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

C

cache - Variable in class org.peace_tools.data.DataStore

A weak hash map that serves as a cache to hold MST, EST, and cluster data file entries in it.

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

A combo-box to select the type of caching that must be used to cache intermediate values to improve performance of the analyzer.

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

The size of the cache (number of entries maintained in the cache) to be used for analysis.

cacheSize - Variable in class org.peace_tools.workspace.FWAnalyzer

The size of each cache entry (per EST) in number of distance/similarity metrics that are to be cached to avoid having to recompute metrics.

cacheType - Variable in class org.peace_tools.workspace.FWAnalyzer

The type of cache that was used to hold the data distance/similarity metric when the analysis was conducted.

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

Helper method invoked when user clicks cancel button.

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

Helper method invoked when user clicks cancel button.

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

Helper method invoked when user clicks cancel button.

cancel() - Method in class org.peace_tools.generic.WizardDialog

Helper method invoked when user clicks cancel button.

CANCEL_MSG - Variable in class org.peace_tools.views.DBClassifierEditor

A conventional message to be displayed to the user prior to canceling out of this dialog.

cancelButton - Variable in class org.peace_tools.generic.WizardDialog

The "Cancel" button that is displayed at the bottom of the wizard in a separate panel.

canExecute() - Method in class org.peace_tools.core.FileInfo

Determine if this entry is executable.

canRead() - Method in class org.peace_tools.core.FileInfo

Determine if this entry is readable.

CANT_ABORT_JOB - Static variable in class org.peace_tools.core.JobMenuHelper

An error message that is formatted (to fill-in missing information) and displayed to the user if aborting a job fails.

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

A message that is formatted and displayed to the user when a server corresponding to a given job entry could not be located in the work space.

CANT_FIND_SERVER - Static variable in class org.peace_tools.core.JobMenuHelper

An error message that is formatted (to fill-in missing information) and displayed to the user when a server entry could not be successfully located to abort a job.

CANT_MAKE_VIEW - Static variable in class org.peace_tools.core.ViewFactory

A static message that is to be displayed if a view could not be opened.

canWrite() - Method in class org.peace_tools.core.FileInfo

Determine if this entry is writable.

CAUTION_MSG - Static variable in class org.peace_tools.core.job.VerifyWizardPage

A simple caution message that is displayed at the bottom of the wizard page.

center - Variable in class org.peace_tools.core.server.ServerWizard

The DnDTabbedPane to which the actual PEACE installer tab must be added.

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

The permanent tab that is always present in in the main frame.

centerPanel(Window, Window) - Static method in class org.peace_tools.generic.Utilities

Helper method to center a given child on a parent.

CHANGE_LOG_FILE_NAME - Static variable in class org.peace_tools.views.LogPane

A string constant to ensure that the action command associated with a swing component and its action listener are consistently used without causing any issues.

CHANGE_LOG_LEVEL - Static variable in class org.peace_tools.views.LogPane

A string constant to ensure that the action command associated with a swing component and its action listener are consistently used without causing any issues.

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

A tool bar style button that permits the user to change the colors associated with the selected clusters.

changeCredentialsOnly - Variable in class org.peace_tools.core.server.ServerTypeWizardPage

If this flag is set to true, then this wizard permits the user only to change the credentials associated with a remote server.

changedUpdate(DocumentEvent) - Method in class org.peace_tools.core.PEACEInstaller

Implementation for method in DocumentListener to scroll to end of the document.

changePage(int, int) - Method in class org.peace_tools.generic.WizardDialog

Helper method to perform the tasks related with page switching.

CHECK_BOX_ITEM - Static variable in class org.peace_tools.generic.Utilities

Constant that can be supplied to the createMenuItem method

CHECK_MSG - Variable in class org.peace_tools.views.DBClassifierEditor

A String.format() style message to be displayed to the user while prompting to enter data string for validating a given regular expression.

