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

L

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

A long value representing the time the file was last modified, measured in milliseconds since the epoch (00:00:00 GMT, January 1, 1970), or 0L if the file does not exist or if an I/O error occurs

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

The time stamp value of the last time the status of this job was updated.

launchMainFrame(String, boolean) - Method in class org.peace_tools.core.PEACE

Call back method from the work space chooser.

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

Helper method to layout the button panel to the bottom of the wizard.

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

Helper method to layout the sequence panel in the wizard.

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

Helper method to layout the title panel in the wizard.

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

This method is called from the showWizard method just before the wizard is made visible.

LeafIcons - Static variable in class org.peace_tools.views.DataSetTreeView

The static set of icons that are repeatedly used by the custom cell renderer used by this tree view class.

LeafIcons - Static variable in class org.peace_tools.views.MSTFileView

The static set of icons that are repeatedly used by the custom cell renderer used by this tree view class.

LevelIcons - Static variable in class org.peace_tools.views.UserLogPane

The set of icons/images used by the StatusTimeStamp class to provide an aggregate view of both status and time stamps for every entry in the user log.

LinuxInstallFiles - Static variable in class org.peace_tools.core.PEACEInstaller

The list of files to be installed on a Linux machine.

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

The action listener to be notified when this thread exists with a status of FINISHING or ERROR.

listeners - Static variable in class org.peace_tools.generic.dndTabs.DnDTabbedPane

The list of listeners that have been added for this DnDTabbedPane.

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

The list of log listeners that are interested in receiving call back information whenever log information changes.

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

The list of listeners that are currently registered to receive notifications on changes that have occured to various entries in the workspace.

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

The set of list model listeners that were added to this model.

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

The actual JTable that provides a graphical view of the data sets in the form of a list.

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

Helper method to load author information from various files.

loadCluster(File) - Static method in class org.peace_tools.data.ClusterFile

This method loads cluster data into an in-memory format.

loadCluster(String, InputStream) - Static method in class org.peace_tools.data.ClusterFile

This method loads cluster data into an in-memory format.

loadCoreWorkspaceData(Document, String) - Static method in class org.peace_tools.workspace.Workspace

Helper method to simply load the top-level Directory for the Workspace and the creation time stamp for this workspace from a DOM document.

loadESTs(File) - Static method in class org.peace_tools.data.ESTList

Load ESTs from a given FASTA file and build a new ESTList.

loadESTs(String, InputStream) - Static method in class org.peace_tools.data.ESTList

Load ESTs from a stream that provides FASTA data.

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

This is a helper method that is invoked just before a remote session establishes connection with a server.

loadMST(File) - Static method in class org.peace_tools.data.MST

This method loads MST data into an in-memory format.

loadMST(String, InputStream) - Static method in class org.peace_tools.data.MST

This method loads MST data into an in-memory format.

loadWorkspaceList(boolean, JComboBox) - Method in class org.peace_tools.core.WorkspaceChooser

This is a helper method that is used to load the list of previously used work space paths from the default ".workspace_list" file in the default working directory.

LocalServerSession - Class in org.peace_tools.core.session

A local server session to run jobs on the local host.

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

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

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

If this flag is set to true, then this wizard permits the user only to change the install path on the server.

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

If this flag is set to true, then this wizard permits the user only to change the install path on the server.

log - Variable in class org.peace_tools.core.job.SubmitJobWizardPage

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

Log - Class in org.peace_tools.generic

This is an abstract base class that provides the core features for managing log entries.

Log(Log.LogLevel, String) - Constructor for class org.peace_tools.generic.Log

A constructor for the Log.

log(String) - Static method in class org.peace_tools.generic.ProgrammerLog

This method logs the specified message in the programmer log.

log(Exception) - Static method in class org.peace_tools.generic.ProgrammerLog

This method logs the specified message in the programmer log.

log(Log.LogLevel, String, String) - Static method in class org.peace_tools.generic.UserLog

This method logs the specified message at the given level.

log - Variable in class org.peace_tools.views.LogPane

This instance variable holds a reference to the actual log class from which this log pane is displaying log entries.

log - Variable in class org.peace_tools.views.UserLogPane

The table to which we write our log into.

Log.LogLevel - Enum in org.peace_tools.generic

This enumeration provides a convenient mechanism for referring to different error levels when generating logs.

Log.LogLevel() - Constructor for enum org.peace_tools.generic.Log.LogLevel

logArea - Variable in class org.peace_tools.views.ProgrammerLogPane

The table to which we write our log into.

logChanged(boolean, boolean, boolean) - Method in interface org.peace_tools.generic.LogListener

This is the only call back method in this interface.

logChanged(boolean, boolean, boolean) - Method in class org.peace_tools.views.LogPane

This method implements the LogListener interface method to update the GUI to reflect the current state of the logger associated with this log pane.

logChanged(boolean, boolean, boolean) - Method in class org.peace_tools.views.ProgrammerLogPane

This method overrides the default implementation in the base class to update the programmer logs displayed by this component.

logEntries - Variable in class org.peace_tools.generic.ProgrammerLog

This instance variable holds all the user logs that have been generated thus far via the log() method in this class.

logEntries - Variable in class org.peace_tools.generic.UserLog

This instance variable holds all the user logs that have been generated thus far via the log() method in this class.

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

The log file stream to which the data is currently being written as logs are being generated.

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

The file we are writing to (if any).

logLevelList - Variable in class org.peace_tools.views.LogPane

A combo box to permit the user to set the level at which logs are to be saved by this logger.

LogListener - Interface in org.peace_tools.generic

Interface for "Views" that are interested in receiving log changes.

LogPane - Class in org.peace_tools.views

This is an abstract base class that provides the core features for displaying log entries.

LogPane(Log, boolean) - Constructor for class org.peace_tools.views.LogPane

A constructor for the LogPane.

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

A toggle button which when checked (or depressed) indicates that the y-axis must be drawn on a logarithmic scale rather than on a linear scale.

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

A convenience constant to set the smallest y-axis value when the data is displayed on a log scale.

LOW_COLOR_MSG - Static variable in class org.peace_tools.views.overlap.ClusterList

A fixed message that is displayed to the user to indicate that some of the clusters have duplicate colors.

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

Message to be displayed to the user to indicate that there is a low memory situation when loading a file.

LowMemoryException - Exception in org.peace_tools.data

A simple exception to report a low memory condition.

LowMemoryException() - Constructor for exception org.peace_tools.data.LowMemoryException

The default constructor.

LowMemoryException(String) - Constructor for exception org.peace_tools.data.LowMemoryException

Constructor to create an exception with the given message.