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saveDelayedWorkspace() - Method in class org.peace_tools.core.MainFrame
This method is a helper method to save the workspace from a separate thread.
saveInfo(DnDTabbedPane, Component) - Method in class org.peace_tools.generic.dndTabs.DnDTabPos
Helper method to save information about the given tab.
saveLogsButton - Variable in class org.peace_tools.views.LogPane
A toggle button that can be in "on" or "off" state to indicate if logs are to be saved to the specified fileName (if it is not null) or not.
savePosition(Container, Component) - Method in class org.peace_tools.generic.dndTabs.DnDTabPos
Method to save the relative position of a given child window.
savePosition(Component, Component) - Method in class org.peace_tools.generic.dndTabs.DnDTabPos
Recursive helper method to save relative position.
saveSelectedESTs() - Method in class org.peace_tools.views.ClusterTreeTableView
Helper method to save the selected ESTs.
saveSelectedESTs() - Method in class org.peace_tools.views.ESTTableView
Helper method to save the selected ESTs.
saveWorkspace(Dialog) - Method in class org.peace_tools.core.MainFrame
Save the workspace data directly.
saveWorkspace() - Method in class org.peace_tools.workspace.Workspace
Save the current work space configuration information.
saveWorkspaceList(JComboBox) - Method in class org.peace_tools.core.WorkspaceChooser
This is a helper method that is used to save the current list of work space paths to the work space list file.
saveWorkspaceViaDOM() - Method in class org.peace_tools.workspace.Workspace
This method can be used to save the work space configuration to disk.
SAVING_ERROR - Static variable in class org.peace_tools.core.MainFrame
This message is displayed when the work space file could not be saved successfully.
sc - Static variable in class org.peace_tools.views.DetailView
A shared style context that contains the various styles that are used to layout information in the DefaultStyledDocument objects created and used by this class.
SELECT_EST_MSG - Variable in class org.peace_tools.views.ClusterTreeTableView
A simple message that is displayed to the user.
SELECT_EST_MSG - Variable in class org.peace_tools.views.ESTTableView
A simple message that is displayed to the user.
selectedBorder - Variable in class org.peace_tools.views.DBClassifierEditor.ColorRenderer
The border to be used to draw color boxes when the row is selected in the table.
selectedCluster - Variable in class org.peace_tools.data.OverlapModel
Instance variable to track the currently selected/visible cluster entry in a combo box.
selectionStats - Variable in class org.peace_tools.views.overlap.ClusterList
A simple non-editable text field to display cluster selection statistics.
Separator - Static variable in class org.peace_tools.core.WorkspaceChooser
A simple separator to make the license text look pretty.
seqCounter - Variable in class org.peace_tools.workspace.JobList
Sequence counter that is maintained on a per-work space basis to generate unique/valid IDs for each new job entry added to this list.
seqCounter - Variable in class org.peace_tools.workspace.ServerList
Sequence counter that is maintained on a per-work space basis to generate unique/valid IDs for each new server entry added to this list.
seqCounter - Variable in class org.peace_tools.workspace.Workspace
Sequence counter that is maintained on a per-work space basis to generate unique/valid IDs for each new entry that is added to this workspace.
seqTitles - Variable in class org.peace_tools.generic.WizardDialog
The array of sequence titles that are displayed to the left of the wizard dialog.
sequence - Variable in class org.peace_tools.data.EST
The actual sequence of base pairs associated with this EST.
sequencePanel - Variable in class org.peace_tools.generic.WizardDialog
A custom column panel that is displayed to the left of the wizard.
serialVersionUID - Static variable in class org.peace_tools.core.AboutDialog
A generated serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.dataset.DataSetWizard
The generated serialization UID (need to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.core.dataset.ESTInfoWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.dataset.SummaryWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.DeleteDialog
A generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.FileCopyDialog
A serialization constant (to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.core.job.AnalyzerWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.job.ClusterWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.job.FiltersWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.job.HeuristicsWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.job.JobInfoWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.job.JobWizard
The generated serialization UID (need to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.core.job.MSTWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.job.SubmitJobWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.job.VerifyWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.MainFrame
A generated serial version ID.
