in class edu.ucsb.nceas.morpho.framework.FileUtils
Copy one file to another, given Files as inputs
copy(File, File, Hashtable) - Static method in class edu.ucsb.nceas.morpho.framework.FileUtils
Copy one file to another, given Files as inputs, and substitute special tokens with their corresponding values
copy(String, String) - Static method in class edu.ucsb.nceas.morpho.framework.FileUtils
Copy one file to another, given their file names as inputs
copy(String, String, Hashtable) - Static method in class edu.ucsb.nceas.morpho.framework.FileUtils
Copy one file to another, given their file names as inputs, and substitute special tokens with their corresponding values
counter - Static variable in class edu.ucsb.nceas.morpho.editor.DocFrame
counter for name
createElement(String) - Method in class edu.ucsb.nceas.metaedit.ElementFactory
 
createElement(String) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
createElement(String) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
createObject(Constructor, Object[]) - Static method in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
createTextNode(char[], int, int, boolean) - Method in class edu.ucsb.nceas.metaedit.ElementFactory
 
createTextNode(String, boolean) - Method in class edu.ucsb.nceas.metaedit.ElementFactory
 
createTextNode(String, boolean) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
createTextNode(String, boolean) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
CustomTreeCellRenderer - class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer.
 
CustomTreeCellRenderer() - Constructor for class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 

D

datadir - Variable in class edu.ucsb.nceas.morpho.framework.DataStore
 
DataPackage - class edu.ucsb.nceas.morpho.datapackage.DataPackage.
class that represents a data package.
DataPackage(String, String, Vector, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.datapackage.DataPackage
Create a new data package object with an id, location and associated relations.
DataPackageGUI - class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI.
Class that implements a GUI to edit a data package
DataPackageGUI(ClientFramework, DataPackage) - Constructor for class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
DataPackageInterface - interface edu.ucsb.nceas.morpho.framework.DataPackageInterface.
All component plugins that handle access to data packages should implement this interface and register themselves as a service provider for the interface withthe framework.
DataPackagePanel - class edu.ucsb.nceas.morpho.editor.DataPackagePanel.
DataPackagePanel is an example of a plug-in panel to be used by the XML editor.
DataPackagePanel(DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.DataPackagePanel
 
DataPackagePlugin - class edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin.
Class that implements the plugin for package editing
DataPackagePlugin() - Constructor for class edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin
Construct the plugin.
DataStore - class edu.ucsb.nceas.morpho.framework.DataStore.
creates an abstract class for getting files from any dataStore using the same methods.
DataStore(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.framework.DataStore
create a new FileSystemDataStore for a ClientFramework
DataStoreInterface - interface edu.ucsb.nceas.morpho.framework.DataStoreInterface.
creates an interface for getting files from any dataStore using the same methods.
debug(int, String) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
 
debug(int, String) - Static method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Print debugging messages based on severity level, where severity level 1 are the most critical and higher numbers are more trivial messages.
deepNodeCopy(DefaultMutableTreeNode) - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
delete(String) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
Deletes the package from the specified location
delete(String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin
Deletes the package.
delete(String, String) - Method in interface edu.ucsb.nceas.morpho.framework.DataPackageInterface
This method is called to delete a datapackage from metacat or the local disk.
deleteFile(String) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
 
deleteFile(String) - Method in class edu.ucsb.nceas.morpho.framework.MetacatDataStore
deletes a file from metacat.
deleteFile(String) - Method in interface edu.ucsb.nceas.morpho.framework.DataStoreInterface
Deletes the file with an id of name.
deleteFile(String) - Method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
deletes a file from the local file system.
deleteTriplesInTriplesFile(String, DataPackage, ClientFramework) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
method to delete triples with a specified string from the triples file
DELIMITER - Static variable in class edu.ucsb.nceas.morpho.framework.FileUtils
 
DFHPanel - class edu.ucsb.nceas.morpho.editor.DFHPanel.
DFHPanel is an example of a class that can be dynamically loaded at run time to edit a specific part of an XML document tree.
DFHPanel() - Constructor for class edu.ucsb.nceas.morpho.editor.DFHPanel
Default constructor.
DFHPanel(DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.DFHPanel
The primary constructor used to dynamically load the class.
doc - Variable in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
DocFrame - class edu.ucsb.nceas.morpho.editor.DocFrame.
DocFrame is a container for an XML editor which shows combined outline and nested panel views of an XML document.
DocFrame() - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
This constructor builds the contents of the DocFrame Display
DocFrame(ClientFramework, String, String) - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
This constructor actual handles the creation of a tree and panel for displaying and editing the information is an XML document, as represented in the String 'doctext'
DocFrame(ClientFramework, String, String, String, String) - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
this version of the constructor is needed so that each DocFrame can 'remember' the id and location parameters used to create it
DocFrame(ClientFramework, String, String, String, String, String, String) - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
this version allows one to create a new DocFrame and set the initially selected nodename/nodetext
DocFrame(ClientFramework, String, Vector, String, String, String, String) - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
this version will create a new DocFrame using a Vector of XML strings.
DocFrame(File) - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
 
DocFrame(String) - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
Constructor which adds a title string to the Frame
DocFrame(String, String) - Constructor for class edu.ucsb.nceas.morpho.editor.DocFrame
Constructor which adds a title and passes the xml to display as a string; puts XML into tree
documentJTree - Variable in class edu.ucsb.nceas.metaedit.XMLPanels
 
documentPublicID - Variable in class edu.ucsb.nceas.metaedit.DocumentTypeInfo
The Public ID for the document
documentTypeDescription - Variable in class edu.ucsb.nceas.metaedit.DocumentTypeInfo
A more verbose description of the document type.
DocumentTypeInfo - class edu.ucsb.nceas.metaedit.DocumentTypeInfo.
Stores information related to the document type in a consolidated structure.
DocumentTypeInfo(String, String, String, String) - Constructor for class edu.ucsb.nceas.metaedit.DocumentTypeInfo
Constructor that initializes all document type information fields to the passed in values.
DocumentTypeInfo(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metaedit.DocumentTypeInfo
 
documentTypeName - Variable in class edu.ucsb.nceas.metaedit.DocumentTypeInfo
The label used to name and access the document type.
documentTypeRoot - Variable in class edu.ucsb.nceas.metaedit.DocumentTypeInfo
The root element of the document type.
documentTypeURL - Variable in class edu.ucsb.nceas.metaedit.DocumentTypeInfo
The file or network location of the document DTD.
download() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
Downloads a metacat package to the local disk
download(String) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin
Downloads the package from metacat.
download(String) - Method in interface edu.ucsb.nceas.morpho.framework.DataPackageInterface
This method is called to download a datapackage from metacat to the local disk.
dtd - Variable in class edu.ucsb.nceas.morpho.editor.DTDTree
 
dtdtree - Variable in class edu.ucsb.nceas.morpho.editor.DocFrame
 
DTDTree - class edu.ucsb.nceas.morpho.editor.DTDTree.
class for creating a treeModel based on structure defined in DTD.
DTDTree() - Constructor for class edu.ucsb.nceas.morpho.editor.DTDTree
 
DTDTree(String) - Constructor for class edu.ucsb.nceas.morpho.editor.DTDTree
 
dtm - Variable in class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 
dtm - Variable in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 

E

edit_plugin - class edu.ucsb.nceas.morpho.editor.edit_plugin.
A basic JFC 1.1 based application.
edit_plugin() - Constructor for class edu.ucsb.nceas.morpho.editor.edit_plugin
 
edit_plugin(ClientFramework, String) - Constructor for class edu.ucsb.nceas.morpho.editor.edit_plugin
 
edit_plugin(String) - Constructor for class edu.ucsb.nceas.morpho.editor.edit_plugin
Creates a new instance of JFrame1 with the given title.
editingCanceled(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.EntityGUI
 
editingCanceled(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
editingCanceled(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
editingCanceled(String, String, String) - Method in class edu.ucsb.nceas.morpho.editor.edit_plugin
 
editingCanceled(String, String, String) - Method in class edu.ucsb.nceas.morpho.editor.EditorController
 
editingCanceled(String, String, String) - Method in interface edu.ucsb.nceas.morpho.framework.EditingCompleteListener
this method handles canceled editing
editingCompleted(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.EntityGUI
this is called whenever the editor exits.
editingCompleted(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
this is called whenever the editor exits.
editingCompleted(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
this is called whenever the editor exits.
editingCompleted(String, String, String) - Method in class edu.ucsb.nceas.morpho.editor.edit_plugin
 
editingCompleted(String, String, String) - Method in class edu.ucsb.nceas.morpho.editor.EditorController
 
editingCompleted(String, String, String) - Method in interface edu.ucsb.nceas.morpho.framework.EditingCompleteListener
This method is called when editing is complete
EditingCompleteListener - interface edu.ucsb.nceas.morpho.framework.EditingCompleteListener.
Any object that is interested in being notified when editing of an XML document is complete and obtaining a copy of the edited (new) document should implement this interface and register with the editor document
EditorController - class edu.ucsb.nceas.morpho.editor.EditorController.
A basic JFC 1.1 based application.
EditorController() - Constructor for class edu.ucsb.nceas.morpho.editor.EditorController
 
EditorController(ClientFramework, String) - Constructor for class edu.ucsb.nceas.morpho.editor.EditorController
 
EditorController(String) - Constructor for class edu.ucsb.nceas.morpho.editor.EditorController
Creates a new instance of JFrame1 with the given title.
EditorInterface - interface edu.ucsb.nceas.morpho.framework.EditorInterface.
All component plugins that require the editing of XML documents should implement this interface and register themselves as a service provider for the interface with the framework.
EditorPlugin - class edu.ucsb.nceas.morpho.editor.EditorPlugin.
 