CHECK_RESULT_MSG - Variable in class org.peace_tools.views.DBClassifierEditor

A String.format() style message to be displayed to the user after validating a regular expression against a data string entered by the user.

checkAllServerStatus() - Method in class org.peace_tools.core.MainFrame

Method to ensure status of servers are as expected right after start up.

checkAndClassify() - Method in class org.peace_tools.views.ClusterSummaryView

Helper method to check and launch classification from another thread.

checkAndClose() - Method in class org.peace_tools.views.DBClassifierEditor

Helper method to check and close the dialog.

checkChangePage(int, int) - Method in class org.peace_tools.generic.WizardDialog

Helper method to perform the tasks related with page switching.

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

This array list contains the list of child nodes for this node.

children - Variable in class org.peace_tools.data.ClusterNode

This array list contains the list of child clusters and EST nodes contained by this cluster node.

ClassifierList - Class in org.peace_tools.workspace

A class to encapsulate information about a list of DBClassifier entries that have already been configured in this work space.

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

The default constructor.

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

The list of data base classifiers that are used to classify and group ESTs obtained from different data bases.

classifiers - Variable in class org.peace_tools.workspace.ClassifierList

The list of DB classifier objects that have been configured and added to this list.

classify(ESTList, ProgressMonitor) - Method in class org.peace_tools.data.ClusterFile

Method to recompute (as needed) the classification of ESTs in clusters.

classify(ESTList, ProgressMonitor) - Method in class org.peace_tools.data.ClusterNode

Method to compute classification statistics for this cluster node.

classify(ArrayList<DBClassifier>) - Method in class org.peace_tools.data.EST

Method to determine the classifier that identifies this EST.

classify(ProgressMonitor) - Method in class org.peace_tools.data.ESTList

Method classify all the ESTs in this list.

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

A toggle button which when checked (or depressed) indicates that the bars must also include the classification information for each cluster displayed in the graph.

clearLog() - Method in class org.peace_tools.generic.Log

This method clears the log and writes a special message to the PrintStream, if one exists.

CLU_INFO - Static variable in class org.peace_tools.core.job.ClusterWizardPage

A simple text message that is displayed to the user when the user selects the CLU analyzer.

CLU_INFO - Static variable in class org.peace_tools.core.job.HeuristicsWizardPage

A simple text message that is displayed to the user when the user selects the CLU analyzer.

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

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

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

A hash map to quickly look-up color for a given cluster ID.

ClusterColorMapper - Interface in org.peace_tools.views.overlap

A simple interface to map a clusterID to a Color object.

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

The cluster entry that is finally created by this job wizard when the final wizard page is displayed.

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

Field to read/display the install path where the MST file will be saved after it is generated on the server.

ClusterFile - Class in org.peace_tools.data

The top-level class that encapsulates all the pertinent information regarding a cluster data file.

ClusterFile(String) - Constructor for class org.peace_tools.data.ClusterFile

The constructor creates an empty cluster object.

clusterFile - Variable in class org.peace_tools.data.ClusterTreeTableModel

Reference to the cluster file that contains the cluster data to be adapted and interfaced by this model.

clusterFile - Variable in class org.peace_tools.data.OverlapModel

Reference to the cluster file that contains the cluster information that was used to generate this pre-alignment model.

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

The set of clusters that we are working with.

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

The ID of the cluster to which the EST Entry belongs.

clusterList - Variable in class org.peace_tools.data.OverlapModel

This list contains the list of clusters (that may be sorted) being displayed to the user.

ClusterList - Class in org.peace_tools.views.overlap

A combo-box like custom component to display list of clusters from a tool bar.

ClusterList(OverlapModel, ClusterColorMapper, JComponent) - Constructor for class org.peace_tools.views.overlap.ClusterList

The default constructor.

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

The list that displays the list of clusters currently present in the memory model.

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

The list that displays the list of clusters currently present in the memory model and permits the user to change colors.

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

The optional list of clustering data files that are currently associated with this data set.

ClusterListCellRenderer - Class in org.peace_tools.views.overlap

A custom cell renderer to efficiently display large cluster list.

ClusterListCellRenderer(ClusterColorMapper) - Constructor for class org.peace_tools.views.overlap.ClusterListCellRenderer

The default constructor.