serialVersionUID - Static variable in class org.peace_tools.core.server.ServerAddingEntryWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.server.ServerInfoWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.server.ServerTypeWizardPage
A serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.core.server.ServerWizard
This is a generated serial version ID.
serialVersionUID - Static variable in class org.peace_tools.core.WorkspaceChooser
The generated serial version ID to keep the Java compiler happy about serializing this class.
serialVersionUID - Static variable in class org.peace_tools.data.DataSetTableModel
A generated serial version ID for serializing the information in this class (if needed).
serialVersionUID - Static variable in class org.peace_tools.data.ESTTableModel
A generated serialization UID included just to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.data.JobListTableModel
A generated serial version ID for serializing the information in this class (if needed).
serialVersionUID - Static variable in exception org.peace_tools.data.LowMemoryException
A generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.data.ServerListTableModel
A generated serial version ID for serializing the information in this class (if needed).
serialVersionUID - Static variable in class org.peace_tools.generic.CustomBorder
A generated serialization values.
serialVersionUID - Static variable in class org.peace_tools.generic.CustomPanel
The serial version ID associated with this class for serialization.
serialVersionUID - Static variable in class org.peace_tools.generic.dndTabs.DnDTabbedPane
A generated serial version ID.
serialVersionUID - Static variable in class org.peace_tools.generic.dndTabs.DnDTabButton
A generated serialization UID to keep the complier happy
serialVersionUID - Static variable in class org.peace_tools.generic.GenericWizardPage
The generated serial UID for serializing this class.
serialVersionUID - Static variable in class org.peace_tools.generic.IconTreeNode
A generated serialization UID (just to keep the compiler happy).
serialVersionUID - Static variable in class org.peace_tools.generic.WizardDialog
Generated serial version ID for serializing this class.
serialVersionUID - Static variable in class org.peace_tools.views.ClusterSummaryView
Generated serialization UID (merely to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.views.ClusterSummaryView.TickLine
A generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.ClusterTreeTableView
A generated serial version ID for serialization (more realistically to keep the compiler happy).
serialVersionUID - Static variable in class org.peace_tools.views.CustomTableCellRenderer
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.DataSetFileListView
A generated serial version ID for serialization (more realistically to keep the compiler happy).
serialVersionUID - Static variable in class org.peace_tools.views.DataSetFileListView.ServerNameStatusRenderer
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.DataSetPopupMenu
A generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.DataSetTreeView.DataSetRenderer
 
serialVersionUID - Static variable in class org.peace_tools.views.DataSetTreeView
A generated serial version ID.
serialVersionUID - Static variable in class org.peace_tools.views.DBClassifierEditor.ColorEditor
The generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.DBClassifierEditor.ColorRenderer
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.DBClassifierEditor
Generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.DetailView
A generated serialization UID just to keep the Java compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.ESTTableView
A generated serialization UID (included just to keep the compiler happy).
serialVersionUID - Static variable in class org.peace_tools.views.GenericHTMLView
A generated serialization UID to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.JobDetailsView
A generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.JobListView.JobNameStatusRenderer
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.JobListView.JobStatusRenderer
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.JobListView
A generated serial version ID for serialization (more realistically to keep the compiler happy).
serialVersionUID - Static variable in class org.peace_tools.views.LogPane
A serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.MSTFileView.DataSetRenderer
 
serialVersionUID - Static variable in class org.peace_tools.views.MSTFileView
A generated serial version ID.
serialVersionUID - Static variable in class org.peace_tools.views.overlap.ClusterList
Generated serialization UID (merely to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.views.overlap.ClusterListCellRenderer
Generated serialization UID (merely to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.views.overlap.OverlapPanel
Generated serialization UID (merely to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.views.overlap.OverlapView
Generated serialization UID (merely to keep the compiler happy)
serialVersionUID - Static variable in class org.peace_tools.views.overlap.Ruler
A generated serialization UID just to keep the compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.ProgrammerLogPane
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.ServerJobsView
A generated serialization UID to keep compiler happy.