EditorPlugin() - Constructor for class edu.ucsb.nceas.morpho.editor.EditorPlugin
Construct the editor plugin.
edu.ucsb.nceas.metaedit - package edu.ucsb.nceas.metaedit
 
edu.ucsb.nceas.morpho.datapackage - package edu.ucsb.nceas.morpho.datapackage
 
edu.ucsb.nceas.morpho.datapackage.wizard - package edu.ucsb.nceas.morpho.datapackage.wizard
 
edu.ucsb.nceas.morpho.editor - package edu.ucsb.nceas.morpho.editor
 
edu.ucsb.nceas.morpho.framework - package edu.ucsb.nceas.morpho.framework
 
edu.ucsb.nceas.morpho.framework.tests - package edu.ucsb.nceas.morpho.framework.tests
 
edu.ucsb.nceas.morpho.query - package edu.ucsb.nceas.morpho.query
 
ElementChoice - class edu.ucsb.nceas.metaedit.ElementChoice.
Internal window dialog for choosing an element from a list of appendable types or from a list of insertable types.
ElementChoice() - Constructor for class edu.ucsb.nceas.metaedit.ElementChoice
Construct a new ElementChoice dialog in the containing frame.
ElementFactory - class edu.ucsb.nceas.metaedit.ElementFactory.
An extended TreeFactory adding new capabilities to the TreeElement produced by TreeFactory (e.g.
ElementFactory.TreeElement - class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement.
An extended TXElement with additioanl methods such as getPath(...).
ElementFactory.TreeElement(String) - Constructor for class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
ElementFactory() - Constructor for class edu.ucsb.nceas.metaedit.ElementFactory
 
endDocument() - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
endDocument() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Unused SAX handler
endElement(String, String, String) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
endElement(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleParser
 
endElement(String, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
 
endElement(String, String, String) - Method in class edu.ucsb.nceas.morpho.query.Query
callback method used by the SAX Parser when the end tag of an element is detected.
endElement(String, String, String) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
SAX handler callback that is called upon the end of an element when parsing an XML document.
endPrefixMapping(String) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
endPrefixMapping(String) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Unused SAX handler
EntityGUI - class edu.ucsb.nceas.morpho.datapackage.EntityGUI.
Class that implements a GUI to edit an entity
EntityGUI(DataPackage, String, String, DataPackageGUI, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.datapackage.EntityGUI
Creates a new entity editor.
eval(Node, String) - Static method in class edu.ucsb.nceas.morpho.framework.XPathAPI
Evaluate XPath string to an XObject.
eval(Node, String, Node) - Static method in class edu.ucsb.nceas.morpho.framework.XPathAPI
Evaluate XPath string to an XObject.
execute() - Method in class edu.ucsb.nceas.morpho.query.Query
Run the query against the local data store and metacat, depending on how the searchMetacat and searchLocal flags are set.
execute() - Method in class edu.ucsb.nceas.morpho.query.LocalQuery
Run the query against the local document store

F

FileSystemDataStore - class edu.ucsb.nceas.morpho.framework.FileSystemDataStore.
implements and the DataStoreInterface for accessing files on the local file system.
FileSystemDataStore(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
create a new FileSystemDataStore for a ClientFramework
FileUtils - class edu.ucsb.nceas.morpho.framework.FileUtils.
This class provides convenience methods for manipulating filesystem objects, such as copying from one file to another.
FileUtils() - Constructor for class edu.ucsb.nceas.morpho.framework.FileUtils
 
fireCancelEvent(ChangeEvent) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
fireCancelEvent(ChangeEvent) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
fireEditingCanceledEvent(DocFrame, String) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
Fire off notifications to EditingCanceledListeners when the editing has been completed
fireEditingCompleteEvent(DocFrame, String) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
Fire off notifications to EditingCompleteListeners when the editing has been completed
fireStopEvent(ChangeEvent) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
fireStopEvent(ChangeEvent) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
focusGained(FocusEvent) - Method in class edu.ucsb.nceas.metaedit.XMLPanels
 
focusGained(FocusEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
focusGained(FocusEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners
 
focusLost(FocusEvent) - Method in class edu.ucsb.nceas.metaedit.XMLPanels
 
focusLost(FocusEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
focusLost(FocusEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners
 

G

get(String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Gets the value(s) corresponding to a key string (i.e.
get(String, int) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Gets the value(s) corresponding to a key string (i.e.
getAbstractState() - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
returns state of Abstract checkbox
getAllIdentifiers() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
returns a vector containing a distinct set of all of the file ids that make up this package
getAllowsChildren() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
getAllState() - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
get state of 'All' check box
getAppendableElements(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
Create a Vector of names that are appendable as children on the element specified in selectedTreeElement.
getAppendableElements(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
Create a Vector of names that are appendable as children on the element specified in selectedTreeElement.
getAppendablesInProperOrder(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
getAppendablesInProperOrder(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
getAttribute(String) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get an attribute value by name
getAttributes() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
returns a hashtable of vectors with the basic values in it.
getAttributes() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the attributes as a string
getCardinality() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getCellEditorValue() - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
getCellEditorValue() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor
 
getCellEditorValue() - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
getChildAt(int) - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
getChildCount() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
getChildren() - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
Retrieve an Enumeration of query terms for this QueryGroup
getChildren() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the an enumeration of the children of this node
getChosenElementToAppend() - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Determine the currently selected element name from the list.
getChosenElementToInsert() - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Determine the currently selected element name from the insertables list.
getClipboardObject() - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
 
getCollection() - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
return a vector of Triple objects that represent this collection.
getCollectionByObject(String) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
returns a vector of triples with the given object
getCollectionByRelationship(String) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
returns a vector of triples with the given relationship
getCollectionBySubject(String) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
returns a vector of triples with the given subject
getColumnClass(int) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Return the Class for each column so that they can be rendered correctly.
getColumnCount() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.AttrJTableModel
 
getColumnCount() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Return the number of columns in this result set
getColumnName(int) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.AttrJTableModel
 
getColumnName(int) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Determine the name of a column by its index
getConfigFileTypeAttributes(ClientFramework, String) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
gets the file types from the config file and hashes them by a specified attribute
getConfiguration() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Get the configuration object associated with the framework.
getContentModelString(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
getContentModelString(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
getContentType() - Method in class edu.ucsb.nceas.morpho.framework.MultipartForm
Get the content header after encoding.
getContentType(String) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
Determine the content type for a given element type.
getContentType(String) - Method in class edu.ucsb.nceas.metaedit.IBMParser
Determine the content type for a given element type.
getCookie() - Static method in class edu.ucsb.nceas.morpho.framework.HttpMessage
return the cookie that this message object contains
getData(DefaultMutableTreeNode, Hashtable, Hashtable) - Method in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
getData(DefaultMutableTreeNode, Hashtable, Hashtable) - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
getDepth() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
Returns the depth of the tree rooted at this node -- the longest distance from this node to a leaf.
getDescriptions() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
 
getDoc() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
Returns the document as an XMLElement object.
getDoc(File, String) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
parses file with the dom parser and returns a dom Document
getDocID() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the doc id of this node
getDoctype() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
Returns the public identifier of the doctype that this config file represents
getDocumentDOM() - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
getDocumentDOM() - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
getDocumentJTree() - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
getDocumentJTree() - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
getDocumentJTree() - Method in class edu.ucsb.nceas.metaedit.IBMParser
getDocumentTree returns the JTree to the MetaDoc for display.
getDocumentTypeInfo() - Method in class edu.ucsb.nceas.metaedit.NewDialog
Determine info associated with the document type as specified by the user.
getDocumentTypeName() - Method in class edu.ucsb.nceas.metaedit.NewDialog
Determine the name of the document type as specified by the user.
getDtd() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
Returns the path to the dtd that this config file represents
getDTD() - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
getDTD() - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
getDTDAttrDecls(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
Determine the attributes declared in the DTD for a given node.
getDTDAttrDecls(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
Determine the attributes declared in the DTD for a given node.
getEditor() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getEditor(ClientFramework) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
gets the editor context and returns it
getElementInfo(DefaultMutableTreeNode, Hashtable, Hashtable) - Method in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
getElementInfo(DefaultMutableTreeNode, Hashtable, Hashtable) - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
getElements(DefaultMutableTreeNode) - Method in class edu.ucsb.nceas.morpho.editor.DFHPanel
given a DefaultMutableTreeNode, build a Hashtable of all elements that have text i.e.
getElements(DefaultMutableTreeNode) - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
given a DefaultMutableTreeNode, build a Hashtable of all elements that have text i.e.
getFilterDocList() - Method in class edu.ucsb.nceas.morpho.query.Query
Accessor method to return a vector of the filter doc types as defined in the <filterdoctype> tag in the pathquery dtd.
getFrameObjects() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
 
