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

A

abortJob(Job) - Method in class org.peace_tools.core.JobMenuHelper

Method to abort a job running on a server.

ABOUT_ERROR - Static variable in class org.peace_tools.core.HelpMenuHelper

This message is displayed when the default system browser could not be launched to display help.

AboutDialog - Class in org.peace_tools.core

AboutDialog(JFrame) - Constructor for class org.peace_tools.core.AboutDialog

The constructor.

AbstractMenuHelper - Class in org.peace_tools.core

The base class for various menu helpers.

AbstractMenuHelper(AbstractMenuHelper.HelperType, MainFrame) - Constructor for class org.peace_tools.core.AbstractMenuHelper

AbstractMenuHelper.ActionType - Enum in org.peace_tools.core

Enumeration to enable referring to a specific type of action.

AbstractMenuHelper.ActionType() - Constructor for enum org.peace_tools.core.AbstractMenuHelper.ActionType

AbstractMenuHelper.HelperType - Enum in org.peace_tools.core

Enumeration to enable convenient identification/classification of menu helper objects.

AbstractMenuHelper.HelperType() - Constructor for enum org.peace_tools.core.AbstractMenuHelper.HelperType

accept(ActionEvent) - Method in class org.peace_tools.core.WorkspaceChooser

This is a refactored (to keep code clutter to a minimum in the actionPerformed() method) method that is called only from the actionPerformed() method whenever the user clicks on the "Accept" button in the license tab.

ActionCmds - Static variable in class org.peace_tools.core.FileMenuHelper

The strings for the action commands generated by the various menu items in the help menu.

ActionCmds - Static variable in class org.peace_tools.core.HelpMenuHelper

The strings for the action commands generated by the various menu items in the help menu.

ActionCmds - Static variable in class org.peace_tools.core.ServerMenuHelper

The strings for the action commands generated by the various menu items in the help menu.

ActionCmds - Static variable in class org.peace_tools.core.ViewMenuHelper

The strings for the action commands generated by the various menu items in the help menu.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.dataset.ESTInfoWizardPage

This method handles the tasks performed when the "Browse" button is clicked.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.DeleteDialog

Handle clicking of OK or Cancel buttons.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.FileMenuHelper

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.HelpMenuHelper

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.job.AnalyzerWizardPage

Action listener to enable/disable frame depending on analyzer selected.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.job.ClusterWizardPage

Method to handle clicking of "Browse" button.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.job.FiltersWizardPage

Method to handle clicking of check boxes.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.job.HeuristicsWizardPage

Method to handle clicking of check boxes.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.job.MSTWizardPage

Method to handle clicking of "Browse" button.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.JobMenuHelper

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.MainFrame

The action performed method that handles various application-level events.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.server.ServerInfoWizardPage

This method handles the tasks performed when the "Browse" button is clicked.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.server.ServerTypeWizardPage

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.ServerConnectionTester

Handle user clicking the "Interrupt" button.

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.ServerMenuHelper

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.ViewMenuHelper

actionPerformed(ActionEvent) - Method in class org.peace_tools.core.WorkspaceChooser

This method handles the actions associated with various controls in the dialog.

actionPerformed(ActionEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabButton

Close tab when button is clicked.

actionPerformed(ActionEvent) - Method in class org.peace_tools.generic.WizardDialog

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.ClusterTreeTableView

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.DataSetPopupMenu

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.DataSetTreeView

Action listener to handle call backs from pop up menu items.

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.DBClassifierEditor

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.DetailView

Method to intercept clicks on "Refresh" button.

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.ESTTableView

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.LogPane

The event-callback handler for the "Choose..." button, the "SaveLogs" button, and the combo box.

actionPerformed(ActionEvent) - Method in class org.peace_tools.views.overlap.ClusterList

add(MSTData) - Method in class org.peace_tools.workspace.DataSet

Add a new Minimum Spanning Tree (MST) data file to this data set.

add(MSTClusterData) - Method in class org.peace_tools.workspace.DataSet

Add a new MST-based clustering data file to this data set.

add(Job) - Method in class org.peace_tools.workspace.JobList

Method to add a new job entry to the job list.

add(Server) - Method in class org.peace_tools.workspace.ServerList

Method to add a new server entry to this server list.

addActionListener(ActionListener) - Method in class org.peace_tools.views.DataSetPopupMenu

Add a given action listener to all menu items.

addChild(ClusterNode) - Method in class org.peace_tools.data.ClusterNode

Add another cluster as the child cluster of this cluster node.

addChild(MSTNode) - Method in class org.peace_tools.data.MSTNode

Add another MSTNode as the child node of this node.

addDataSet(DataSet) - Method in class org.peace_tools.workspace.Workspace

Method to add a new data set to the workspace.

addElement(Element, String, String) - Static method in class org.peace_tools.workspace.DOMHelper

Helper method to add a new element to a given DOM node.

addKnownHost(String, int, String, byte[]) - Method in class org.peace_tools.core.session.RemoteServerSession

Method to add a new host entry to the list of known hosts.

addListDataListener(ListDataListener) - Method in class org.peace_tools.data.OverlapModel

Adds a listener to be notified when the data associated with the model changes.

addListener(DnDTabListener) - Static method in class org.peace_tools.generic.dndTabs.DnDTabbedPane

Add a listener to be notified when a tab in this panel is deleted.

addLog(String) - Method in class org.peace_tools.core.PEACEInstaller

Helper method to add informational output.

addLog(String, String) - Method in class org.peace_tools.core.PEACEInstaller

Helper method to add string to output and scroll it.

addLogFileNameControls(JToolBar) - Method in class org.peace_tools.views.LogPane

This is a refactored utility method that is used in the constructor to create the log file display area, the "Change..." button, and the toggle button to enable/disabling writing logs to the file.