serialVersionUID - Static variable in class org.peace_tools.views.ServerListView
A generated serial version ID for serialization (more realistically to keep the compiler happy).
serialVersionUID - Static variable in class org.peace_tools.views.ServerListView.ServerNameStatusRenderer
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.UserLogPane
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.views.UserLogPane.StatusTimeStamp
The general serial version UID to enable serialization of this class as per Java requirements.
serialVersionUID - Static variable in class org.peace_tools.workspace.WorkspaceEvent
A generated serialization UID (required as the base class is defined to be serializable).
server - Variable in class org.peace_tools.core.job.SubmitJobWizardPage
The session to the server on which the job is to be submitted.
server - Variable in class org.peace_tools.core.JobMonitor
Information regarding the server on which the job (that this monitor is monitoring) is running.
server - Variable in class org.peace_tools.core.PEACEInstaller
This is the server entry that is being currently installed via this wizard.
server - Variable in class org.peace_tools.core.server.ServerAddingEntryWizardPage
Information about the actual server entry being edited.
server - Variable in class org.peace_tools.core.server.ServerInfoWizardPage
Information about the actual server entry being edited.
server - Variable in class org.peace_tools.core.server.ServerTypeWizardPage
Information about the actual server entry being edited.
server - Variable in class org.peace_tools.core.server.ServerWizard
This is the server entry that is being currently edited via this wizard.
server - Variable in class org.peace_tools.core.ServerConnectionTester
The server to which this class is attempting to establish is a connection to verify that the GUI can actually connect to the server.
server - Variable in class org.peace_tools.core.ServerMenuHelper
The currently selected server entry (if any).
server - Variable in class org.peace_tools.core.session.ServerSession
The server data entry that provides the necessary information to connect to the server.
server - Variable in class org.peace_tools.views.DetailView
The server from where the details are bing displayed.
Server - Class in org.peace_tools.workspace
Class to encapsulate information regarding a Server entry in a PEACE work space configuration file.
Server(String, String, String, String, String, Duration, boolean) - Constructor for class org.peace_tools.workspace.Server
The constructor.
Server.ServerStatusType - Enum in org.peace_tools.workspace
Different enumerations defining the last known operational status of a given Server entry.
Server.ServerStatusType() - Constructor for enum org.peace_tools.workspace.Server.ServerStatusType
 
SERVER_ICON - Static variable in class org.peace_tools.views.PropertiesTreeMaker
A static constant to refer to the server icon position in the PropertiesTreeMaker.CustomIcons array.
SERVER_IN_BAD_STATUS - Static variable in class org.peace_tools.core.MainFrame
This message is displayed by the main frame when a server entry is in an unexpected state on start up.
SERVER_INFO - Static variable in class org.peace_tools.views.JobDetailsView
A format string to format the information on a Job/server.
ServerAddingEntryWizardPage - Class in org.peace_tools.core.server
This class serves as the last page in a ServerWizard.
ServerAddingEntryWizardPage(WizardDialog, Server) - Constructor for class org.peace_tools.core.server.ServerAddingEntryWizardPage
The constructor.
ServerConnectionTester - Class in org.peace_tools.core
 
ServerConnectionTester(MainFrame, Server) - Constructor for class org.peace_tools.core.ServerConnectionTester
The constructor.
serverID - Variable in class org.peace_tools.workspace.JobBase
A cross reference to the server on which this Job has been scheduled.
ServerInfoWizardPage - Class in org.peace_tools.core.server
This class serves as the second interactive page in a ServerWizard.
ServerInfoWizardPage(WizardDialog, Server, boolean) - Constructor for class org.peace_tools.core.server.ServerInfoWizardPage
The constructor.