getFrames() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
 
getFramework() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Get a reference to the framework
getHashtable(String, String, String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Assume that there is some parent node which has a subset of child nodes that are repeated e.g.
getHelp() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getIcon() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getIconName() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getID() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
returns the id of the head of this package (i.e.
getIdentifier() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
gets the identifier of the package file
getIdentifier() - Method in class edu.ucsb.nceas.morpho.query.Query
Accessor method to return the identifier of this Query
getIdString() - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
getIndex(TreeNode) - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
getInsertableBefore(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
Creates a Vector of element names that are insertable as siblings after the element that is specified in selectedTreeElement.
getInsertableBefore(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
Creates a Vector of element names that are insertable as siblings after the element that is specified in selectedTreeElement.
getItem() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getJTextAreaInFocus() - Method in class edu.ucsb.nceas.metaedit.XMLPanels
 
getKeywordsState() - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
returns state of Keywords check box
getLength() - Method in class edu.ucsb.nceas.morpho.framework.MultipartForm
Get the length in bytes of this form after encoding.
getLevel() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
getLocation() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
returns the location of the data package.
getLocationString() - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
getMainFrame() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
 
getMetacatInputStream(Properties) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Send a request to Metacat
getMetacatInputStream(Properties, boolean) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Send a request to Metacat
getMetacatString(Properties) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Send a request to Metacat
getMetacatString(Properties, boolean) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Send a request to Metacat
getName() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getNextId() - Method in class edu.ucsb.nceas.morpho.datapackage.AccessionNumber
returns the next local id from the config file returns null if configXML was unable to increment the id number
getNode(String) - Method in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
getNode(String) - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
getNodeID() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the id of this node
getNodeIndex() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get nodeIndex of the node
getNodeList() - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
 
getNodeType() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the type of this node
getObject() - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
get the object of this triple
getOperator() - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
Retrieve the operator for this QueryGroup
getOwnerList() - Method in class edu.ucsb.nceas.morpho.query.Query
Accessor method to return a vector of the owner fields as defined in the <owner> tag in the pathquery dtd.
getParent() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
getParentID() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the parent id of this node
getParts(String) - Method in class edu.ucsb.nceas.morpho.datapackage.AccessionNumber
Returns a vector with all components of the accession number.
getPassword() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
get password associated with this framework
getPath() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
Returns the path from the root, to get to this node.
getPathContent(File, String, ClientFramework) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
gets the content of a tag in a given xml file with the given path
getPathContent(String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
gets the content of a tag in a given xml file with the given path
getPathExpression() - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
get the path expression parameter
getPathToRoot(TreeNode, int) - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
Builds the parents of node up to and including the root node, where the original node is the last element in the returned array.
getPCDATA() - Method in class edu.ucsb.nceas.metaedit.Inputer
Determine the text in the text field.
getPCValue() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getPreferredSize() - Method in class edu.ucsb.nceas.morpho.query.WrappedTextRenderer
Get the preferred size for this text area
getPresentWorkingDir() - Method in class edu.ucsb.nceas.metaedit.MetaEditor
 
getProfile() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Get the profile for the currently logged in user.
getProperty(String) - Method in class edu.ucsb.nceas.metaedit.Options
Gets the list of DTD schemas for perusal
getQuery() - Method in class edu.ucsb.nceas.morpho.query.QueryDialog
Get the Query built using this dialog box
getQuery() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Get the query that was used to construct these results
getQueryGroup() - Method in class edu.ucsb.nceas.morpho.query.Query
get the QueryGroup used to express query constraints
getQueryTitle() - Method in class edu.ucsb.nceas.morpho.query.Query
Accessor method to return the title of this Query
getRelatedFiles() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
returns a hashtable of the related files taken from the triples.
getRelationship() - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
get the relationship of this triple
getResultsVector() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
get the resultsVector
getResultsVector() - Method in class edu.ucsb.nceas.morpho.query.HeadResultSet
get the resultsVector
getReturnDocList() - Method in class edu.ucsb.nceas.morpho.query.Query
Accessor method to return a vector of the return document types as defined in the <returndoctype> tag in the pathquery dtd.
getReturnFieldList() - Method in class edu.ucsb.nceas.morpho.query.Query
Accessor method to return a vector of the extended return fields as defined in the <returnfield> tag in the pathquery dtd.
getRoot() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
Returns the public identifier of the doctype that this config file represents
getRootEditor() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
getRootNodeID() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the root node id of this node
getRowCount() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.AttrJTableModel
 
getRowCount() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Return the number of records in this result set
getRowCount() - Method in class edu.ucsb.nceas.morpho.query.HeadResultSet
Return the number of records in this result set
getRowHeight() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Return the correct row height for table rows
getSaveString() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
getSaveString() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
getSaveString() - Method in class edu.ucsb.nceas.metaedit.MetaDoc
get the xml text
getSchemata() - Method in class edu.ucsb.nceas.metaedit.Options
Gets the list of DTD schemas for perusal
getSearchLocal() - Method in class edu.ucsb.nceas.morpho.query.Query
determine if we should search locally
getSearchMetacat() - Method in class edu.ucsb.nceas.morpho.query.Query
determine if we should search metacat
getSearchMode() - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
return the value of the combobox which contains the search mode (i.e.
getSearchMode() - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
get the searchmode parameter
getSearchMode() - Method in class edu.ucsb.nceas.morpho.query.TaxonTermPanel
return the value of the combobox which contains the search mode (i.e.
getServiceProvider(Class) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to get a reference to an object that implements a particular interface
getSessionCookie() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
 
getSiteList() - Method in class edu.ucsb.nceas.morpho.query.Query
Accessor method to return a vector of the site fields as defined in the <site> tag in the pathquery dtd.
getStringFromFile(File) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
returns the string representation of a file
getSubject() - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
get the subject of this triple
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.ucsb.nceas.morpho.query.WrappedTextRenderer
Return self as rendering components, delegating the display mainly to the superclass JTextArea
getTagAttrDeclsArray(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
getTagAttrDeclsArray(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
getTagName() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Get the name of this node
getTaxonRank() - Method in class edu.ucsb.nceas.morpho.query.TaxonTermPanel
return the value of the combobox which contains the taxonomic rank (i.e.
getTitleState() - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
returns state of Title checkbox
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
Set up the rendering for the new icons and text for the tree
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class edu.ucsb.nceas.morpho.editor.XMLTreeCellRenderer
required method for a TreeCellRenderer uses icon in userobject for each nodeinstead of an icon which is based on whether node is leaf or branch.
getTriple() - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
return this triple as a vector of strings
getTripleFileDom() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
returns the dom representation of the triple file.
getTriples() - Method in class edu.ucsb.nceas.morpho.datapackage.TripleParser
returns the TripleCollection of all of the triples in this document
getTriples() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
gets the triplesCollection created by this object
getTriplesFile() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
gets the file that contains the package information.
getUserName() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Get the username associated with this framework
getUserObject(Object) - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
getValue() - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
get the text that is to be seached for.
getValue() - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
get the Value parameter
getValue() - Method in class edu.ucsb.nceas.morpho.query.TaxonTermPanel
get the text that is to be seached for.
getValue(String) - Method in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
getValue(String) - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
getValueAt(int, int) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.AttrJTableModel
 
getValueAt(int, int) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Determine the value of a column by its row and column index
getValueAt(int, int) - Method in class edu.ucsb.nceas.morpho.query.HeadResultSet
Determine the value of a column by its row and column index
getValuesForPath(String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
 
getXML() - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard
gets the xml produced from the wizard
greenAsterisk - Static variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
greenOne - Static variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
greenPlus - Static variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
greenQuestionMark - Static variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
greenSquare - Static variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 

H

HeadResultSet - class edu.ucsb.nceas.morpho.query.HeadResultSet.
A HeadResultSet encapsulates the list of results returned from either a local query or a Metacat query, but only presents the most recent revision of a document as part of the Table Model.
HeadResultSet(Query, String, InputStream, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.HeadResultSet
Construct a HeadResultSet instance given a query object and a InputStream that represents an XML encoding of the results.
HeadResultSet(Query, String, Vector, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.HeadResultSet
Construct a HeadResultSet instance from a vector of vectors; for use with LocalQuery
ht - Variable in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
ht - Variable in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
htnodes - Variable in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
htnodes - Variable in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
HttpMessage - class edu.ucsb.nceas.morpho.framework.HttpMessage.
 