addLogLevelChanger(JToolBar) - Method in class org.peace_tools.views.LogPane

This is a utility method that is invoked just from the constructor to create a combo box that permits the user to change the log level.

addLogListener(LogListener) - Method in class org.peace_tools.generic.Log

Adds a log listener (typically a view derived off of LogPane) to the set of listeners to be notified whenever log information changes.

addMouseAdapter(JComponent) - Method in class org.peace_tools.views.DataSetFileListView

A refactored helper method to add a mouse adapter.

addMouseAdapter(JTree) - Method in class org.peace_tools.views.DataSetTreeView

A refactored helper method to add a mouse adapter.

addMouseAdapter(JComponent) - Method in class org.peace_tools.views.JobListView

A refactored helper method to add a mouse adapter.

addMouseAdapter(JComponent) - Method in class org.peace_tools.views.ServerListView

A refactored helper method to add a mouse adapter.

addPage(WizardPage) - Method in class org.peace_tools.generic.WizardDialog

Adds a new wizard page to the list of wizard dialog pages.

addParameter(Param) - Method in class org.peace_tools.workspace.Filter

Add a parameter to the filter.

addParameter(Param) - Method in class org.peace_tools.workspace.Heuristic

Add a parameter to the heuristic.

addPropertiesRenderer(JTree) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Method to set a custom cell renderer to handle icons better.

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

Add a new server entry.

addThread(Thread) - Method in class org.peace_tools.generic.WizardDialog

Adds a given worker thread to the wizard.

addToESTEntryTable(int, ESTEntry) - Method in class org.peace_tools.data.OverlapModel

Add an entry to the specified row in the estEntryTable.

addTreeModelListener(TreeModelListener) - Method in class org.peace_tools.data.ClusterTreeTableModel

Adds a listener to be notified when the data associated with the data set changes.

addTreeModelListener(TreeModelListener) - Method in class org.peace_tools.data.DataSetTreeModel

Adds a listener to be notified when the data associated with the data set changes.

addTreeModelListener(TreeModelListener) - Method in class org.peace_tools.data.MSTTreeModel

Adds a listener to be notified when the data associated with the data set changes.

addView(JComponent, String, ViewFactory.ViewType) - Method in class org.peace_tools.core.ViewFactory

Utility method to add a newly created view to display and internal tables.

addWorkspaceListener(WorkspaceListener) - Method in class org.peace_tools.workspace.Workspace

Add a workspace listener to receive change notification events from this workspace.

addXAxisLabels(Rectangle) - Method in class org.peace_tools.views.ClusterSummaryView

Helper method to create X-axis labels.

addYAxisLabels(Rectangle) - Method in class org.peace_tools.views.ClusterSummaryView

Helper method to create Y-axis labels.

adjustCheckBox(JCheckBox, String) - Method in class org.peace_tools.core.job.FiltersWizardPage

Helper method to correctly format, enhance, and layout a given check box.

adjustCheckBox(JCheckBox, String) - Method in class org.peace_tools.core.job.HeuristicsWizardPage

Helper method to correctly format, enhance, and layout a given check box.

adjustDimension(Component, int, int) - Static method in class org.peace_tools.generic.Utilities

Helper method to set the preferred and maximum size of a component.

adjustFont(Component, int, int, int) - Static method in class org.peace_tools.generic.Utilities

Utility method to change the font size set for a given component.

alignmentMetric - Variable in class org.peace_tools.data.ESTEntry

The alignment metric generated by a given EST analyzer indicating some of the alignment relationship between this node and its parent node.

alignmentMetric - Variable in class org.peace_tools.data.MSTNode

The alignment metric generated by a given EST analyzer indicating some of the alignment relationship between this node and its parent node.

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

Information about the distance/similarity analyzer that was used to create this MST data set.

analyzerList - Variable in class org.peace_tools.core.job.AnalyzerWizardPage

A combo-box to select the type of frame/word algorithm to be used for computing similarity metric.

ANALYZERS - Static variable in class org.peace_tools.core.job.AnalyzerWizardPage

The list of analyzers that the user can choose from to compare two ESTs to determine similarity or distance.

AnalyzerWizardPage - Class in org.peace_tools.core.job

This class serves as an interactive page in a JobWizard.

AnalyzerWizardPage(JobWizard) - Constructor for class org.peace_tools.core.job.AnalyzerWizardPage

The constructor.

applyClassifiers(boolean) - Method in class org.peace_tools.views.DBClassifierEditor

Helper method to validate regular expressions and apply them to the work space.

area - Variable in class org.peace_tools.views.ClusterSummaryView

The area in the graph pane where the actual graph is drawn.

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

The 4 block arrow cursors that are internally used by this DnD handler.

attributes - Variable in class org.peace_tools.core.FileInfo

The various attributes defining the file.

AuthorImages - Variable in class org.peace_tools.core.AboutDialog

The icons to be displayed for each author to make the about dialog a bit more fancy.

AuthorList - Variable in class org.peace_tools.core.AboutDialog

The list of authors and their information to be loaded from text files in PEACE install directory.

awp - Variable in class org.peace_tools.core.job.HeuristicsWizardPage

A reference to the analyzer wizard page from where the the frame size set for the analyzer is obtained and used to seed the frame size for the t/v heuristic.

awp - Variable in class org.peace_tools.core.job.JobWizard

The analyzer wizard page contains the analyzer information to be used for constructing the MST for this job.

axisScale - Variable in class org.peace_tools.views.ClusterSummaryView

The x and y axis scale controllers.

axisScale - Variable in class org.peace_tools.views.overlap.OverlapView

The row and column size scale controllers.