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

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dataSet - Variable in class org.peace_tools.core.dataset.DataSetWizard

This is the server entry that is being currently edited via this wizard.

dataSet - Variable in class org.peace_tools.core.dataset.ESTInfoWizardPage

Information about the actual data set entry being edited.

dataSet - Variable in class org.peace_tools.core.dataset.SummaryWizardPage

Information about the actual data set entry being edited.

DataSet - Class in org.peace_tools.workspace

The top-level data set that encapsulates the meta data regarding data files that are all related to a single EST file.

DataSet(String, String, String) - Constructor for class org.peace_tools.workspace.DataSet

Constructor to create a Data Set entry.

dataSet - Variable in class org.peace_tools.workspace.MSTClusterData

Reference to the data set that logically contains this MSTData element.

dataSet - Variable in class org.peace_tools.workspace.MSTData

Reference to the data set that logically contains this MSTData element.

DATASET_ERROR - Static variable in class org.peace_tools.core.DeleteDialog

Message to be displayed to the user (after formatting) to report error when deleting a workspace entry.

DATASET_ICON - Static variable in class org.peace_tools.views.PropertiesTreeMaker

A static constant to refer to the data set icon position in the PropertiesTreeMaker.CustomIcons array.

DataSetFileListView - Class in org.peace_tools.views

This class provides a tabular view of the list of files that are currently configured in this work space.

DataSetFileListView(MainFrame) - Constructor for class org.peace_tools.views.DataSetFileListView

The default constructor.

DataSetFileListView.ServerNameStatusRenderer - Class in org.peace_tools.views

A inner class to serve as a special renderer that puts file names along with a suitable icon.

DataSetFileListView.ServerNameStatusRenderer() - Constructor for class org.peace_tools.views.DataSetFileListView.ServerNameStatusRenderer

Default constructor.

dataSetList - Variable in class org.peace_tools.core.job.JobInfoWizardPage

A combo-box to select the data set to be used for this job.

dataSetList - Variable in class org.peace_tools.workspace.Workspace

The list of data sets that have been configured for use in this work space.

DataSetPopupMenu - Class in org.peace_tools.views

Class to generate and handle pop-up menus for data set viewers.

DataSetPopupMenu(MainFrame, boolean) - Constructor for class org.peace_tools.views.DataSetPopupMenu

Creates all the menu entries to be displayed in the menu.

DataSetTableModel - Class in org.peace_tools.data

DataSetTableModel() - Constructor for class org.peace_tools.data.DataSetTableModel

The default constructor.

dataSetTree - Variable in class org.peace_tools.views.DataSetTreeView

The actual JTree that provides a hierarchical view of the data files currently configured on this work space.

DataSetTreeModel - Class in org.peace_tools.data

A bridge class between a Workspace and a JTree.

DataSetTreeModel() - Constructor for class org.peace_tools.data.DataSetTreeModel

The default constructor.

DataSetTreeView - Class in org.peace_tools.views

DataSetTreeView(MainFrame) - Constructor for class org.peace_tools.views.DataSetTreeView

The constructor creates the tree view using the data from the current work space.

DataSetTreeView.DataSetRenderer - Class in org.peace_tools.views

A tree cell renderer that essentially provides a better representative set of Icons to make the overall display look a bit prettier.

DataSetTreeView.DataSetRenderer() - Constructor for class org.peace_tools.views.DataSetTreeView.DataSetRenderer

DataSetWizard - Class in org.peace_tools.core.dataset

This class serves as the top-level class for adding a new data set entry to the work space.

DataSetWizard(String, MainFrame) - Constructor for class org.peace_tools.core.dataset.DataSetWizard

The constructor for the data set wizard.

DataStore - Class in org.peace_tools.data

A helper class to load and maintain data files.

DataStore() - Constructor for class org.peace_tools.data.DataStore

The constructor.

dataStore - Static variable in class org.peace_tools.data.DataStore

The globally unique singleton instance of this class that is shared by all the other classes that require data files to be loaded.

dbClassifier - Variable in class org.peace_tools.data.EST

Index of the classifier in the Work space's classifier list with which this EST is associated.

DBClassifier - Class in org.peace_tools.workspace

Database (DB) Classifier to distinguish ESTs from different databases.

DBClassifier(String, String, int, boolean) - Constructor for class org.peace_tools.workspace.DBClassifier

Constructor to create a classifier object with the fixed value fields initialized to specific values.

DBClassifierEditor - Class in org.peace_tools.views

This class provides a comprehensive editor for modifying the DBClassifierEditor.

DBClassifierEditor(MainFrame) - Constructor for class org.peace_tools.views.DBClassifierEditor

The constructor.

