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

G

generateClusterLookupTable(int, ClusterNode, int[]) - Static method in class org.peace_tools.data.OverlapModel

Helper method to build a table (simple array) that provides clusterID for each fragment.

generateESTEntries(MSTNode, int, int[], int, int, ArrayList<Long>) - Method in class org.peace_tools.data.OverlapModel

Recursive method to generate ESTEntry objects with alignment information.

GenericHTMLView - Class in org.peace_tools.views

A HTML-based view to display simple HTML data.

GenericHTMLView(String, MainFrame) - Constructor for class org.peace_tools.views.GenericHTMLView

The default and only constructor.

GenericWizardPage - Class in org.peace_tools.generic

This class serves as a generic wizard page.

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

The default constructor.

get() - Static method in class org.peace_tools.data.DataStore

Obtain reference to the globally unique singleton instance.

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

Method to get a reference to the process-wide, unique instance of the PEACE workspace.

getActionListener() - Method in class org.peace_tools.core.AbstractMenuHelper

The action listener to handle actions created by this menu helper.

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

getActionListener() - Method in class org.peace_tools.core.HelpMenuHelper

getActionListener() - Method in class org.peace_tools.core.JobMenuHelper

getActionListener() - Method in class org.peace_tools.core.ServerMenuHelper

getActionListener() - Method in class org.peace_tools.core.ViewMenuHelper

getAlignmentMetric() - Method in class org.peace_tools.data.MSTNode

Returns the distance metric value set for this node.

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

This method is a convenience method that can be used to obtain a FWAnalyzer object containing information from this page.

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

Obtain the currently selected analyzer.

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

Obtain the currently selected analyzer.

getBackground(Object) - Method in class org.peace_tools.views.ClusterTreeTableView.DataSetRenderer

Provide background for a given object.

getBorderInsets(Component) - Method in class org.peace_tools.generic.CustomBorder

Returns the insets of the border.

getBorderInsets(Component, Insets) - Method in class org.peace_tools.generic.CustomBorder

Reinitialize the insets parameter with this Border's current Insets.

getCacheSize() - Method 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.

getCacheType() - Method in class org.peace_tools.workspace.FWAnalyzer

The type of cache that was used to cache distance/similarity metrics generated during MST construction.

getCellEditorValue() - Method in class org.peace_tools.views.DBClassifierEditor.ColorEditor

Implementation for method in CellEditor interface to return the color value set by the user.

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

Obtain the permanent, center pane for this frame.

getChild(Object, int) - Method in class org.peace_tools.data.ClusterTreeTableModel

Returns the child cluster or EST node for a given parent node.

getChild(Object, int) - Method in class org.peace_tools.data.DataSetTreeModel

This method provides the actual child object to be displayed in a JTree depending on the data in the Workspace.

getChild(Object, int) - Method in class org.peace_tools.data.MSTTreeModel

This method provides the actual child object to be displayed in a JTree under a given node.

getChildCount(Object) - Method in class org.peace_tools.data.ClusterTreeTableModel

Return the number of child nodes for a given cluster node.

getChildCount(Object) - Method in class org.peace_tools.data.DataSetTreeModel

This method provides the child count depending on the data in the Workspace.

getChildCount(Object) - Method in class org.peace_tools.data.MSTTreeModel

This method provides the child count for a given node.

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

Obtain the child nodes associated with this node.

getChildren() - Method in class org.peace_tools.data.MSTNode

Obtain the child nodes for this node.

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

Obtain the classifier list set for this work space.

getClassifiers() - Method in class org.peace_tools.workspace.ClassifierList

Obtain reference to a clone of list of classifiers.

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

Obtain the cluster entry created and added by this wizard.

getClusterData(String, Component) - Method in class org.peace_tools.data.DataStore

Method to load/get a given cluster file.

getClusterData(String) - Method in class org.peace_tools.workspace.DataSet

Obtain the MSTClusterData entry for a given job ID.

getClusterData(String) - Method in class org.peace_tools.workspace.Workspace

Obtain the MSTClusterData entry for a given job ID.

getClusterEntry(String, String, JobSummary) - Method in class org.peace_tools.core.job.ClusterWizardPage

Helper method to create a MSTCluster data.

getClusterFile() - Method in class org.peace_tools.data.ClusterTreeTableModel

Obtain the cluster file from where cluster data was obtained.

getClusterFile() - Method in class org.peace_tools.data.OverlapModel

Obtain the cluster file information from where this pre-alignment model was built.