ClusterListCellRenderer.CustomIcon - Class in org.peace_tools.views.overlap

A simple, custom icon class.

ClusterListCellRenderer.CustomIcon() - Constructor for class org.peace_tools.views.overlap.ClusterListCellRenderer.CustomIcon

Default constructor.

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

The scroll pane that contains the ClusterList.clusterList so that the list can scroll when the there are a large number of clusters.

ClusterNode - Class in org.peace_tools.data

A class that represents a single cluster in a cluster tree.

ClusterNode(ClusterNode, boolean, int, String) - Constructor for class org.peace_tools.data.ClusterNode

Constructor to create a Cluster.

clusterOrESTID - Variable in class org.peace_tools.data.ClusterNode

A number that is assigned to this node.

ClusterSummaryView - Class in org.peace_tools.views

View to display a graph of clusters to provide a summary view.

ClusterSummaryView(MainFrame, ClusterFile, ESTList, MSTClusterData) - Constructor for class org.peace_tools.views.ClusterSummaryView

The default constructor.

ClusterSummaryView.TickLine - Class in org.peace_tools.views

A simple component to draw vertical or horizontal ticks.

ClusterSummaryView.TickLine() - Constructor for class org.peace_tools.views.ClusterSummaryView.TickLine

clusterTable - Variable in class org.peace_tools.views.ClusterTreeTableView

The actual Tree-table that provides a graphical view of the list of clusters in a given cluster file.

clusterTable - Variable in class org.peace_tools.views.ESTTableView

The actual Tree-table that provides a graphical view of the list of clusters in a given cluster file.

ClusterTreeTableModel - Class in org.peace_tools.data

The tree table model that provides a facade to display cluster information in a tree-table.

ClusterTreeTableModel(ClusterFile, ESTList, MSTClusterData) - Constructor for class org.peace_tools.data.ClusterTreeTableModel

The constructor.

ClusterTreeTableView - Class in org.peace_tools.views

The tree table model that provides a combination of a tree and table to display cluster information in a convenient form.

ClusterTreeTableView(ClusterTreeTableModel, MainFrame) - Constructor for class org.peace_tools.views.ClusterTreeTableView

The default constructor.

ClusterTreeTableView.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.

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

The default constructor.

ClusterWizardPage - Class in org.peace_tools.core.job

This class serves as an interactive page in a JobWizard.

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

The constructor.

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

Helper method to create a collapsed pane with message.

color - Variable in class org.peace_tools.views.DBClassifierEditor.ColorEditor

The color value that was last set by the user.

color - Variable in class org.peace_tools.views.overlap.ClusterListCellRenderer.CustomIcon

The color with which the square area of the icon is to be painted.

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

The RGB color code associated with this entry.

colorCodes - Variable in class org.peace_tools.generic.CustomBorder

Create a custom border using 4 character codes for top, left, bottom, right.

ColorColumnEditor - Variable in class org.peace_tools.views.DBClassifierEditor

An instance of the color renderer that is used to render the third column in the table with a suitable colored label.

ColorColumnRenderer - Variable in class org.peace_tools.views.DBClassifierEditor

An instance of the color renderer that is used to render the third column in the table with a suitable colored label.

colorIcon - Variable in class org.peace_tools.views.overlap.ClusterListCellRenderer

The icon that is used in the label created by the getListCellRendererComponent method.

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

Helper to look-up color for a given cluster ID.

colorMapper - Variable in class org.peace_tools.views.overlap.ClusterListCellRenderer

The ClusterColorMapper that provides the coloring information for rendering the colored icons with each entry.

colorMapper - Variable in class org.peace_tools.views.overlap.OverlapPanel

Helper to look-up color for a given cluster ID.

colors - Variable in class org.peace_tools.generic.CustomBorder

An array of four colors corresponding to top, left, bottom, right borders

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

The starting column position for this entry.

colScale - Variable in class org.peace_tools.views.overlap.OverlapPanel

The scale to be applies when rendering a single column.

colScale - Variable in class org.peace_tools.views.overlap.Ruler

The scale to be applies when rendering a single column.

columization - Variable in class org.peace_tools.views.ESTTableView

A checkbox that can be used by the user to enable or disable column-wise display of nucleotide sequences.

