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

R

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

Constant that can be supplied to the createMenuItem method

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

A tool bar style button that permits the user to assign random colors to each cluster.

read(PushbackInputStream) - Method in class org.peace_tools.data.EST

Method to read an EST from a given input stream.

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

Bit value indicating if this entry is readable.

readFullStream(InputStream) - Static method in class org.peace_tools.generic.Utilities

This is a helper method to read small text data from a stream into a String.

readline(InputStream) - Method in class org.peace_tools.data.EST

Helper method to read a line from a given input stream.

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

This is a helper method to read small text files (like license information) into a string.

reallyQuit() - Method in class org.peace_tools.core.FileMenuHelper

Double check before exiting.

recheckDelay - Variable in class org.peace_tools.core.JobMonitor

The delay in milliseconds for which the main thread must sleep before checking back for updates.

refreshButton - Variable in class org.peace_tools.views.DetailView

The refresh button that the user can click to reload the job information.

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

A simple error message to be displayed to the user whenever a invalid regular expression is entered.

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

The regular expression that is used to identify a given database name.

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

This instance variable indicates if this server entry represents a local or a remote server.

RemoteServerSession - Class in org.peace_tools.core.session

A remote server session based on the secure shell (SSH) protocol.

RemoteServerSession(Component, Server) - Constructor for class org.peace_tools.core.session.RemoteServerSession

The constructor merely passes parameters to the base class that initializes the instance variables.

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

The panel that contains the data entry fields related to a remote server entry.

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

Remove an existing Minimum Spanning Tree (MST) data file from this data set.

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

Remove an existing MST-based clustering data file from this data set.

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

Method to remove a job entry.

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

Method to remove a server entry to this server list.

removeDataSet(DataSet) - Method in class org.peace_tools.core.DeleteDialog

Helper method to delete a data set along with all underlying entries and files.

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

Method to add a new data set to the workspace.

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

Removes a listener from the list of listeners maintained by this class.

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

Remove a listener to be notified from this tab.

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

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

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

Remove a tab (or component) from this DnDTabbedPane.

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

Remove a given worker thread from the list of worker threads.

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

Removes a listener from the list of listeners maintained by this class.

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

Removes a listener from the list of listeners maintained by this class.

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

Removes a listener from the list of listeners maintained by this class.

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

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

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

Remove a workspace listener from the listeners to receive notification events from this workspace.

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

Variable to indicate the information about a fragment that should be rendered.

reserveID() - Method in class org.peace_tools.workspace.Workspace

Reserves the next sequence number for use in a data set.

reserveJobID() - Method in class org.peace_tools.workspace.JobList

Reserves the next job ID for use in a job object.

reserveServerID() - Method in class org.peace_tools.workspace.ServerList

Reserves the next server ID for use in a server object.

resetDynamicInfo() - Method in class org.peace_tools.views.JobDetailsView

Helper method to reset outputs, errors, and scripts to "unavailable" status.

resetDynamicInfo() - Method in class org.peace_tools.views.ServerJobsView

Helper method to reset outputs, errors, and scripts to "unavailable" status.

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

Helper method to resize/scale the graph.

restorePosition(Container, Component) - Method in class org.peace_tools.generic.dndTabs.DnDTabPos

Primary interface to restore position of a tab.

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

Deletes an empty directory on the server.

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

Deletes an empty directory on the server.

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

Remove an empty directory on the server.

root - Variable in class org.peace_tools.data.ClusterFile

The root of the cluster node.

root - Variable in class org.peace_tools.data.MST

The root of the MST node.

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

The scale to be applies when rendering a single row.

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

The scale to be applies when rendering a single row.

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

The preferred height of the horizontal ruler.

RULE_WIDTH - Static variable in class org.peace_tools.views.overlap.Ruler

The preferred width of the vertical ruler.

Ruler - Class in org.peace_tools.views.overlap

The overlap panel that displays the actual overlap image.

Ruler(int, int, Ruler.Orientation) - Constructor for class org.peace_tools.views.overlap.Ruler

The only constructor.

Ruler.Orientation - Enum in org.peace_tools.views.overlap

Enumerations to define the two types of rulers that this class can be used for.

Ruler.Orientation() - Constructor for enum org.peace_tools.views.overlap.Ruler.Orientation

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

This is a helper method that is used to validate a given FASTA file.

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

This method is called when the user clicks the OK button to delete entry(s).

run() - Method in class org.peace_tools.core.FileCopyDialog

Thread method to do the actual copying operation.

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

Method to perform various tasks involved in successfully creating and submitting a job on a remote server.

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

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

This method is invoked from a separate thread from the pageChanging() method.

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

This method is invoked from a separate thread from the pageChanging() method.

run() - Method in class org.peace_tools.core.ServerConnectionTester

The background thread method that performs the connection test.

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

Perform classification from a separate thread.

run() - Method in class org.peace_tools.views.JobDetailsView

The thread method that retrieves and populates job information.

run() - Method in class org.peace_tools.views.ServerJobsView

The thread method that retrieves and populates job information.

runCommand(ServerSession, String, String, String[]) - Method in class org.peace_tools.views.DetailView

Helper method to run the job runner on the server and return outputs.

runtime - Variable in class org.peace_tools.workspace.JobBase

The actual CPU time that the job took to run on the server.