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

Obtain the cluster id associated with an EST node.

getClusterID() - Method in class org.peace_tools.data.ESTEntry

Returns the ID of the cluster to which this entry belongs.

getClusterList() - Method in class org.peace_tools.workspace.DataSet

Obtain the list of clustering data files encapsulated by this data set.

getColor(int, Component) - Method in class org.peace_tools.generic.CustomBorder

Helper method to get the color associated with a given side of the border.

getColor(Integer) - Method in interface org.peace_tools.views.overlap.ClusterColorMapper

Return the Color associated with a given cluster ID.

getColor(Integer) - Method in class org.peace_tools.views.overlap.OverlapView

getColor() - Method in class org.peace_tools.workspace.DBClassifier

Obtain the color code for shading database entry.

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

Obtain the current column scaling factor being used.

getColumn() - Method in class org.peace_tools.data.ESTEntry

Obtain the starting column position where this entry is to be placed.

getColumnClass(int) - Method in class org.peace_tools.data.ClusterTreeTableModel

Obtain the class that describes the data type of a given column.

getColumnClass(int) - Method in class org.peace_tools.data.DataSetTableModel

Obtain the class that describes the data type of a given column.

getColumnClass(int) - Method in class org.peace_tools.data.ESTTableModel

Obtain the class that describes the data type of a given column.

getColumnClass(int) - Method in class org.peace_tools.data.JobListTableModel

Obtain the class that describes the data type of a given column.

getColumnCount() - Method in class org.peace_tools.data.ClusterTreeTableModel

This method overrides the interface method in RowModel to return the number of columns in the TreeTable.

getColumnCount() - Method in class org.peace_tools.data.DataSetTableModel

Method to obtain the columns that are to be displayed in a

getColumnCount() - Method in class org.peace_tools.data.ESTTableModel

This method overrides the interface method in TableModel to return the number of columns in the Table.

getColumnCount() - Method in class org.peace_tools.data.JobListTableModel

Method to obtain the columns that are to be displayed by in a Job table.

getColumnCount() - Method in class org.peace_tools.data.ServerListTableModel

Method to obtain the columns that are to be displayed by in a Server table.

getColumnName(int) - Method in class org.peace_tools.data.ClusterTreeTableModel

This method overrides the interface method in RowModel to return the title for the columns.

getColumnName(int) - Method in class org.peace_tools.data.DataSetTableModel

Override the default names that are set for the columns displayed in the job table.

getColumnName(int) - Method in class org.peace_tools.data.ESTTableModel

This method overrides the interface method in RowModel to return the title for the columns.

getColumnName(int) - Method in class org.peace_tools.data.JobListTableModel

Override the default names that are set for the columns displayed in the job table.

getColumnName(int) - Method in class org.peace_tools.data.ServerListTableModel

Override the default names that are set for the columns displayed in the job table.

getCPUs() - Method in class org.peace_tools.workspace.JobSummary

The total number of CPUS that was computed and stored in this summary when the JobSummary object was created.

getCPUsPerNode() - Method in class org.peace_tools.workspace.Job

Obtain the number of CPUs on each node that were requested for running this job.

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

Obtain the index of the current page being displayed in this wizard.

getDataSet() - Method in class org.peace_tools.core.job.JobInfoWizardPage

Obtain the data set that has been selected by the user.

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

Helper method to obtain the currently selected data set.

getDataSet() - Method in class org.peace_tools.workspace.MSTClusterData

Obtain the data set that logically contains this MST Data.

getDataSet() - Method in class org.peace_tools.workspace.MSTData

Obtain the data set that logically contains this MST Data.

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

Obtain the list of data sets associated with this workspace.

getDBClassifier() - Method in class org.peace_tools.data.EST

Obtain the classifier index with which this EST is associated.

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

Helper method to determine the default working directory for PEACE.

getDescription() - Method in class org.peace_tools.core.job.JobInfoWizardPage

Obtain the description for the job.

getDescription() - Method in class org.peace_tools.workspace.DataSet

Obtain the user supplied description for this this data.

getDescription() - Method in class org.peace_tools.workspace.DBClassifier

Obtain the user supplied description for this this classifier.

getDescription() - Method in class org.peace_tools.workspace.Job

Obtain the user supplied description for this this job.

getDescription() - Method in class org.peace_tools.workspace.MSTClusterData

Obtain the user supplied description for this this data.

getDescription() - Method in class org.peace_tools.workspace.MSTData

Obtain the user supplied description for this this data.

getDescription() - Method in class org.peace_tools.workspace.Server

Obtain the user-specified description for this entry.

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

Obtain the permanent desktop panel for this frame.