HttpMessage(URL) - Constructor for class edu.ucsb.nceas.morpho.framework.HttpMessage
 

I

IBMParser - class edu.ucsb.nceas.metaedit.IBMParser.
Implementation of the ParserDriver interface for the IBM XML parser (xml4j).
IBMParser(String, String, String, MetaEditor) - Constructor for class edu.ucsb.nceas.metaedit.IBMParser
Construct a new IBMParser with the given DTD filename.
ignorableWhitespace(char[], int, int) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
ignorableWhitespace(char[], int, int) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Unused SAX handler
incChildNum() - Method in class edu.ucsb.nceas.morpho.query.BasicNode
increase childNum when new child for the node is created
incRev(String) - Method in class edu.ucsb.nceas.morpho.datapackage.AccessionNumber
returns an id with an incremented id.
incRev(String, boolean) - Method in class edu.ucsb.nceas.morpho.datapackage.AccessionNumber
parses id and adds a revision number to it.
incRevInTriples(File, String, String) - Method in class edu.ucsb.nceas.morpho.datapackage.AccessionNumber
searches an xml file for triples.
index - Variable in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
index - Variable in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
init() - Method in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
init() - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
initialize(ClientFramework) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin
The plugin must store a reference to the ClientFramework in order to be able to call the services available through the framework.
initialize(ClientFramework) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
The plugin must store a reference to the ClientFramework in order to be able to call the services available through the framework.
initialize(ClientFramework) - Method in class edu.ucsb.nceas.morpho.editor.edit_plugin
 
initialize(ClientFramework) - Method in class edu.ucsb.nceas.morpho.editor.EditorController
 
initialize(ClientFramework) - Method in interface edu.ucsb.nceas.morpho.framework.PluginInterface
This method is called after the Plugin has been created in order to allow the plugin a chance to initialize variables, create menus and toolbars, and store a reference to the framework.
initialize(ClientFramework) - Method in class edu.ucsb.nceas.morpho.query.QueryPlugin
The plugin must store a reference to the ClientFramework in order to be able to call the services available through the framework.
Inputer - class edu.ucsb.nceas.metaedit.Inputer.
Internal window dialog for editing the text in PCDATA elements
Inputer() - Constructor for class edu.ucsb.nceas.metaedit.Inputer
Construct a new Inputer Dialog for use throughout the duration of the program.
InputerCellEditor - class edu.ucsb.nceas.metaedit.InputerCellEditor.
 
InputerCellEditor() - Constructor for class edu.ucsb.nceas.metaedit.InputerCellEditor
Construct a new Inputer Dialog for use throughout the duration of the program.
InputerCellRenderer - class edu.ucsb.nceas.metaedit.InputerCellRenderer.
 
InputerCellRenderer() - Constructor for class edu.ucsb.nceas.metaedit.InputerCellRenderer
Construct a new Inputer Dialog for use throughout the duration of the program.
insert(String, String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Inserts another node before the first element with the name contained in 'key', otherwise appends it to the end of the config file (last element in root node)
insertElement(ElementFactory.TreeElement, ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
insertElement(ElementFactory.TreeElement, ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
insertIdInFile(File, String) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
inserts a documents id into a specified path in the document.
internalFrameActivated(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
handler method that is called when this document is selected and becomes the active frame in a set of JInternalFrames, part of the implementation of the InternalFrameListener interface
internalFrameActivated(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
internalFrameClosed(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
internalFrameClosed(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
internalFrameClosing(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
internalFrameClosing(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
internalFrameDeactivated(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
internalFrameDeactivated(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
internalFrameDeiconified(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
internalFrameDeiconified(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
internalFrameIconified(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
internalFrameIconified(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
internalFrameOpened(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
internalFrameOpened(InternalFrameEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
isCaseSensitive() - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
determine if the QueryTerm is case sensitive
isCellEditable(EventObject) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
isCellEditable(EventObject) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
isCellEditable(int, int) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.AttrJTableModel
 
isConnected() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Determines if the framework has a valid login
isLeaf() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
isSearchStarted() - Method in class edu.ucsb.nceas.morpho.query.QueryDialog
determine whether the query should be executed
itemStateChanged(ItemEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard
not used in this implementation

J

jtaToNodeHash - Variable in class edu.ucsb.nceas.metaedit.XMLPanels
 
jtaToTextNodeHash - Variable in class edu.ucsb.nceas.metaedit.XMLPanels
 

L

loadSavedQueries() - Method in class edu.ucsb.nceas.morpho.query.ResultPanel
Load the saved queries into the Search menu so that the user can launch any queries they saved from previosu sessions.
LOCAL - Static variable in class edu.ucsb.nceas.morpho.datapackage.DataPackage
used to signify that this package is located locally
LocalDocTypesPanel - class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel.
 
LocalDocTypesPanel() - Constructor for class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
Default constructor.
LocalDocTypesPanel(DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
LocalQuery - class edu.ucsb.nceas.morpho.query.LocalQuery.
LocalQuery is a class designed to execute a query defined in an XML document that follows the PathQuery DTD.
LocalQuery(Query, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.LocalQuery
Basic Constuctor for the class
LockedPanel - class edu.ucsb.nceas.morpho.editor.LockedPanel.
Locked panel is an example of a very simple plug-in panel to be used by the XML editor.
LockedPanel(DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.LockedPanel
 
logIn() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Log into metacat
logOut() - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Log out of metacat

M

main(String[]) - Static method in class edu.ucsb.nceas.metaedit.mdeBean
 
main(String[]) - Static method in class edu.ucsb.nceas.metaedit.MetaEditor
Call the constructor for this class to create a new instance.
main(String[]) - Static method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
 
main(String[]) - Static method in class edu.ucsb.nceas.morpho.datapackage.TripleParser
command line test method.
main(String[]) - Static method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShell
Test method
main(String[]) - Static method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
 
main(String[]) - Static method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard
Test method that allows command line execution.
main(String[]) - Static method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
 
main(String[]) - Static method in class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 
main(String[]) - Static method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
main(String[]) - Static method in class edu.ucsb.nceas.morpho.editor.edit_plugin
The entry point for this application.
main(String[]) - Static method in class edu.ucsb.nceas.morpho.editor.EditorController
The entry point for this application.
main(String[]) - Static method in class edu.ucsb.nceas.morpho.framework.MetacatDataStore
Test method
main(String[]) - Static method in class edu.ucsb.nceas.morpho.framework.SplashFrame
Test the frame
main(String[]) - Static method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
Test method
main(String[]) - Static method in class edu.ucsb.nceas.morpho.framework.ClientFramework
The entry point for this application.
main(String[]) - Static method in class edu.ucsb.nceas.morpho.query.Query
Main routine for testing
main(String[]) - Static method in class edu.ucsb.nceas.morpho.query.LocalQuery
Main routine for testing
mdeBean - class edu.ucsb.nceas.metaedit.mdeBean.
 
mdeBean() - Constructor for class edu.ucsb.nceas.metaedit.mdeBean
 
merge(ResultSet) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Merge a ResultSet onto this one using the docid as the join column
merge(ResultSet) - Method in class edu.ucsb.nceas.morpho.query.HeadResultSet
Merge a ResultSet onto this one using the docid as the join column
METACAT - Static variable in class edu.ucsb.nceas.morpho.datapackage.DataPackage
used to signify that this package is located on a metacat server
MetacatDataStore - class edu.ucsb.nceas.morpho.framework.MetacatDataStore.
implements and the DataStoreInterface for accessing files on the Metacat
MetacatDataStore(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.framework.MetacatDataStore
Constructor to create this object in conjunction with a ceartain framework.
MetacatUploadException - exception edu.ucsb.nceas.morpho.framework.MetacatUploadException.
This exception is thrown when a service request is made of an object and that object can not properly handle the request, either because it is not designed to handle it, or there was an error in trying to handle it.
MetacatUploadException(String) - Constructor for class edu.ucsb.nceas.morpho.framework.MetacatUploadException
 
MetaDoc - class edu.ucsb.nceas.metaedit.MetaDoc.
A component used to store and display an XML document utilizing a JTree for hirearchichal storage of the nodes.
MetaDoc(String, String) - Constructor for class edu.ucsb.nceas.metaedit.MetaDoc
Create a new MetaDoc and its principal components.
MetaDoc(String, String, String, MetaEditor) - Constructor for class edu.ucsb.nceas.metaedit.MetaDoc
Create a new XML file, create a JTree to contain it, and load the root node and its immediate children into the tree.
MetaEditor - class edu.ucsb.nceas.metaedit.MetaEditor.
Main class for the editing environment, used for displaying editor components and a menu bar for selecting actions.
MetaEditor() - Constructor for class edu.ucsb.nceas.metaedit.MetaEditor
Create a new instance of the class and set up the major visual components of the editor.
mouseClicked(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
mouseClicked(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners
 
mouseEntered(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
mouseEntered(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners
 
mouseExited(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
mouseExited(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners
 
mousePressed(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
mousePressed(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners
 
mouseReleased(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
mouseReleased(MouseEvent) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.CustomCellEditor.JComboBoxWithListeners
 
MultipartForm - class edu.ucsb.nceas.morpho.framework.MultipartForm.
This class represents name/value pairs and files in a byte array using the multipart/form-data encoding.
MultipartForm(NVPair[], NVPair[]) - Constructor for class edu.ucsb.nceas.morpho.framework.MultipartForm
Create a new form with form data and files using the multipart/form-data encoding.
MultipartForm(NVPair[], NVPair[], FilenameMangler) - Constructor for class edu.ucsb.nceas.morpho.framework.MultipartForm
Create a new form with form data and files using the multipart/form-data encoding and use the given FilenameMangler to alter filenames before encoding.