ServerJobsView - Class in org.peace_tools.views
Class to display list of jobs/processes running on a server.
ServerJobsView(Server, String) - Constructor for class org.peace_tools.views.ServerJobsView
The constructor.
serverList - Variable in class org.peace_tools.core.job.MSTWizardPage
The combo box that permits the user to select the server to be used for running the job.
ServerList - Class in org.peace_tools.workspace
A class to encapsulate information about a list of servers that have already been configured in this work space.
ServerList() - Constructor for class org.peace_tools.workspace.ServerList
The default constructor.
serverList - Variable in class org.peace_tools.workspace.Workspace
The list of Server classes that have been configured for use in this work space.
ServerListTableModel - Class in org.peace_tools.data
A bridge class between Server entries in a workspace and a JTable.
ServerListTableModel() - Constructor for class org.peace_tools.data.ServerListTableModel
The default constructor.
ServerListView - Class in org.peace_tools.views
This class provides a tabular view of the list of servers that are currently configured in this work space.
ServerListView(MainFrame) - Constructor for class org.peace_tools.views.ServerListView
The default constructor.
ServerListView.ServerNameStatusRenderer - Class in org.peace_tools.views
A simple renderer that uses a JLabel to render server name and icon indicating job status.
ServerListView.ServerNameStatusRenderer() - Constructor for class org.peace_tools.views.ServerListView.ServerNameStatusRenderer
 
ServerMenuHelper - Class in org.peace_tools.core
The server menu helper for the application.
ServerMenuHelper(MainFrame) - Constructor for class org.peace_tools.core.ServerMenuHelper
The constructor.
serverName - Variable in class org.peace_tools.workspace.JobSummary
The domain name (or IP address) of the server on which the job was actually run.
ServerNameRenderer - Variable in class org.peace_tools.views.ServerListView
An instance of the cell renderer that is used to render the first column in the table with a suitable status icon.
servers - Variable in class org.peace_tools.workspace.ServerList
The list of Server objects that have been configured and added to this list.
serverSession - Variable in class org.peace_tools.core.server.ServerInfoWizardPage
This instance variable is used to manage the connection to the server just for testing purposes.
ServerSession - Class in org.peace_tools.core.session
A common base class for local and remote connections.
ServerSession(Server, Component) - Constructor for class org.peace_tools.core.session.ServerSession
The constructor merely initializes the instance variables to the values supplied as parameters.
ServerSession.OSType - Enum in org.peace_tools.core.session
Enumerations to provide a more convenient mechanism for referring to the actual type of the server that this server session has been connected to.
ServerSession.OSType() - Constructor for enum org.peace_tools.core.session.ServerSession.OSType
 
ServerStatusIcons - Static variable in class org.peace_tools.views.ServerListView
The list of icons that are used by this table cell renderer to provide visual cues about the current status of this server.
serverTable - Variable in class org.peace_tools.views.ServerListView
The actual JTable that provides a graphical view of the list of servers currently configured on this workspace.
serverTypes - Variable in class org.peace_tools.core.server.ServerTypeWizardPage
The combo box that permits the user to choose between a local and remote server setting.
ServerTypeWizardPage - Class in org.peace_tools.core.server
This class serves as the first interactive page in a ServerWizard.
ServerTypeWizardPage(WizardDialog, Server, boolean) - Constructor for class org.peace_tools.core.server.ServerTypeWizardPage
The constructor.
ServerWizard - Class in org.peace_tools.core.server
This class serves as the top-level class for adding a new server entry to the work space.
ServerWizard(String, MainFrame, DnDTabbedPane) - Constructor for class org.peace_tools.core.server.ServerWizard
The constructor.
session - Variable in class org.peace_tools.core.FileCopyDialog
The server session to be used for copying the necessary files.
session - Variable in class org.peace_tools.core.JobMonitor
The session (local/remote) to the server on which the job is running.
SESSION_PURPOSE - 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 as the reason for making a remote server connection.