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

The tab (JComponent) to be moved via this DnD handler.

computeFont(Graphics) - Method in class org.peace_tools.views.overlap.OverlapPanel

Compute the font that will fit letters within each fragment rectangle.

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

Method to compute and return statistics about this cluster.

computeStatistics() - Method in class org.peace_tools.data.ESTList

Method to compute and return statistics about the set of ESTs encapsulated in this list.

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

Connect to the server in order to perform various operations.

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

Connect to the server in order to perform various operations.

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

Connect to the server in order to perform various operations.

connection - Variable in class org.peace_tools.core.session.RemoteServerSession

The connection to the remote server via which the remote server can be accessed for performing various operations.

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

The background thread that is attempting to connect to the remote server.

container - Variable in class org.peace_tools.core.PEACEInstaller

The top-level container that logically contains all the GUI elements associated with this installer.

contentPane - Variable in class org.peace_tools.views.ClusterTreeTableView

The main content pane that contains the summary pane along with the tree table.

contextItemList - Variable in class org.peace_tools.core.AbstractMenuHelper

The list of main menu items created by this helper.

copy(InputStream, String, String, String) - Method in class org.peace_tools.core.session.LocalServerSession

Copy given data from an input stream to a given file on the local machine.

copy(OutputStream, String, String, JProgressBar) - Method in class org.peace_tools.core.session.LocalServerSession

Copy file from one directory to a given output stream.

copy(InputStream, String, String, String) - Method in class org.peace_tools.core.session.RemoteServerSession

Copy given data from an input stream to a given file on the remote machine.

copy(OutputStream, String, String, JProgressBar) - Method in class org.peace_tools.core.session.RemoteServerSession

Copy file from a remote machine to a given output stream.

copy(InputStream, String, String, String) - Method in class org.peace_tools.core.session.ServerSession

Copy given data from an input stream to a given file on the server.

copy(OutputStream, String, String, JProgressBar) - Method in class org.peace_tools.core.session.ServerSession

Copy file from a remote machine to a given output stream.

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

Helper method to copy EST data file to shared space if needed.

copyInstallFiles(ServerSession) - Method in class org.peace_tools.core.PEACEInstaller

This is a helper method that is used to copy the install files to the server.

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

A simple copyright message.

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

A custom panel that actually has the PEACE logo as the background image.

cp - Variable in class org.peace_tools.core.WorkspaceChooser

A custom panel that actually has the PEACE logo as the background image.

CPU_INFO_MSG - Static variable in class org.peace_tools.core.job.MSTWizardPage

A generic informational message that is displayed to the user to provide information about the u/v heuristic.

cpus - Variable in class org.peace_tools.workspace.JobSummary

The total number of CPUs (Nodes * CPUsPerNode) that were used for running the job.

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

The number of CPUS per Nodes (on a cluster) that were requested for running this job.

create(Job, ActionListener) - Static method in class org.peace_tools.core.JobMonitor

The primary API method to create a job monitor thread.

create(ClusterFile, ESTList, MST, MSTClusterData) - Static method in class org.peace_tools.data.OverlapModel

The constructor.

create(Element) - Static method in class org.peace_tools.workspace.ClassifierList

Helper method to utilize data from a DOM tree to create a suitable ClassifierList entry.

create(Element) - Static method in class org.peace_tools.workspace.DataSet

Helper method to utilize data from a DOM tree to create a suitable DataSet entry.

create(Element) - Static method in class org.peace_tools.workspace.DBClassifier

Helper method to utilize data from a DOM tree to create a suitable DBClassifier entry.

create(Element) - Static method in class org.peace_tools.workspace.Filter

Helper method to utilize data from a DOM tree to create a suitable Filter entry.

create(Element) - Static method in class org.peace_tools.workspace.FWAnalyzer

Helper method to utilize data from a DOM tree to create a suitable FWAnalyzer entry.