N

newDataFile(String, File) - Method in class edu.ucsb.nceas.morpho.framework.MetacatDataStore
method to create a new data file on metacat.
NewDialog - class edu.ucsb.nceas.metaedit.NewDialog.
Internal window dialog for choosing a document type for new documents
NewDialog(Frame, String, boolean, Options) - Constructor for class edu.ucsb.nceas.metaedit.NewDialog
Construct a new NewDialog window for the document type of new documents.
newDocument() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
newDocument() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
newDocument() - Method in class edu.ucsb.nceas.metaedit.MetaEditor
Create a new document by choosing a document type definition from the predefined list.
newFile(String, Reader, boolean) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
 
newFile(String, Reader, boolean) - Method in class edu.ucsb.nceas.morpho.framework.MetacatDataStore
Create and save a new file to metacat using the "insert" action.
newFile(String, Reader, boolean) - Method in interface edu.ucsb.nceas.morpho.framework.DataStoreInterface
create a new file with an id of name in the datastore and return a File object that represents it.
newFile(String, Reader, boolean) - Method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
returns a File object in the local repository.
newNode(Object) - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
node - Variable in class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 
node - Variable in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
node - Variable in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
NodeInfo - class edu.ucsb.nceas.morpho.editor.NodeInfo.
NodeInfo is a class used as a UserObject for a specialized JTree model.
NodeInfo(String) - Constructor for class edu.ucsb.nceas.morpho.editor.NodeInfo
creates a new NodeInfo object with the indicated name.
nodeMap - Variable in class edu.ucsb.nceas.morpho.editor.DFHPanel
 
nodeMap - Variable in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
normalize(String) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
Normalizes the given string.
normalize(String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Normalizes the given string.

O

openDataPackage(String, String, Vector) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin
 
openDataPackage(String, String, Vector) - Method in interface edu.ucsb.nceas.morpho.framework.DataPackageInterface
This method is called to open a data package that resides either locally (location=local) or on a Metacat server (location=metacat).
openDocument() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
openDocument() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
openDocument() - Method in class edu.ucsb.nceas.metaedit.MetaEditor
Display the file chooser dialog to select an XML file, and open that file.
openDocument(File) - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
openDocument(File) - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
openDocument(File) - Method in class edu.ucsb.nceas.metaedit.MetaEditor
Open the given file object, skipping File dialog
openEditor(String) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
 
openEditor(String) - Method in interface edu.ucsb.nceas.morpho.framework.EditorInterface
This method is called to open a XML editor that resides either
openEditor(String, EditingCompleteListener) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
 
openEditor(String, String, String, EditingCompleteListener) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
 
openEditor(String, String, String, EditingCompleteListener) - Method in interface edu.ucsb.nceas.morpho.framework.EditorInterface
This method is called to open a XML editor with the indicated xmltext and an editingCompletedListener to be notified when the editing is completed
openEditor(String, String, String, String, String, EditingCompleteListener) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
 
openEditor(String, String, String, String, String, EditingCompleteListener) - Method in interface edu.ucsb.nceas.morpho.framework.EditorInterface
This method is called to open a XML editor with the indicated xmltext and an editingCompletedListener to be notified when the editing is completed, the nodename and nodevalue parameters indicated node to be selected when documement is opened
openEditor(Vector, String, String, String, String, EditingCompleteListener) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
 
openEditor(Vector, String, String, String, String, EditingCompleteListener) - Method in interface edu.ucsb.nceas.morpho.framework.EditorInterface
 
openFile(String) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
 
openFile(String) - Method in class edu.ucsb.nceas.morpho.framework.MetacatDataStore
Opens a file from Metacat and returns a File object that represents the metacat file.
openFile(String) - Method in interface edu.ucsb.nceas.morpho.framework.DataStoreInterface
open a file from a datastore with the id of name and return a File object that represents it.
openFile(String) - Method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
opens a file with the given name.
openFile(String, ClientFramework) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
opens a file on metacat or local.
openFile(String, String, ClientFramework) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
figures out a files location if it is not known and opens it.
openResultRecord(int) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Open a given row index of the result set using a delegated handler class
openResultRecord(int) - Method in class edu.ucsb.nceas.morpho.query.HeadResultSet
Open a given row index of the result set using a delegated handler class
openResultRecord(Vector) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Open a given row of the result set using a delegated handler class
Options - class edu.ucsb.nceas.metaedit.Options.
Class for storing, editing, and displaying application specific options, including the name to URL mappings for document types.
Options(JFrame, boolean, String) - Constructor for class edu.ucsb.nceas.metaedit.Options
Construct a new internal Options window and set its dimension and location.

P

PackageUtil - class edu.ucsb.nceas.morpho.datapackage.PackageUtil.
This class contains static utility methods that are used throughtout the other *.morpho.datapackage.* classes.
PackageUtil() - Constructor for class edu.ucsb.nceas.morpho.datapackage.PackageUtil
 
PackageWizard - class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard.
This class builds a custom frame based on a configuration file.
PackageWizard() - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard
constructor which initializes the window based on the paramater values in the wizard tag of the xml configuration document.
PackageWizard(ClientFramework, Container, String) - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard
constructor which creates a package wizard frame in the given contentPane using the given framefile (xml configuration file).
PackageWizardParser - class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser.
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the Package Wizard
PackageWizardParser(FileReader, String) - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
 
PackageWizardShell - class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShell.
This is the shell of the package wizard.
PackageWizardShell() - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShell
 
PackageWizardShell(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShell
 
PackageWizardShellParser - class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser.
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the Package Wizard
PackageWizardShellParser(FileReader, String) - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
 
parseDTD() - Method in class edu.ucsb.nceas.morpho.editor.DTDTree
parses a dtd file and creates a tree of document instance
parseId(String) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
Parses a dotted notation id into a file path.
parseIdFromMessage(String) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
parses the id of a file from the message that metacat returns
ParserDriver - interface edu.ucsb.nceas.metaedit.ParserDriver.
Interface defining methods needed to extract DTD information from a variety of parsers.
PluginInterface - interface edu.ucsb.nceas.morpho.framework.PluginInterface.
All component plugins that are to be included in the ClientFramework must implement this interface so that the services of the ClientFramework such as menu and toolbar actions, and session control, are available to the plugin component.
PreviewFrame - class edu.ucsb.nceas.metaedit.PreviewFrame.
Internal window frame for displaying the XML source that is being edited in the tree.
PreviewFrame() - Constructor for class edu.ucsb.nceas.metaedit.PreviewFrame
Construct a new internal PreviewFrame window and set its dimension and location.
previewXML() - Method in class edu.ucsb.nceas.metaedit.MetaDoc
Display the XML text in the preview window.
previewXMLFile() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
previewXMLFile() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
previewXMLFile() - Method in class edu.ucsb.nceas.metaedit.MetaEditor
Display the document in the XML Preview window.
print(Node) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
This method can 'print' any DOM subtree.
print(Node) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
This method can 'print' any DOM subtree.
printDoc(XMLElement) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
prints a string representation of the doc object
printDoctype(Document) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
prints out the doctype part of and xml document.
printExtendedSQL(String) - Method in class edu.ucsb.nceas.morpho.query.Query
This method prints sql based upon the <returnfield> tag in the pathquery document.
printGetDocByDoctypeSQL(String) - Static method in class edu.ucsb.nceas.morpho.query.Query
 
printPackageSQL() - Static method in class edu.ucsb.nceas.morpho.query.Query
Prints sql that returns all relations in the database.
printPackageSQL(String) - Static method in class edu.ucsb.nceas.morpho.query.Query
Prints sql that returns all relations in the database that were input under a specific docid
printPackageSQL(String, String) - Static method in class edu.ucsb.nceas.morpho.query.Query
Returns all of the relations that has a certain docid in the subject or the object.
printRelationSQL(String) - Static method in class edu.ucsb.nceas.morpho.query.Query
 
printSQL(boolean) - Method in class edu.ucsb.nceas.morpho.query.Query
create a SQL serialization of the query that this instance represents
printSQL(boolean) - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
create a SQL serialization of the query that this instance represents
printSQL(boolean) - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
create a SQL serialization of the query that this instance represents
processingInstruction(String, String) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
processingInstruction(String, String) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Unused SAX handler
ProfileDialog - class edu.ucsb.nceas.morpho.framework.ProfileDialog.
A graphical window for creating a new user profile with user provided information.
ProfileDialog(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.framework.ProfileDialog
Construct a dialog and set the framework
ProfileDialog(ClientFramework, boolean) - Constructor for class edu.ucsb.nceas.morpho.framework.ProfileDialog
Construct the dialog

Q

Query - class edu.ucsb.nceas.morpho.query.Query.
A Class that represents a structured query, and can be constructed from an XML serialization conforming to @see pathquery.dtd.
Query(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.Query
construct an instance of the Query class, manually setting the Query constraints rather that readin from an XML stream
Query(Reader, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.Query
construct an instance of the Query class from an XML Stream
Query(String, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.Query
construct an instance of the Query class from an XML String
QueryDialog - class edu.ucsb.nceas.morpho.query.QueryDialog.
Dialog which collects search information from user to be used to create a Query
QueryDialog(ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.QueryDialog
Construct a new instance of the query dialog
QueryDialog(Frame, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.QueryDialog
Construct a new instance of the query dialog
QueryGroup - class edu.ucsb.nceas.morpho.query.QueryGroup.
A group of terms and other groups in a query, allowing arbitrarily nested hierarchiies that can be combined using union or intersection.
QueryGroup(String) - Constructor for class edu.ucsb.nceas.morpho.query.QueryGroup
construct a new QueryGroup
QueryPlugin - class edu.ucsb.nceas.morpho.query.QueryPlugin.
 