SessionFactory - Class in org.peace_tools.core.session
A helper factory class to create a suitable session depending on server.
SessionFactory() - Constructor for class org.peace_tools.core.session.SessionFactory
Default constructor.
set(ArrayList<DBClassifier>) - Method in class org.peace_tools.workspace.ClassifierList
Method to set a new set of classifier entries.
setBasesPerCol(int) - Method in class org.peace_tools.data.ESTTableModel
Method to change the number of bases to be displayed in each column.
setButtonStatus() - Method in class org.peace_tools.generic.WizardDialog
Method to suitably set status of buttons in the wizard.
setButtonStatus(int, int, int) - Method in class org.peace_tools.generic.WizardDialog
Method to enable or disable back and/or next buttons.
setColor(Integer, Color) - Method in interface org.peace_tools.views.overlap.ClusterColorMapper
Set a color to be used for rendering fragments in the given cluster.
setColor(Color) - Method in class org.peace_tools.views.overlap.ClusterListCellRenderer.CustomIcon
Set the color to be used to render the icon.
setColor(Integer, Color) - Method in class org.peace_tools.views.overlap.OverlapView
 
setColor(int) - Method in class org.peace_tools.workspace.DBClassifier
Set a color to shade ESTs identified by this classifier.
setColors(List<Color>) - Method in class org.peace_tools.views.overlap.ClusterList
Sets color for selected or all clusters to given color.
setColumnWidths() - Method in class org.peace_tools.views.ESTTableView
Utility method to set the column widths.
setDataSet(DataSet) - Method in class org.peace_tools.workspace.MSTClusterData
Set the data set that this object logically belongs to.
setDataSet(DataSet) - Method in class org.peace_tools.workspace.MSTData
Set the data set that this object logically belongs to.
setDataSetTreeView(DataSetTreeView) - Method in class org.peace_tools.views.DataSetFileListView
Set the reference to the data set tree view to be synchronized with this table.
setDescription(String) - Method in class org.peace_tools.workspace.DataSet
Set an user supplied description for this this data.
setDescription(String) - Method in class org.peace_tools.workspace.DBClassifier
Set a description for this entry The description is persisted in the work space configuration file and loaded when a work space is opened in the GUI.
setDescription(String) - Method in class org.peace_tools.workspace.Job
Set a description for this job.
setDescription(String) - Method in class org.peace_tools.workspace.Server
Change the description set for this server entry.
setDockCue(DnDTabbedPane.Location) - Method in class org.peace_tools.generic.dndTabs.DnDTabbedPane
This method must be used to set/clear the current docking cue associated with this DndTabPane.
setEnabled(String, boolean) - Method in class org.peace_tools.core.AbstractMenuHelper
Helper method to update status of all items for a given action command.
setEnabled(JMenuItem, boolean) - Static method in class org.peace_tools.generic.Utilities
Utility method to update menu item text that uses HTML.
setEnabled(Container, boolean) - Static method in class org.peace_tools.generic.Utilities
Helper method to recursively enable/disable a component and its children.
setEnabled(boolean) - Method in class org.peace_tools.workspace.DBClassifier
Indicate if this classifier must be used to group/classify ESTs.
setESTList(ESTList) - Method in class org.peace_tools.core.dataset.DataSetWizard
Set the list of ESTs associated with this data set.
setFileName(String) - Method in class org.peace_tools.generic.Log
Set a file to which user logs are to be written for persistent storage.
setID(String) - Method in class org.peace_tools.workspace.DataSet
Set the workspace-wide ID for this DataSet.
setID(String) - Method in class org.peace_tools.workspace.Server
Set the unique ID for this server.
setImage(String) - Method in class org.peace_tools.generic.CustomPanel
Set the image to be used for the background This method can be used to set the image that must be used as the background by the CustomPanel object.
setInfo(Icon, String, Dimension) - Method in class org.peace_tools.generic.dndTabs.DnDTabPos
Set initial information for restoring a window.