DBClassifierEditor.ColorEditor - Class in org.peace_tools.views

Custom cell editor to display color chooser dialog to change colors.

DBClassifierEditor.ColorEditor() - Constructor for class org.peace_tools.views.DBClassifierEditor.ColorEditor

DBClassifierEditor.ColorRenderer - Class in org.peace_tools.views

A simple renderer that uses a JLabel to render the color for a DB classifier.

DBClassifierEditor.ColorRenderer(JTable) - Constructor for class org.peace_tools.views.DBClassifierEditor.ColorRenderer

The constructor to setup initial configuration for rendering colors.

decode(char) - Static method in class org.peace_tools.generic.Log

Utility method to convert an encoded log level character (obtained via a call to the encode() method) to corresponding LogLevel enumeration value.

defaultRenderer - Variable in class org.peace_tools.views.JobListView.JobStatusRenderer

The label with a given status string that is used when the job is in a non-running status.

defaultViewFactory - Variable in class org.peace_tools.core.MainFrame

The default view factory that is used to create all the views associated with this main frame.

DeleteDialog - Class in org.peace_tools.core

DeleteDialog(MainFrame, Object) - Constructor for class org.peace_tools.core.DeleteDialog

The constructor.

deleteFiles - Variable in class org.peace_tools.core.DeleteDialog

A check box to determine if the user wants the physical file to be deleted as well.

deleteLocalFile(String) - Method in class org.peace_tools.core.DeleteDialog

Helper method to delete a local file.

deleteRemoteDir(Server, String) - Method in class org.peace_tools.core.DeleteDialog

Helper method to recursively delete file on server.

deleteServer() - Method in class org.peace_tools.core.ServerMenuHelper

Helper method to verify and delete server entry.

deleteTab(Component) - Method in class org.peace_tools.generic.dndTabs.DnDTabbedPane

Delete (and remove) a given tab component.

delJobFiles(Job) - Method in class org.peace_tools.core.DeleteDialog

Helper method to delete files for a given job.

delPath - Variable in class org.peace_tools.core.DeleteDialog

This label is used to display the actual path being deleted when physical file deletion is requested.

deployRunnerScript() - Method in class org.peace_tools.core.job.SubmitJobWizardPage

This is a helper method that is used to deploy the job runner script to the server.

description - Variable in class org.peace_tools.core.dataset.ESTInfoWizardPage

Field to read and edit a brief description about the server.

description - Variable in class org.peace_tools.core.job.ClusterWizardPage

A brief description about the cluster file.

description - Variable in class org.peace_tools.core.job.JobInfoWizardPage

Field to read and edit a brief description about the job.

description - Variable in class org.peace_tools.core.server.ServerInfoWizardPage

Field to read and edit a brief description about the server.

description - Variable in class org.peace_tools.workspace.DataSet

A user defined description for this EST data file.

description - Variable in class org.peace_tools.workspace.DBClassifier

A user defined description for this DB classifier enttry.

description - Variable in class org.peace_tools.workspace.Job

A user defined description for this job.

description - Variable in class org.peace_tools.workspace.MSTClusterData

A user defined description for this file.

description - Variable in class org.peace_tools.workspace.MSTData

A user defined description for this file.

description - Variable in class org.peace_tools.workspace.Server

A user-assigned description for this server entry.

desktop - Variable in class org.peace_tools.core.MainFrame

This is the parent component of all the tabs and tabbed panes that constitute the visual layout of the main frame.

DetailView - Class in org.peace_tools.views

A common base class shared by JobDetailsView and ServerJobsView.

DetailView(String, String, Server) - Constructor for class org.peace_tools.views.DetailView

The constructor.

dialog - Variable in class org.peace_tools.core.ServerConnectionTester

The dialog that is being used to display some message and progress information to the user.

DIR_ATTRIB - Static variable in class org.peace_tools.core.FileInfo

Bit value indicating if this entry is a directory.

DISCLAIMER - Static variable in class org.peace_tools.core.Version

The standard disclaimer message.

disconnect() - Method in class org.peace_tools.core.session.LocalServerSession

Method to disconnect from a remote server.

disconnect() - Method in class org.peace_tools.core.session.RemoteServerSession

Method to disconnect from a remote server.

disconnect() - Method in class org.peace_tools.core.session.ServerSession

Disconnect and close connection to a server.

disposeDialog() - Method in class org.peace_tools.core.DeleteDialog

Helper method to hide and dispose this dialog.

DnDTabbedPane - Class in org.peace_tools.generic.dndTabs

DnDTabbedPane() - Constructor for class org.peace_tools.generic.dndTabs.DnDTabbedPane

The default constructor.