QueryPlugin() - Constructor for class edu.ucsb.nceas.morpho.query.QueryPlugin
Construct the query plugin.
QueryTerm - class edu.ucsb.nceas.morpho.query.QueryTerm.
A single term in a query, containing the path to be searched, the value to match, and any relevant search modifiers.
QueryTerm(boolean, String, String) - Constructor for class edu.ucsb.nceas.morpho.query.QueryTerm
Construct a new instance of a query term for a free text search (using the value only)
QueryTerm(boolean, String, String, String) - Constructor for class edu.ucsb.nceas.morpho.query.QueryTerm
Construct a new instance of a query term for a structured search (matching the value only for those nodes in the pathexpr)

R

reconstructEmptyTXElementInTree(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
redSquare - Static variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
Icons to indicate different conditions of nodes or subtrees.
refreshQuery() - Method in class edu.ucsb.nceas.morpho.query.ResultPanel
Refresh the results by running the query again to produce a new ResulSet
removeActiveDoc(MetaDoc) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Tell the active document to stop listening to the append/insert buttons.
removeCellEditorListener(CellEditorListener) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
removeCellEditorListener(CellEditorListener) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
removeChildren(String, int) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
removes all children of the specified parent
removeElement(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
removeElement(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
removeMenuItem(String, int) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to remove a menu item from a menu based on the index of the menu item.
removeNode(String, int) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
deletes indicated node
removeTriple(Triple) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
removes the specified triple from the collection and returns it.
removeWindow(JFrame) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
This method is called by plugins to de-register a Window that the plugin has created.
ResultFrame - class edu.ucsb.nceas.morpho.query.ResultFrame.
Display a ResultSet in a table view in window using an embedded ResultPanel to construct the table.
ResultFrame(ClientFramework, ResultSet) - Constructor for class edu.ucsb.nceas.morpho.query.ResultFrame
Construct a new ResultFrame and display the result set
ResultFrame(ClientFramework, ResultSet, int) - Constructor for class edu.ucsb.nceas.morpho.query.ResultFrame
Construct a new ResultFrame and display the result set
ResultPanel - class edu.ucsb.nceas.morpho.query.ResultPanel.
Display a ResultSet in a table view in a panel that can be embedded in a window or tab or other location
ResultPanel(ResultSet) - Constructor for class edu.ucsb.nceas.morpho.query.ResultPanel
Construct a new ResultPanel and display the result set.
ResultPanel(ResultSet, boolean, boolean) - Constructor for class edu.ucsb.nceas.morpho.query.ResultPanel
Construct a new ResultPanel and display the result set
ResultPanel(ResultSet, boolean, boolean, int) - Constructor for class edu.ucsb.nceas.morpho.query.ResultPanel
Construct a new ResultPanel and display the result set
ResultSet - class edu.ucsb.nceas.morpho.query.ResultSet.
A ResultSet encapsulates the list of results returned from either a local query or a Metacat query.
ResultSet(Query, String, InputStream, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.ResultSet
Construct a ResultSet instance given a query object and a InputStream that represents an XML encoding of the results.
ResultSet(Query, String, Vector, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.query.ResultSet
Construct a ResultSet instance from a vector of vectors; for use with LocalQuery
resultsVector - Variable in class edu.ucsb.nceas.morpho.query.ResultSet
Store each row of the result set as a row in a Vector
reviseQuery() - Method in class edu.ucsb.nceas.morpho.query.ResultPanel
Revise the query by loading it into the QueryDialog GUI
rootNode - Variable in class edu.ucsb.nceas.morpho.editor.DocFrame
 
rootNode - Variable in class edu.ucsb.nceas.morpho.editor.DTDTree
 

S

save() - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Save the configuration file
save() - Method in class edu.ucsb.nceas.morpho.query.Query
Save an XML serialized version of the query in the profile directory
saveAttrTable() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
saveDocument() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
saveDocument() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
saveDocumentAs() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
saveDocumentAs() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
saveDocumentToDatabase() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
saveDocumentToDatabase() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
saveDOM(Node) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
This method wraps the 'print' method to send DOM back to the XML document (file) that was used to create the DOM.
saveFile(String, Reader) - Method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
 
saveFile(String, Reader, boolean) - Method in class edu.ucsb.nceas.morpho.framework.DataStore
 
saveFile(String, Reader, boolean) - Method in class edu.ucsb.nceas.morpho.framework.MetacatDataStore
Save an xml metadata file (which already exists) to metacat using the "update" action.
saveFile(String, Reader, boolean) - Method in interface edu.ucsb.nceas.morpho.framework.DataStoreInterface
save a file to the datastore with the id of name.
saveFile(String, Reader, boolean) - Method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
 
saveFile(String, Reader, boolean, String) - Method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
Saves a file with the given name.
saveOptions() - Method in class edu.ucsb.nceas.metaedit.Options
Saves our options in a properties file for later loading
saveQuery() - Method in class edu.ucsb.nceas.morpho.query.ResultPanel
Save a query in the user's profile so they can run it again later.
saveTempFile(String, Reader) - Method in class edu.ucsb.nceas.morpho.framework.FileSystemDataStore
 
selected - Variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
Whether or not the item that was last configured is selected.
selectNodeList(Node, String) - Static method in class edu.ucsb.nceas.morpho.framework.XPathAPI
Use an XPath string to select a nodelist.
selectNodeList(Node, String, Node) - Static method in class edu.ucsb.nceas.morpho.framework.XPathAPI
Use an XPath string to select a nodelist.
selectSingleNode(Node, String) - Static method in class edu.ucsb.nceas.morpho.framework.XPathAPI
Use an XPath string to select a single node.
selectSingleNode(Node, String, Node) - Static method in class edu.ucsb.nceas.morpho.framework.XPathAPI
Use an XPath string to select a single node.
sendDataFile(String, File) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
sends a data file to the metacat using "multipart/form-data" encoding
sendGetMessage() - Method in class edu.ucsb.nceas.morpho.framework.HttpMessage
Performs a GET request to the previously given servlet with no query string
sendGetMessage(Properties) - Method in class edu.ucsb.nceas.morpho.framework.HttpMessage
Performs a GET request to the previously given servlet Builds a query string from the supplied Properties list.
sendPostData(Properties) - Method in class edu.ucsb.nceas.morpho.framework.HttpMessage
Sends post data using url encoding.
sendPostData(Properties, Properties) - Method in class edu.ucsb.nceas.morpho.framework.HttpMessage
Sends post data using multipart/form-data encoding.
sendPostMessage() - Method in class edu.ucsb.nceas.morpho.framework.HttpMessage
Performs a POST request with no query parameters
sendPostMessage(Properties) - Method in class edu.ucsb.nceas.morpho.framework.HttpMessage
Deprecated. Replaced by #sendPostData(Properties args)
separator - Variable in class edu.ucsb.nceas.morpho.framework.DataStore
 
SEPARATOR_FOLLOWING - Static variable in class edu.ucsb.nceas.morpho.framework.ClientFramework
 
SEPARATOR_PRECEDING - Static variable in class edu.ucsb.nceas.morpho.framework.ClientFramework
Constant to indicate a spearator should precede an action
ServiceExistsException - exception edu.ucsb.nceas.morpho.framework.ServiceExistsException.
This exception is thrown when a plug registers a service under a serviceName that has previously been registered.
ServiceExistsException(String) - Constructor for class edu.ucsb.nceas.morpho.framework.ServiceExistsException
 
ServiceNotHandledException - exception edu.ucsb.nceas.morpho.framework.ServiceNotHandledException.
This exception is thrown when a service request is made of an object and that object can not properly handle the request, either because it is not designed to handle it, or there was an error in trying to handle it.
ServiceNotHandledException(String) - Constructor for class edu.ucsb.nceas.morpho.framework.ServiceNotHandledException
 
