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

W

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

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

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

The size of the window or the frame size that was used for analyzing EST sequences.

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

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

wizard - Variable in class org.peace_tools.core.job.FiltersWizardPage

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

wizard - Variable in class org.peace_tools.core.job.MSTWizardPage

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

wizard - Variable in class org.peace_tools.core.job.VerifyWizardPage

A reference to the wizard dialog that logically owns this page.

wizard - Variable in class org.peace_tools.core.server.ServerAddingEntryWizardPage

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

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

A reference to the wizard dialog that logically owns this page.

WizardDialog - Class in org.peace_tools.generic

A extended wizard dialog class.

WizardDialog(Frame) - Constructor for class org.peace_tools.generic.WizardDialog

The constructor.

WizardPage - Interface in org.peace_tools.generic

A simple interface that is implemented by all wizard pages so that they can be displayed in a wizard dialog.

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

This combo box is provided to permit the user to select a suitable word size to be used for analysis.

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

The word size that was used for analyzing EST sequences.

workerThreads - Static variable in class org.peace_tools.core.MainFrame

A thread group that contains various worker threads.

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

The list of worker threads that various pages may have spawned.

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

The selected work space that is set after the user successfully chooses a work space.

Workspace - Class in org.peace_tools.workspace

The top-level Workspace class that stores and manages all the data associated with a PEACE Workspace.

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

The default constructor.

workspace - Static variable in class org.peace_tools.workspace.Workspace

The process-wide, unique instance of the workspace object.

workspaceChanged(WorkspaceEvent) - Method in class org.peace_tools.data.DataSetTableModel

Translates work space change notifications to table changes.

workspaceChanged(WorkspaceEvent) - Method in class org.peace_tools.data.DataSetTreeModel

workspaceChanged(WorkspaceEvent) - Method in class org.peace_tools.data.JobListTableModel

workspaceChanged(WorkspaceEvent) - Method in class org.peace_tools.data.ServerListTableModel

workspaceChanged(WorkspaceEvent) - Method in class org.peace_tools.views.ClusterSummaryView

Intercept and update graph if classifiers change.

workspaceChanged(WorkspaceEvent) - Method in interface org.peace_tools.workspace.WorkspaceListener

This method is invoked on all workspace listeners registered with the current Workspace.

WorkspaceChooser - Class in org.peace_tools.core

This class provides a pretty sophisticated dialog box that is displayed initially to the user to select a work space.

WorkspaceChooser(JFrame, PEACE) - Constructor for class org.peace_tools.core.WorkspaceChooser

The constructor.

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

The directory where all the files associated with this workpsace are stored.

WorkspaceEvent - Class in org.peace_tools.workspace

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

Constructor to create an event that can be used to report change in the status of a complete data set.

WorkspaceEvent(MSTData, WorkspaceEvent.Operation) - Constructor for class org.peace_tools.workspace.WorkspaceEvent

Constructor to create an event that can be used to report change in the status of a MST data file.

WorkspaceEvent(MSTClusterData, WorkspaceEvent.Operation) - Constructor for class org.peace_tools.workspace.WorkspaceEvent

Constructor to create an event that can be used to report change in the status of a MST cluster data file.

WorkspaceEvent(Job, WorkspaceEvent.Operation) - Constructor for class org.peace_tools.workspace.WorkspaceEvent

Constructor to create an event that can be used to report change in the status of a job entry.

WorkspaceEvent(Server, WorkspaceEvent.Operation) - Constructor for class org.peace_tools.workspace.WorkspaceEvent

Constructor to create an event that can be used to report change in the status of a server entry.

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

Constructor to create an event that can be used to report change to the list of DB classifiers.

WorkspaceEvent.EntryType - Enum in org.peace_tools.workspace

Enumeration for the different types of Workpace entries that can be reported via a WorkspaceEvent object.

WorkspaceEvent.EntryType() - Constructor for enum org.peace_tools.workspace.WorkspaceEvent.EntryType

WorkspaceEvent.Operation - Enum in org.peace_tools.workspace

Enumeration for the different types of operations on a Workspace entity that can be reported via a WorkspaceEvent object.

WorkspaceEvent.Operation() - Constructor for enum org.peace_tools.workspace.WorkspaceEvent.Operation

WorkspaceListener - Interface in org.peace_tools.workspace

A simple interface class that is used to report changes occuring to the currently active, global Workspace.

write(ESTList, PrintStream) - Method in class org.peace_tools.data.ClusterNode

Method to dump the EST data out in FASTA file format.

write(PrintStream) - Method in class org.peace_tools.data.EST

Method to dump the EST data out in FASTA file format.

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

Bit value indicating if this entry is writable.

writeESTs(PrintStream) - Method in class org.peace_tools.data.ESTList

Writes ESTs in FASTA format to a given writer.

writeESTs(File) - Method in class org.peace_tools.data.ESTList

Writes ESTs in FASTA format to a given file.

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

The actual work space entry to be removed by this dialog.

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

A handy reference to the workspace entry from which the data for this cluster table model was actually obtained.

wsEntry - Variable in class org.peace_tools.data.MSTTreeModel

A handy reference to the workspace entry from which the data for this MST tree model was actually obtained.

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

A handy reference to the workspace entry from which the data for this overlap model was partially obtained.

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

The list of work spaces that the user can choose from or edit to start up the GUI session.