create(Element) - Static method in class org.peace_tools.workspace.Heuristic

Helper method to utilize data from a DOM tree to create a suitable Heuristic entry.

create(Element) - Static method in class org.peace_tools.workspace.Job

Helper method to utilize data from a DOM tree to create a suitable Job entry.

create(Element) - Static method in class org.peace_tools.workspace.JobList

Helper method to utilize data from a DOM tree to create a suitable JobList entry.

create(Element) - Static method in class org.peace_tools.workspace.JobSummary

Helper method to utilize data from a DOM tree to create a suitable JobSummary entry.

create(Element) - Static method in class org.peace_tools.workspace.MSTClusterData

Helper method to utilize data from a DOM tree to create a suitable MSTClusterData entry.

create(Element) - Static method in class org.peace_tools.workspace.MSTData

Helper method to utilize data from a DOM tree to create a suitable MSTData entry.

create(Element) - Static method in class org.peace_tools.workspace.Server

Helper method to utilize data from a DOM tree to create a suitable Server entry.

create(Element) - Static method in class org.peace_tools.workspace.ServerList

Helper method to utilize data from a DOM tree to create a suitable ServerList entry.

createAuthorList(JTabbedPane) - Method in class org.peace_tools.core.AboutDialog

Helper method to create the "Authors" tab in the dialog.

createButton(String, String, String, ActionListener, String, boolean) - Static method in class org.peace_tools.generic.Utilities

This method is a utility method to create generic buttons.

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

This is a helper method that is used to create the cache type and cache size entry boxes.

createChooserDialog(boolean) - Method in class org.peace_tools.core.WorkspaceChooser

This is a helper method that creates the work space chooser dialog that prompts the user to choose a work space for this session of the GUI.

createCloseButtonPanel() - Method in class org.peace_tools.core.AboutDialog

Helper method to create and add panel with version information along with the close button.

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

Helper method to create the cluster file entry dialog box along with a "Browse" button.

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

Creates the cluster list used to display clusters.

createCursors(DnDTabbedPane) - Static method in class org.peace_tools.generic.dndTabs.DnDTabHandler

This is a helper method that is used to create some of the custom cursors used by this class.

createDefault(String) - Static method in class org.peace_tools.workspace.Workspace

Method to create default work space met data in a given directory.

createDefaultView(String, String, ViewFactory.ViewType, Object) - Method in class org.peace_tools.core.ViewFactory

Helper method to create a default view for a given data type.

createDialog(JFrame) - Method in class org.peace_tools.core.ServerConnectionTester

Helper method to create the dialog to be displayed.

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

Helper method to create entries in the work space.

createFileMenu(JToolBar, AbstractMenuHelper) - Method in class org.peace_tools.core.FileMenuHelper

Helper method to create the file menu.

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

This is a helper method that is used to create the frame and word entry boxes.

createGraph() - Method in class org.peace_tools.views.ClusterSummaryView

Helper method to configure and setup the graph panel to draw the actual cluster graph.

createHelpMenu(JToolBar) - Method in class org.peace_tools.core.HelpMenuHelper

Helper method to create the help menu.

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

This is a refactored utility method to create informational labels.

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

This is a refactored utility method to create informational labels.

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

This is a helper method that is used to create a valid directory where this job's files will be copied.

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

Helper method to create the job entry to be added to the workspace.

createJobMenu(JToolBar, AbstractMenuHelper) - Method in class org.peace_tools.core.JobMenuHelper

Helper method to create the job menu.

createJobThreads() - Method in class org.peace_tools.core.MainFrame

Method to create threads for all jobs whose status is to be monitored.

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

Helper method to create a thread to periodically poll a job.

createLabel(String, String) - Method in class org.peace_tools.core.FileCopyDialog

Helper method to create a label with succinct file name.

createLabeledComponents(String, String, int, boolean, Component...) - Static method in class org.peace_tools.generic.Utilities

This method is a helper method to lay out components vertically.

createLabels(float, int, int, int, boolean, Rectangle, ArrayList<JLabel>) - Method in class org.peace_tools.views.ClusterSummaryView

Helper method to create the axis labels.