ServiceProvider - interface edu.ucsb.nceas.morpho.framework.ServiceProvider.
All component plugins that provide services must implement this interface so that the framework can identify them.
set_eChoiceVisible(boolean) - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
set_eChoiceVisible(boolean) - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
set_inputer(boolean) - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
set_inputer(boolean) - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
set(String, int, String) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
used to set a value corresponding to 'key'; value is changed in DOM structure in memory
setAbstractState(boolean) - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
set state of Abstract check box
setActiveDoc(MetaDoc) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Tell the append/insert buttons, when they are pressed to pass their ActionEvent to the actionPerformed method in the current document.
setActiveDoc(MetaDoc) - Method in class edu.ucsb.nceas.metaedit.MetaEditor
Set the currently active document.
setActiveDoc(MetaDoc) - Method in class edu.ucsb.nceas.metaedit.Inputer
Tell okButton, when it is pressed to pass its ActionEvent to the actionPerformed method in the current document.
setAllState(boolean) - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
set state of 'All' check box
setAppendablesList(Vector) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Fill the list of appendable elements with the element names from the given Vector.
setAttr(Hashtable) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
Change an attribute value given a set of defaults from the attribute declarations.
setAttr(Hashtable) - Method in class edu.ucsb.nceas.metaedit.Inputer
Set this pane's descriptive text area to the value of the 'description' attribute.
setAttr(Hashtable) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
Change an attribute value given a set of defaults from the attribute declarations.
setAttrFrame() - Method in class edu.ucsb.nceas.metaedit.MetaEditor
 
setAttribute(String, String) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Add a new attribute to this node, or set its value
setAttrTable(ElementFactory.TreeElement, Enumeration, TXAttribute[]) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame
 
setCardinality(String) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setCaseSensitive(boolean) - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
set if the QueryTerm is case sensitive
setClipboardObject(Object) - Method in class edu.ucsb.nceas.morpho.editor.EditorPlugin
 
setContainer(DocFrame) - Method in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
setController(EditorPlugin) - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
setCookie(String) - Static method in class edu.ucsb.nceas.morpho.framework.HttpMessage
return the cookie that this message object contains
setDocID(String) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Set the doc id of this node
setDoctype(String) - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
setDocumentLocator(Locator) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
setDocumentLocator(Locator) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Unused SAX handler
setEditor(MetaEditor) - Method in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
setEditor(String) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setFile(File) - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
setFilterDocList(Vector) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set the list of filter docs of this query
setHelp(String) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setIcon(String) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setIdentifier(String) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set the identifier of this query
setInsertablesList(Vector) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Fill the list of insertable elements with the element names from the given Vector.
setItem(boolean) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setJTextAreaInFocus(JTextArea) - Method in class edu.ucsb.nceas.metaedit.XMLPanels
 
setKeywordsState(boolean) - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
set state of Keywords check box
setMainContentPane(Component) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Set the content pane of the main Morpho window to display the component indicated.
setMDEHome(String) - Method in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
setName(String) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setNodeID(long) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Set the id of this node
setNodeIndex(int) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Set the node index of this node
setNodeType(String) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Set the type of this node
setObject(String) - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
Set the object of this triple
setOperator(String) - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
Set the operator for this QueryGroup
setOwnerList(Vector) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set the list of owners used to constrain this query
setParentID(long) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Set the parent id of this node
setParser(IBMParser) - Method in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
setPassword(String) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Set the password associated with this framework
setPathExpression(String) - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
set the path expression parameter
setPCValue(String) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setProfile(ConfigXML) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Set the profile for the currently logged in user (on startup, or when switching profiles).
setProfile(String) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Set the profile associated with this framework based on its name
setQuery(Query) - Method in class edu.ucsb.nceas.morpho.query.QueryDialog
Set the query that should be displayed and edited in the dialog
setQuery(Query) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Set the query that was used to construct these results (for use by LocalQuery)
setQueryGroup(QueryGroup) - Method in class edu.ucsb.nceas.morpho.query.Query
set the QueryGroup used to express query constraints
setQueryTitle(String) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set the title of this query
setRelationship(String) - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
Set the relationship of this triple
setResults(ResultSet) - Method in class edu.ucsb.nceas.morpho.query.ResultPanel
Set the ResultSet (usually as a result of refreshing or revising a Query)
setResultsVector(Vector) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
set the resultsVector
setReturnDocList(Vector) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set the list of return docs of this query
setReturnFieldList(Vector) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set the list of fields to be returned by this query
setRootEditor(String) - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
setRootElementName(String) - Method in class edu.ucsb.nceas.morpho.editor.DTDTree
 
setRootNodeID(long) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Set the root node id of this node
setSearchLocal(boolean) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set searchLocal
setSearchMetacat(boolean) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set searchMetacat
setSearchMode(String) - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
set the search mode field
setSearchMode(String) - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
set the searchmode parameter
setSearchMode(String) - Method in class edu.ucsb.nceas.morpho.query.TaxonTermPanel
set the search mode field
setSiteList(Vector) - Method in class edu.ucsb.nceas.morpho.query.Query
method to set the list of sites used to constrain this query
setSubject(String) - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
Set the subject of this triple
setTagName(String) - Method in class edu.ucsb.nceas.morpho.query.BasicNode
Set the name of this node
setTaxonRank(String) - Method in class edu.ucsb.nceas.morpho.query.TaxonTermPanel
set the taxon rank field
setText(String) - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
setTitle(String) - Method in class edu.ucsb.nceas.morpho.query.ResultFrame
Override setTitle to update the name and framework menus as well
setTitleState(boolean) - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
set state of Title check box
setTree(JTree) - Method in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
setTreeModel(DefaultTreeModel) - Method in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
setTreeValueFlag(boolean) - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
setUp() - Method in class edu.ucsb.nceas.morpho.framework.tests.ConnectTest
Establish a testing framework by initializing appropriate objects
setUserName(String) - Method in class edu.ucsb.nceas.morpho.framework.ClientFramework
Set the username associated with this framework
setUserObject(Object) - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
setValue(String) - Method in class edu.ucsb.nceas.morpho.query.SubjectTermPanel
set the text that is to be seached for.
setValue(String) - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
set the value parameter
setValue(String) - Method in class edu.ucsb.nceas.morpho.query.TaxonTermPanel
set the text that is to be seached for.
setValueAt(Object, int, int) - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.AttrJTableModel
 
setVisible(boolean) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizard
sets the visibility of the package wizard panel
setVisible(boolean) - Method in class edu.ucsb.nceas.morpho.editor.DocFrame
 
setVisible(boolean) - Method in class edu.ucsb.nceas.morpho.framework.SplashFrame
Show or hide the window.
shouldSelectCell(EventObject) - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
shouldSelectCell(EventObject) - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
show() - Method in class edu.ucsb.nceas.metaedit.NewDialog
Update the document type list before showing the dialog.
showOptions() - Method in class edu.ucsb.nceas.metaedit.AbstractMdeBean
 
showOptions() - Method in class edu.ucsb.nceas.metaedit.mdeBean
 
showOptions() - Method in class edu.ucsb.nceas.metaedit.Options
Displays the options dialog as a modal dialog
showOptions() - Method in class edu.ucsb.nceas.metaedit.MetaEditor
Show the options dialog box for editing
skippedEntity(String) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
skippedEntity(String) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Unused SAX handler
sortAttributes(NamedNodeMap) - Static method in class edu.ucsb.nceas.morpho.datapackage.PackageUtil
Returns a sorted list of attributes.
sortAttributes(NamedNodeMap) - Method in class edu.ucsb.nceas.morpho.framework.ConfigXML
Returns a sorted list of attributes.
SplashFrame - class edu.ucsb.nceas.morpho.framework.SplashFrame.
GUI window that provides information about Morpho, its contributors, and acknowlegements.
SplashFrame() - Constructor for class edu.ucsb.nceas.morpho.framework.SplashFrame
Construct the window
SplashFrame(boolean) - Constructor for class edu.ucsb.nceas.morpho.framework.SplashFrame
Construct a frame and display a note that the application is loading.
SplashFrame(String) - Constructor for class edu.ucsb.nceas.morpho.framework.SplashFrame
Construct a frame with a title
SplashFrame(String, boolean) - Constructor for class edu.ucsb.nceas.morpho.framework.SplashFrame
Construct a frame and display a note that the application is loading.
startDocument() - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
startDocument() - Method in class edu.ucsb.nceas.morpho.query.ResultSet
SAX handler callback that is called when an XML document is initially parsed.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleParser
 
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardShellParser
This method is called whenever a new start tag is encountered.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.morpho.datapackage.wizard.PackageWizardParser
This method is called whenever a new start tag is encountered.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.morpho.query.Query
callback method used by the SAX Parser when the start tag of an element is detected.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
SAX handler callback that is called upon the start of an element when parsing an XML document.
startPrefixMapping(String, String) - Method in class edu.ucsb.nceas.metaedit.MetaDoc
 
startPrefixMapping(String, String) - Method in class edu.ucsb.nceas.morpho.query.ResultSet
Unused SAX handler
stopCellEditing() - Method in class edu.ucsb.nceas.metaedit.InputerCellRenderer
 
stopCellEditing() - Method in class edu.ucsb.nceas.metaedit.InputerCellEditor
 
SubjectTermPanel - class edu.ucsb.nceas.morpho.query.SubjectTermPanel.
This panel contains all the elements for a single text query term.
SubjectTermPanel() - Constructor for class edu.ucsb.nceas.morpho.query.SubjectTermPanel
Constructor
suite() - Static method in class edu.ucsb.nceas.morpho.framework.tests.ConnectTest
Create a suite of tests to be run together

T

table - Variable in class edu.ucsb.nceas.morpho.editor.AttributeEditDialog
 
table - Variable in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
tableChanged(TableModelEvent) - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
TableDataToNodes() - Method in class edu.ucsb.nceas.morpho.editor.LocalDocTypesPanel
 