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

Obtain the directory where all the files pertaining to this workspace are stored by default.

getDisplayName(Object) - Method in class org.peace_tools.views.ClusterTreeTableView.DataSetRenderer

Provides a name for the node to be displayed on the tree.

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

This method can be used to determine the current docking cue associated with this DndTabPane.

getEditorKit() - Method in class org.peace_tools.views.GenericHTMLView

Create custom editor kit to work around Java bug.

getElement(Document, String) - Static method in class org.peace_tools.workspace.DOMHelper

Utility method to search for a given immediate child element.

getElement(Element, String) - Static method in class org.peace_tools.workspace.DOMHelper

Utility method to search for a given immediate child element.

getElement(NodeList, String) - Static method in class org.peace_tools.workspace.DOMHelper

Helper method to search within a given list of nodes to locate a given element.

getElementAt(int) - Method in class org.peace_tools.data.OverlapModel

Obtain the cluster node in the combo box list at a given index.

getEntry(int) - Method in class org.peace_tools.data.DataSetTableModel

This is a helper method to obtain a file name corresponding to a given row in the work space.

getEntryType() - Method in class org.peace_tools.workspace.WorkspaceEvent

Determine the type of entry regarding which a status change is being reported.

getEST() - Method in class org.peace_tools.data.ESTEntry

Returns the actual EST object set for this node.

getESTAt(int) - Method in class org.peace_tools.data.ESTTableModel

Obtain the EST entry at a given row.

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

Obtain the aggregate classification information for this cluster.

getESTCount(boolean) - Method in class org.peace_tools.data.ClusterNode

Method to determine number of ESTs contained in this cluster node.

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

Obtain the EST id associated with an EST node.

getESTIndex() - Method in class org.peace_tools.data.MSTNode

Obtain the index of the EST associated with this node.

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

This method can be used to obtain the ESTs associated with this data set.

getESTList() - Method in class org.peace_tools.data.ClusterTreeTableModel

Obtain the list of ESTs associated with this model.

getESTList() - Method in class org.peace_tools.data.ESTTableModel

Obtain the list of ESTs associated with this model.

getESTList() - Method in class org.peace_tools.data.MSTTreeModel

Obtain the list of ESTs for which this MST was generated.

getESTList() - Method in class org.peace_tools.data.OverlapModel

Obtain the list of ESTs associated with this model.

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

Obtain the list of ESTs encapsulated by this ESTList.

getExtension(File) - Static method in class org.peace_tools.generic.Utilities

A helper method to determine the extension of a file.

getFarthestPos(MSTNode) - Method in class org.peace_tools.data.OverlapModel

Helper method to determine how far-left the pre-alignment extends given the root is at logical position zero.

getFASTA(String, Component) - Method in class org.peace_tools.data.DataStore

Method to load/get a given FASTA file.

getFileName() - Method in class org.peace_tools.data.ClusterFile

The absolute path to the file name from where the cluster data was originally loaded.

getFileName(int) - Method in class org.peace_tools.data.DataSetTableModel

This is a helper method to obtain a file name corresponding to a given row in the work space.

getFileName() - Method in class org.peace_tools.data.MST

The absolute path to the file name from where the MST data was originally loaded.

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

Obtain the name of the file to which the user logs are being written.

getFilterList() - Method in class org.peace_tools.workspace.Job

Obtain the list of filters that were used to improve quality of clustering.

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

This method is a convenience method that can be used to obtain a FilterList object containing information from this page.

getFiltersCmdLine() - Method in class org.peace_tools.workspace.Job

Command line for PEACE clustering engine to configure filters.

getFiltersSummary() - Method in class org.peace_tools.workspace.JobSummary

Obtain a summary of the filters run as a part of the data.

getForeground(Object) - Method in class org.peace_tools.views.ClusterTreeTableView.DataSetRenderer

Provide foreground for a given object.

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

Obtain the currently set frame size for the analyzer.

getFrameSize() - Method in class org.peace_tools.workspace.FWAnalyzer

The frame/window size that was used to analyze EST sequences.

getFWAnalyzer() - Method in class org.peace_tools.workspace.MSTData

Obtain meta data about the frame/word analyzer that was used to generate metrics (may it be similarity or distance values) that were used to build the MST.

getHelperType() - Method in class org.peace_tools.core.AbstractMenuHelper

Determine the type of helper that this object represents.

getHeuristicList() - Method in class org.peace_tools.workspace.Job

Obtain the list of heuristics that were used to accelerate the process of constructing the MST.