setInstallPath(String) - Method in class org.peace_tools.workspace.Server
Set the directory where the runtime files associated with PEACE are installed on the server.
setJobOverview() - Method in class org.peace_tools.views.JobDetailsView
Helper method to populate first tab in job details.
setLastUpdateTime() - Method in class org.peace_tools.workspace.Job
This is a helper method that is used to set the lastUpdateTimestamp to the current system time.
setLevel(Log.LogLevel) - Method in class org.peace_tools.generic.Log
Sets the Logging level to the specified level.
setMonitor(Thread) - Method in class org.peace_tools.workspace.Job
Set the monitoring thread for this Job.
setName(String) - Method in class org.peace_tools.workspace.Server
Change the server's domain name (or IP address).
setPassword(String) - Method in class org.peace_tools.workspace.Server
Set the password to be used for logging on to a remote server.
setPath(String) - Method in class org.peace_tools.workspace.DataSet
Set the complete file name and path where the actual EST file is located.
setPath(String) - Method in class org.peace_tools.workspace.Job
Set the path where the files for this job are located.
setPermanent(boolean) - Method in class org.peace_tools.generic.dndTabs.DnDTabbedPane
This method should be used to set if a tabbed pane should be permanent or not.
setPerms(File, char, boolean) - Method in class org.peace_tools.core.session.LocalServerSession
Set up the permissions for a given file.
setPollTime(long) - Method in class org.peace_tools.workspace.Server
Change the delay between successive polling efforts on status checks on this server.
setProgress(int, int) - Method in class org.peace_tools.workspace.Job
Set the progress status for this job.
setPurpose(String) - Method in class org.peace_tools.core.session.LocalServerSession
A simple method to set a purpose message for this session.
setPurpose(String) - Method in class org.peace_tools.core.session.RemoteServerSession
A simple method to set a purpose message for this session.
setPurpose(String) - Method in class org.peace_tools.core.session.ServerSession
A simple method to set a purpose message for this session.
setRegExp(String) - Method in class org.peace_tools.workspace.DBClassifier
Set the regular expression for this DB Classifier entry.
setRemote(boolean) - Method in class org.peace_tools.workspace.Server
Method to set if this server entry represents a local or a remote server.
setRenderInfo(int) - Method in class org.peace_tools.views.overlap.OverlapPanel
Set the type of information to be rendered for each fragment.
setRunTime(long) - Method in class org.peace_tools.workspace.JobBase
This method can be used to explicitly set the actual wall clock time that this job used on the server.
setScale(double, double) - Method in class org.peace_tools.views.overlap.OverlapPanel
Method to set the current scales used by this component.
setScale(double, double) - Method in class org.peace_tools.views.overlap.Ruler
Method to set the current scales used by this component.
setSelectedEntry(Object) - Method in class org.peace_tools.views.DataSetFileListView
Method to select entry in the data set table view This is a helper method that is primarily used by the DataSetTreeView to update the selected entry when when the user clicks on a given entry.
setSelectedEntry(Object) - Method in class org.peace_tools.views.DataSetTreeView
Method to select entry in the data set tree view This is a helper method that is primarily used by the DataSetFileListView to update the selected entry when when the selection in the table changes.
setSelectedItem(Object) - Method in class org.peace_tools.data.OverlapModel
Set the selected (item being displayed) item in a combo box.
setSequenceBackground(String) - Method in class org.peace_tools.generic.WizardDialog
Set an image to be used for the sequence panel.
setSplitWindow(Container, DnDTabbedPane.Location, Component, Component, int, int, Dimension) - Static method in class org.peace_tools.generic.dndTabs.DnDTabbedPane
This is a utility method that is used by both DnDTabbedPane and DnDTabPos to create a JSplitPane containing two components organized in a specific manner to occupy a given preferred width/height depending on the type of orientation.
setStartTimestamp(GregorianCalendar) - Method in class org.peace_tools.workspace.Job
This method can be used to explicitly set the time stamp when this job actually started running on the server.