TaxonTermPanel - class edu.ucsb.nceas.morpho.query.TaxonTermPanel.
This panel contains all the elements for a single taxon query term.
TaxonTermPanel() - Constructor for class edu.ucsb.nceas.morpho.query.TaxonTermPanel
Constructor
tearDown() - Method in class edu.ucsb.nceas.morpho.framework.tests.ConnectTest
Release any objects after tests are complete
tempdir - Variable in class edu.ucsb.nceas.morpho.framework.DataStore
 
testInvalidLogin() - Method in class edu.ucsb.nceas.morpho.framework.tests.ConnectTest
Test if the logIn() function works given an invalid username and password
testLogout() - Method in class edu.ucsb.nceas.morpho.framework.tests.ConnectTest
Test if the logOut() function works
testValidLogin() - Method in class edu.ucsb.nceas.morpho.framework.tests.ConnectTest
Test if the logIn() function works given a valid username and password
TextAreaPanel - class edu.ucsb.nceas.morpho.editor.TextAreaPanel.
TextAreaPanel is an example of a special panel editor for use with the DocFrame class.
TextAreaPanel(DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.TextAreaPanel
 
textNodeTojtaHash - Variable in class edu.ucsb.nceas.metaedit.XMLPanels
 
toFormatedXML() - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
return this triple in xml format with easy to read formatting.
toFormatedXML() - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
returns a nicely formatted string representation of this collection in xml the xml looks like this:
topPanel - Variable in class edu.ucsb.nceas.metaedit.XMLPanels
 
topPanel - Variable in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
toString() - Method in class edu.ucsb.nceas.metaedit.ElementFactory.TreeElement
 
toString() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.DataElement
 
toString() - Method in class edu.ucsb.nceas.metaedit.AttrEditFrame.DataElementNAME_TOKEN_GROUP
 
toString() - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
return this triple as a string
toString() - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
return this collection as a string
toString() - Method in class edu.ucsb.nceas.morpho.editor.NodeInfo
 
toString() - Method in class edu.ucsb.nceas.morpho.query.Query
create a String description of the query that this instance represents.
toString() - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
create a String description of the query that this instance represents.
toString() - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
create a String description of the query that this instance represents.
toXml() - Method in class edu.ucsb.nceas.morpho.query.Query
create a XML serialization of the query that this instance represents
toXML() - Method in class edu.ucsb.nceas.metaedit.MetaDoc
Display the XML text in the preview window.
toXML() - Method in class edu.ucsb.nceas.morpho.datapackage.Triple
return this triple in xml format.
toXML() - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
 
toXml(int) - Method in class edu.ucsb.nceas.morpho.query.QueryGroup
create a XML serialization of the query that this instance represents
toXml(int) - Method in class edu.ucsb.nceas.morpho.query.QueryTerm
create a XML serialization of the query that this instance represents
toXML(String) - Method in class edu.ucsb.nceas.morpho.datapackage.TripleCollection
returns a string representation of this collection in xml format.
tree - Variable in class edu.ucsb.nceas.morpho.editor.DocFrame
 
tree - Variable in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
treeModel - Variable in class edu.ucsb.nceas.morpho.editor.DocFrame
 
treeModel - Variable in class edu.ucsb.nceas.morpho.editor.XMLPanels
 
treeModel - Variable in class edu.ucsb.nceas.morpho.editor.DTDTree
 
Triple - class edu.ucsb.nceas.morpho.datapackage.Triple.
This class implements one triple which defines one relationship inside of a package.
Triple() - Constructor for class edu.ucsb.nceas.morpho.datapackage.Triple
create an initialized, blank Triple object
Triple(String, String, String) - Constructor for class edu.ucsb.nceas.morpho.datapackage.Triple
create a new triple with the specified subject relationship and object
Triple(Triple) - Constructor for class edu.ucsb.nceas.morpho.datapackage.Triple
Copy constructor.
TripleCollection - class edu.ucsb.nceas.morpho.datapackage.TripleCollection.
This class implements a collection of triples which make up all of the relationships in a package.
TripleCollection() - Constructor for class edu.ucsb.nceas.morpho.datapackage.TripleCollection
Default Constructor
TripleCollection(File, ClientFramework) - Constructor for class edu.ucsb.nceas.morpho.datapackage.TripleCollection
parses an xml document and pulls any triples out of it.
TripleCollection(Reader) - Constructor for class edu.ucsb.nceas.morpho.datapackage.TripleCollection
read an xml file, build the collection from any triples in the xml file.
TripleCollection(TripleCollection) - Constructor for class edu.ucsb.nceas.morpho.datapackage.TripleCollection
Copy constructor.
TripleCollection(Vector) - Constructor for class edu.ucsb.nceas.morpho.datapackage.TripleCollection
create a collection of triples from a vector of Triple objects.
TripleParser - class edu.ucsb.nceas.morpho.datapackage.TripleParser.
A Class implementing callback bethods for the SAX parser.
TripleParser(Reader, String) - Constructor for class edu.ucsb.nceas.morpho.datapackage.TripleParser
 

U

upload() - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackage
Uploads a local package to metacat
upload(String) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin
Uploads the package to metacat.
upload(String) - Method in interface edu.ucsb.nceas.morpho.framework.DataPackageInterface
This method is called to upload a datapackage that is currently stored locally to metacat
usernameChanged(String) - Method in interface edu.ucsb.nceas.morpho.framework.ConnectionListener
This method is called if there is a change in the username.
usernameChanged(String) - Method in class edu.ucsb.nceas.morpho.query.QueryPlugin
Implement the ConnectionListener interface so we know when to refresh queries.

V

validateElement(ElementFactory.TreeElement) - Method in interface edu.ucsb.nceas.metaedit.ParserDriver
 
validateElement(ElementFactory.TreeElement) - Method in class edu.ucsb.nceas.metaedit.IBMParser
 
valueChanged(ListSelectionEvent) - Method in class edu.ucsb.nceas.metaedit.Options
Processes events generated when the user changes the selection in the list of document types.
valueChanged(ListSelectionEvent) - Method in class edu.ucsb.nceas.metaedit.ElementChoice
Record the selected value whenever the user changes it.
VariablePanel - class edu.ucsb.nceas.morpho.editor.VariablePanel.
VariablePanel is an example of a very plug-in panel to be used by the XML editor.
VariablePanel(DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.VariablePanel
 
VERSION - Static variable in class edu.ucsb.nceas.morpho.framework.ClientFramework
The version of this release of Morpho

W

whitePixel - Static variable in class edu.ucsb.nceas.metaedit.CustomTreeCellRenderer
 
windowActivated(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
windowActivated(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
windowClosed(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
windowClosed(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
windowClosing(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
windowClosing(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
windowDeactivated(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
windowDeactivated(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
windowDeiconified(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
windowDeiconified(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
windowIconified(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
windowIconified(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
windowOpened(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.DataPackageGUI
 
windowOpened(WindowEvent) - Method in class edu.ucsb.nceas.morpho.datapackage.AddMetadataWizard
 
WrappedTextRenderer - class edu.ucsb.nceas.morpho.query.WrappedTextRenderer.
Renders the contents of a table cell as a JTextArea to allow for multiple lines that wrap within the cell.
WrappedTextRenderer(int) - Constructor for class edu.ucsb.nceas.morpho.query.WrappedTextRenderer
Create the renderer with appropriate formatting options set
writeEncodedMultipartForm(OutputStream) - Method in class edu.ucsb.nceas.morpho.framework.MultipartForm
Write the multipart/form-data encoded version of the form to the provided output stream, using a default bufferSize of 4096 bytes for reading in the files.
writeEncodedMultipartForm(OutputStream, int) - Method in class edu.ucsb.nceas.morpho.framework.MultipartForm
Write the multipart/form-data encoded version of the form to the provided output stream, using the provided bufferSize for reading in the files.

X

XMLElement - class edu.ucsb.nceas.morpho.datapackage.wizard.XMLElement.
object that represents an Element and any content inside of it.
XMLElement() - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.XMLElement
 
XMLElement(XMLElement) - Constructor for class edu.ucsb.nceas.morpho.datapackage.wizard.XMLElement
copy constructor
XMLPanels - class edu.ucsb.nceas.metaedit.XMLPanels.
 
XMLPanels - class edu.ucsb.nceas.morpho.editor.XMLPanels.
 
XMLPanels() - Constructor for class edu.ucsb.nceas.morpho.editor.XMLPanels
Default constructor.
XMLPanels(DefaultMutableTreeNode) - Constructor for class edu.ucsb.nceas.morpho.editor.XMLPanels
Constructs a panel tree with the specified root.
XMLPanels(DefaultMutableTreeNode, int) - Constructor for class edu.ucsb.nceas.morpho.editor.XMLPanels
Constructs a panel tree with the specified root.
XMLPanels(JTree, Document, JScrollPane) - Constructor for class edu.ucsb.nceas.metaedit.XMLPanels
 
XMLTreeCellRenderer - class edu.ucsb.nceas.morpho.editor.XMLTreeCellRenderer.
This class is a simple extension of the DefaultTreeCell Renderer that uses an ImageIcon stored in the NodeInfo UserObject of a tree node as the icon of a node when it is displayed in a tree.
XMLTreeCellRenderer() - Constructor for class edu.ucsb.nceas.morpho.editor.XMLTreeCellRenderer
Constructor
XPathAPI - class edu.ucsb.nceas.morpho.framework.XPathAPI.
The methods in this class are convenience methods into the low-level XPath API.
XPathAPI() - Constructor for class edu.ucsb.nceas.morpho.framework.XPathAPI
 

A B C D E F G H I J L M N O P Q R S T U V W X

Copyright © 2000 National Center for Ecological Analysis and Synthesis. All Rights Reserved.