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

This is a helper method that is used to create the necessary information regarding the Low Complexity (LC) filter.

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

This is a helper method that is used to create the necessary information regarding the length filter.

createLicenceTab(JTabbedPane) - Method in class org.peace_tools.core.AboutDialog

This is a helper method that is used to create the license tab in the about dialog.

createLicenceTab(boolean) - Method in class org.peace_tools.core.WorkspaceChooser

This is a helper method that is used to create the license tab in the work space chooser.

createLogViews() - Method in class org.peace_tools.core.ViewFactory

This is a helper method that invoked from the constructor to create the programmer and user log panes.

createMenuItem(int, String, String, ActionListener, String, KeyStroke, boolean, boolean) - Static method in class org.peace_tools.generic.Utilities

This method is a convenience method that provides a simple mechanism for creating a JMenuItem, given the parameters.

createMenuItem(int, String, String, String, ActionListener, String, KeyStroke, boolean, boolean) - Static method in class org.peace_tools.generic.Utilities

This method is a convenience method that provides a simple mechanism for creating a JMenuItem, given the parameters.

createMenus() - Method in class org.peace_tools.core.MainFrame

This is a helper method that invoked from the constructor to create the main menu and associated toolbars.

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

Helper method to create the MST file entry dialog box along with a "Browse" button.

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

Helper method to create a panel with multiple informational notes in them.

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

Helper method to create the description and threshold controls.

createOutputDocs(DefaultStyledDocument[], String[]) - Method in class org.peace_tools.views.DetailView

Helper method to create styled documents.

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

This is a refactored utility method to create informational labels at the top of this panel.

createOverlapView(MSTClusterData) - Method in class org.peace_tools.core.ViewFactory

Method to create a overlap view for a given entry.

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

Helper method to create the overview page.

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

Helper method to create the overview page.

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

Helper method to create the overview page.

createPopupMenu() - Method in class org.peace_tools.views.JobListView

This is a helper method to create the pop-up menu.

createPopupMenu() - Method in class org.peace_tools.views.ServerListView

This is a helper method to create the pop-up menu.

createPropertiesLayout(String, JTree, Component, JToolBar, int) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Method to compute and setup summary information.

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

Helper method to create the combo-box to select a server.

createServerMenu(JToolBar) - Method in class org.peace_tools.core.ServerMenuHelper

Helper method to create the server menu.

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

Helper method to create the server information entry components in this wizard page.

createSession() - Method in class org.peace_tools.core.JobMonitor

This is a helper method that is periodically invoked to check and create a session to the remote server.

createSession(Component, Server) - Static method in class org.peace_tools.core.session.SessionFactory

Factory method to create suitable server session.

createSlider(int) - Method in class org.peace_tools.views.ClusterSummaryView

Helper method to create a slider with suitable scale.

createSplitPane(String, Icon, Component, DnDTabbedPane.Location) - Method in class org.peace_tools.generic.dndTabs.DnDTabbedPane

This method may be used to manually add components either directly to this tabbed pane or around this tabbed pane.

createSplitPane(String, Icon, Component, DnDTabbedPane.Location, double) - Method in class org.peace_tools.generic.dndTabs.DnDTabbedPane

This method may be used to manually add components either directly to this tabbed pane or around this tabbed pane.

createSplitPane(String, Icon, Component, DnDTabbedPane.Location, double, int) - Method in class org.peace_tools.generic.dndTabs.DnDTabbedPane

This method may be used to manually add components either directly to this tabbed pane or around this tabbed pane.

createStandardViews() - Method in class org.peace_tools.core.ViewFactory

This is a helper method that invoked from the constructor to create the standard views (tabs that display various information from the work space) .

createStaticViews() - Method in class org.peace_tools.core.ViewFactory

Method to create the standard set of static views.

createStyles() - Static method in class org.peace_tools.views.DetailView

Helper method to check and create styles.

createSubPanel(int, String, JComponent...) - Static method in class org.peace_tools.generic.Utilities