setStatus(JobBase.JobStatusType) - Method in class org.peace_tools.workspace.Job
Change the status for this job.
setStatus(JobBase.JobStatusType) - Method in class org.peace_tools.workspace.JobBase
Change the status for this job.
setStatus(Server.ServerStatusType) - Method in class org.peace_tools.workspace.Server
Change the status for this server.
setStepStatus(int, boolean) - Method in class org.peace_tools.core.job.SubmitJobWizardPage
Helper method to update the status of a step.
setTableData() - Method in class org.peace_tools.views.DBClassifierEditor
Helper method to copy data from workspace into table model.
setTableView(DataSetFileListView) - Method in class org.peace_tools.views.DataSetTreeView
Set the reference to the file table to be synchronized with this tree.
setTitle(String, String) - Method in class org.peace_tools.generic.GenericWizardPage
This method must be used to set the title and subtitle for this panel.
setTitleBackground(String, Color) - Method in class org.peace_tools.generic.WizardDialog
Set an image to be used for the title panel.
setupAxisLabels() - Method in class org.peace_tools.views.ClusterSummaryView
Helper method to setup x and y axis labels used to draw axis information.
setupToolBar() - Method in class org.peace_tools.views.ClusterSummaryView
Helper method to configure and setup various tools in the tool bar.
setupToolBar() - Method in class org.peace_tools.views.overlap.OverlapView
Helper method to configure and setup various tools in the tool bar.
setUseImageSize(boolean, boolean) - Method in class org.peace_tools.generic.CustomPanel
Method to set if the panel should use the background image size as the preferred size for the panel.
setUserID(String) - Method in class org.peace_tools.workspace.Server
Set the user ID to be used for this server entry.
setValueFor(Object, int, Object) - Method in class org.peace_tools.data.ClusterTreeTableModel
Set the value of the object in this column.
setVisible(boolean) - Method in class org.peace_tools.generic.dndTabs.DnDTabPos
Set the visibility information in this tab.
showDialog() - Method in class org.peace_tools.core.FileCopyDialog
The main method that lays out the components in this wizard and displays the wizard.
showFirstTimeMsg - Variable in class org.peace_tools.core.WorkspaceChooser
Flag that tracks if the first time welcome message has already been displayed or now.
showHelp(Component, String) - Static method in class org.peace_tools.generic.HelpHandler
Displays a given URL.
showStaticView(ViewFactory.ViewType) - Method in class org.peace_tools.core.ViewFactory
Method to display a static view that is currently not visible.
showWizard(String) - Method in class org.peace_tools.generic.WizardDialog
The main method that lays out the components in this wizard and displays the wizard.
size - Variable in class org.peace_tools.core.FileInfo
The size of the file in bytes.
sort(int) - Method in class org.peace_tools.data.ClusterTreeTableModel
Method to change the order in which top-level clusters are ordered.
sort(int) - Method in class org.peace_tools.data.ESTTableModel
Method to change the order in which fragments are ordered.
sort(int) - Method in class org.peace_tools.data.OverlapModel
Method to change the order in which clusters are ordered.
sortedIndexs - Variable in class org.peace_tools.data.ESTTableModel
This array contains a sorted list of indexes of fragments if a sorting scheme has been applied to the data set.
sortedSubClusterIndexs - Variable in class org.peace_tools.data.ClusterTreeTableModel
This array contains a sorted list of indexes of fragments if a sorting scheme has been applied to the data set.
sortOrder - Variable in class org.peace_tools.views.ClusterTreeTableView
Various options on how the clusters in the cluster tree table view are to be sorted.
sortOrder - Variable in class org.peace_tools.views.ESTTableView
Various options on how the clusters in the cluster tree table view are to be sorted.
srvrSession - Variable in class org.peace_tools.core.server.ServerTypeWizardPage
This instance variable is used to manage the connection to the remote server just for testing purposes.