DnDTabbedPane.Location - Enum in org.peace_tools.generic.dndTabs

Preferred docking locations for tabs.

DnDTabbedPane.Location() - Constructor for enum org.peace_tools.generic.dndTabs.DnDTabbedPane.Location

DnDTabButton - Class in org.peace_tools.generic.dndTabs

This is a simple component that provides a custom close button on the currently active tab in a DnDTabbedPane.

DnDTabButton(DnDTabbedPane, int) - Constructor for class org.peace_tools.generic.dndTabs.DnDTabButton

The constructor.

DnDTabHandler - Class in org.peace_tools.generic.dndTabs

This class provides the necessary infrastructure for handling Drag-and-Drop features of a Tab from one TabbedPane to another.

DnDTabHandler(DnDTabbedPane) - Constructor for class org.peace_tools.generic.dndTabs.DnDTabHandler

The constructor.

DnDTabHandler.TransferableTab - Class in org.peace_tools.generic.dndTabs

This inner class provides a wrapper that impelements Transferable interface to simply provide a place holder for DnD operations.

DnDTabHandler.TransferableTab() - Constructor for class org.peace_tools.generic.dndTabs.DnDTabHandler.TransferableTab

The only constructor for creating a transferable tab.

DnDTabListener - Interface in org.peace_tools.generic.dndTabs

Interface to announce deletion of a tab in a DnDTabbedPane.

DnDTabPos - Class in org.peace_tools.generic.dndTabs

Class to remember position of a DnDTabPane.

DnDTabPos() - Constructor for class org.peace_tools.generic.dndTabs.DnDTabPos

The default constructor.

dockCue - Variable in class org.peace_tools.generic.dndTabs.DnDTabbedPane

This instance variable is used to track if this DndTabbedPane should paint a outline on itself to indicate where a tab being dragged will be docked with respect to this window.

DocTitles - Static variable in class org.peace_tools.views.JobDetailsView

The title strings associated with the 4 documents.

doInBackground() - Method in class org.peace_tools.core.PEACEInstaller

DOMHelper - Class in org.peace_tools.workspace

This class contains a collection of static utility method that are used to retrieve or create elements in a given DOM tree.

DOMHelper() - Constructor for class org.peace_tools.workspace.DOMHelper

This class is not meant to be instantiated.

done(boolean) - Method in class org.peace_tools.core.dataset.DataSetWizard

This method overrides the final notification method in this wizard to add the new data set (if wizard was successfully completed) to the workspace.

done(boolean) - Method in class org.peace_tools.core.job.JobWizard

This method overrides the final notification method in this wizard.

done(boolean) - Method in class org.peace_tools.core.server.ServerWizard

This method overrides the final notification method in this class to launch the actuall background installer thread if the wizard successfully completed.

done(boolean) - Method in class org.peace_tools.generic.WizardDialog

Helper method invoked once the wizard is done.

download(ProgressMonitor, String, String) - Static method in class org.peace_tools.generic.Utilities

Helper method for download a file from a given URL.

dragContext - Static variable in class org.peace_tools.generic.dndTabs.DnDTabHandler

This instance variable is filled in by the source pane when a drag operation is started and reset to null once the drag operation is completed.

dragDropEnd(DragSourceDropEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is a part of the DragSourceListener interface.

dragEnter(DragSourceDragEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is a part of the DragSourceListener interface.

dragEnter(DropTargetDragEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is part of the DropTargetListener.

dragExit(DragSourceEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is a part of the DragSourceListener interface.

dragExit(DropTargetEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is part of the DropTargetListener.

dragGestureRecognized(DragGestureEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is a part of the DragGestureListener interface.

dragMouseMoved(DragSourceDragEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is part of the DragSourceMotionListener method.

dragOver(DragSourceDragEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is a part of the DragSourceListener interface.

dragOver(DropTargetDragEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is part of the DropTargetListener.

dragSource - Variable in class org.peace_tools.generic.dndTabs.DnDTabHandler

The drag source object associated with this DnD handler.

drawClassificationBars(Graphics, Rectangle, ClusterNode) - Method in class org.peace_tools.views.ClusterSummaryView

Draw clustering classification information in the graph.

drawGraph(Graphics) - Method in class org.peace_tools.views.ClusterSummaryView

Top-level method to draw the cluster graph.

drop(DropTargetDropEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is part of the DropTargetListener interface.

dropActionChanged(DragSourceDragEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is a part of the DragSourceListener interface.

dropActionChanged(DropTargetDragEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This method is part of the DropTargetListener.

dropDownButton - Variable in class org.peace_tools.views.overlap.ClusterList

The drop down button (with a small triangle) to display cluster pop up list.