This method is a helper method that takes the alignment for a FlowLayout, a label to identify the components, and the actual JComponents themselves and places them in a JPanel with a FlowLayout.

createSummaryInfo() - Method in class org.peace_tools.views.ESTTableView

Method to compute and setup summary information.

createSummaryView(MSTClusterData) - Method in class org.peace_tools.core.ViewFactory

Method to create a graph type of view for a given entry.

createTable() - Method in class org.peace_tools.views.DBClassifierEditor

Helper method to configure and setup various columns in the DB classifier list table.

createTabs() - Method in class org.peace_tools.core.WorkspaceChooser

Helper method to setup the tabs to be displayed in this frame.

createTextView(String) - Method in class org.peace_tools.core.ViewFactory

Helper method to create a textual view for a given file.

createTicks(ArrayList<JLabel>, boolean) - Method in class org.peace_tools.views.ClusterSummaryView

Helper method to create little tick lines on x or y axis.

createToolbar() - Method in class org.peace_tools.views.ClusterTreeTableView

Helper method to configure and setup various tools in the tool bar.

createToolbar() - Method in class org.peace_tools.views.ESTTableView

Helper method to configure and setup various tools in the tool bar.

createToolButton(String, String, String, ActionListener, String, boolean) - Static method in class org.peace_tools.generic.Utilities

This method is a utility method to create tool bar buttons.

createTools() - Method in class org.peace_tools.views.DBClassifierEditor

Helper method to configure and setup various tools in the tool bar.

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

This is a refactored utility method to create informational labels at the top of this panel.

createTopPanel(String, String) - Method in class org.peace_tools.views.DetailView

Helper method to create the controls displayed at the top.

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

This is a helper method that is used to create the necessary information regarding the t/v heuristic.

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

This is a helper method that is used to create the necessary information regarding the u/v heuristic.

createView(Job, Server) - Method in class org.peace_tools.core.ViewFactory

Method to create a graph type of view for a given entry.

createView(Server, String) - Method in class org.peace_tools.core.ViewFactory

Method to create a server job list view.

createView(Object, boolean, boolean) - Method in class org.peace_tools.core.ViewFactory

Method to ease creation of a specific view.

createView(String, String, ViewFactory.ViewType, boolean, boolean, Object) - Method in class org.peace_tools.core.ViewFactory

Method to create a specific view.

createViewMenu(JToolBar, AbstractMenuHelper) - Method in class org.peace_tools.core.ViewMenuHelper

Helper method to create the view menu.

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

This is a helper method that is invoked from the last wizard page (SubmitJobWizardPage) to create the various entries in the work space.

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

The time stamp when this workspace was created.

currentLogLevel - Variable in class org.peace_tools.generic.Log

The current log level at which log messages are being generated.

currentPage - Variable in class org.peace_tools.generic.WizardDialog

The current page that is being displayed by this wizard.

CustomBorder - Class in org.peace_tools.generic

A custom border that draws 4 lines along the edges of a given component based on either color codes or four custom colors.

CustomBorder(String) - Constructor for class org.peace_tools.generic.CustomBorder

Create a custom border using 4 character codes for top, left, bottom, right.

CustomBorder(Color, Color, Color, Color) - Constructor for class org.peace_tools.generic.CustomBorder

Create a custom border with a given set of colors.

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

The static set of icons that are repeatedly used by this class as the user-defined data for selected nodes in the properties tree created by this class.

CustomPanel - Class in org.peace_tools.generic

A Custom panel that can have an Image for its Background

CustomPanel() - Constructor for class org.peace_tools.generic.CustomPanel

Creates a default CustomPanel Object.

CustomPanel(LayoutManager) - Constructor for class org.peace_tools.generic.CustomPanel

Creates a default CustomPanel Object.

CustomTableCellRenderer - Class in org.peace_tools.views

A simple renderer that overrides font in default renderer.

CustomTableCellRenderer() - Constructor for class org.peace_tools.views.CustomTableCellRenderer

The constructor merely initializes the mono space font used to render EST sequences.

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

The wizard page that collects information about the cluster file in which clustering information is to be stored.