STANDARD_MSG - Variable in class org.peace_tools.core.dataset.SummaryWizardPage
A simple standard message to be displayed at the top of this page.
STANDARD_MSG - Variable in class org.peace_tools.core.server.ServerAddingEntryWizardPage
A simple standard message to be displayed at the top of this page.
start() - Method in class org.peace_tools.core.ServerConnectionTester
Starts the background thread to test connection.
startProcess(String) - Method in class org.peace_tools.core.session.LocalServerSession
Helper method to start process to execute command via OS-specific command processor.
startSession() - Method in class org.peace_tools.core.job.SubmitJobWizardPage
This is a helper method that is used to establish a valid session with the remote server on which the job is to be submitted.
startTimestamp - Variable in class org.peace_tools.workspace.Job
The time when this job was actually created and queued to run on a server.
stateChanged(ChangeEvent) - Method in class org.peace_tools.core.job.MSTWizardPage
Listener for CPUs and Nodes/CPU spinner input boxes to update memory.
stateChanged(ChangeEvent) - Method in class org.peace_tools.generic.dndTabs.DnDTabButton
Intercept tab changes and show/hide the close button.
stateChanged(ChangeEvent) - Method in class org.peace_tools.views.ESTTableView
 
stateChanged(ChangeEvent) - Method in class org.peace_tools.views.overlap.OverlapView
Helper method to compute and update scale for the actual display.
staticViewPos - Variable in class org.peace_tools.core.ViewFactory
The last saved positions for the various static views.
staticViews - Variable in class org.peace_tools.core.ViewFactory
The list of static views associated with any main frame.
STATS_ICON - Static variable in class org.peace_tools.views.PropertiesTreeMaker
A static constant to refer to the statistics icon position in the PropertiesTreeMaker.CustomIcons array.
STATS_STR - Variable in class org.peace_tools.core.dataset.SummaryWizardPage
A simple standard message to be displayed at the bottom of this page.
status - Variable in class org.peace_tools.workspace.JobBase
The current runtime status of this job.
status - Variable in class org.peace_tools.workspace.Server
The current operational status of this server.
StatusRenderer - Variable in class org.peace_tools.views.JobListView
An instance of the cell renderer that is used to render the second column in the table to display status or progress information.
StatusStrings - Static variable in class org.peace_tools.data.ServerListTableModel
The set of better formatted status strings to be displayed to the user in the ServerList table associated with this data model.
stepInfo - Variable in class org.peace_tools.core.job.SubmitJobWizardPage
The step information labels to display information about the steps to be done and those that have been completed.
submitJob() - Method in class org.peace_tools.core.job.SubmitJobWizardPage
Helper method to run the job runner on the server.
SubmitJobWizardPage - Class in org.peace_tools.core.job
This class serves as the final page in a JobWizard.
SubmitJobWizardPage(JobWizard) - Constructor for class org.peace_tools.core.job.SubmitJobWizardPage
The constructor.
subTitle - Variable in class org.peace_tools.generic.GenericWizardPage
The subtitle to be set for this wizard page.
SUCCESS_MESSAGE - Static variable in class org.peace_tools.core.job.SubmitJobWizardPage
A generic informational message that is displayed to the user after a job has successfully started up.
SUCCESS_MSG - Static variable in class org.peace_tools.core.JobMenuHelper
A success message that is formatted (to fill-in missing information) and displayed to the user indicating that the job was aborted.
summary - Variable in class org.peace_tools.core.job.VerifyWizardPage
Field to read and edit a brief description about the job.
SummaryWizardPage - Class in org.peace_tools.core.dataset
This class serves as the last page in a DataSetWizard.
SummaryWizardPage(DataSetWizard, DataSet) - Constructor for class org.peace_tools.core.dataset.SummaryWizardPage
The constructor.
SURE_ABORT_JOB - Static variable in class org.peace_tools.core.JobMenuHelper
An verification message that is formatted (to fill-in missing information) and displayed to the user just before a job is aborted on a server.
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