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

This method is a convenience method that can be used to obtain a HeuristicList object containing information from this page.

getHeuristicsCmdLine() - Method in class org.peace_tools.workspace.Job

Command line for PEACE clustering engine to configure heuristics.

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

This method is a convenience method that can be used to obtain a String summarizing the heuristic setup for this job.

getHeuristicsSummary() - Method in class org.peace_tools.workspace.JobSummary

Obtain a summary of the heuristics run as a part of the data.

getIcon() - Method in class org.peace_tools.generic.IconTreeNode

Obtain the icon set for this tree node.

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

This method is a quick little helper method to pull image (icons) using getResource(String).

getIcon(Object) - Method in class org.peace_tools.views.ClusterTreeTableView.DataSetRenderer

Provide an icon for a given object.

getIconHeight() - Method in class org.peace_tools.views.overlap.ClusterListCellRenderer.CustomIcon

getIconWidth() - Method in class org.peace_tools.views.overlap.ClusterListCellRenderer.CustomIcon

getID() - Method in class org.peace_tools.data.EST

Obtain the ID of this EST.

getID() - Method in class org.peace_tools.workspace.DataSet

Obtain the work space wide unique identifier set for this data set.

getID() - Method in class org.peace_tools.workspace.MSTClusterData

Obtain the work space wide unique identifier set for this entry.

getID() - Method in class org.peace_tools.workspace.MSTData

Obtain the work space wide unique identifier set for this data set.

getID() - Method in class org.peace_tools.workspace.Server

Returns the workspace-unique ID assigned for this server entry.

getImage() - Method in class org.peace_tools.generic.CustomPanel

Obtain the image associated with this panel (if any).

getIndexOfChild(Object, Object) - Method in class org.peace_tools.data.ClusterTreeTableModel

Obtain the index of a given child node within its immediate parent.

getIndexOfChild(Object, Object) - Method in class org.peace_tools.data.DataSetTreeModel

This method provides the zero-based logical index of a child node.

getIndexOfChild(Object, Object) - Method in class org.peace_tools.data.MSTTreeModel

This method provides the zero-based logical index of a child node.

getInfo() - Method in class org.peace_tools.data.EST

Obtain the information associated with this EST.

getInstallPath() - Method in class org.peace_tools.workspace.Server

Obtain the directory where the runtime files associated with PEACE are installed on the server.

getIntValue(Element, String) - Static method in class org.peace_tools.workspace.DOMHelper

Utility method to obtain the value of a given element as an integer.

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

Obtain the job entry created and added by this wizard.

getJob(int) - Method in class org.peace_tools.data.JobListTableModel

This is a convenience method to obtain the job data.

getjob(String) - Method in class org.peace_tools.workspace.JobList

Obtain reference to a job object, given its work space wide unique job ID.

getJobID() - Method in class org.peace_tools.workspace.JobBase

Obtain the work space wide unique identifier set for this job.

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

Obtain the JobList that encapsulates the list of Jobs that have been configured in this workspace.

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

Obtain the list of job objects that are currently available in a work space.

getJobSummary() - Method in class org.peace_tools.workspace.MSTClusterData

Obtain meta data about the job that was run to generate the cluster.

getJobSummary() - Method in class org.peace_tools.workspace.MSTData

Obtain meta data about the job that was run to generate the MST.

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

Determine the largest cluster in this cluster node.

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

Returns the time that the file denoted by this abstract file information was last modified.

getLastUpdateTimestamp() - Method in class org.peace_tools.workspace.Job

Returns the last time the status of this job was set/changed.

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

Retrieves the current logging level.

getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.peace_tools.views.overlap.ClusterListCellRenderer

Overrides base class method to provide customized color icon.

getListSelectionListener(JTable) - Method in class org.peace_tools.core.AbstractMenuHelper

The listener to be used in JTable to update tools & menu items.

getListSelectionListener(JTable) - Method in class org.peace_tools.core.FileMenuHelper

getListSelectionListener(JTable) - Method in class org.peace_tools.core.HelpMenuHelper

getListSelectionListener(JTable) - Method in class org.peace_tools.core.JobMenuHelper

getListSelectionListener(JTable) - Method in class org.peace_tools.core.ServerMenuHelper

getListSelectionListener(JTable) - Method in class org.peace_tools.core.ViewMenuHelper

getLocation(int, int) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler

Helper method used to determine where a given x and y coordinates (typically the mouse pointer positions) is with respect to the DnDTabbedPane that owns this handler.

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

Obtain reference to the globally unique instance of the ProgrammerLog.

getLog() - Static method in class org.peace_tools.generic.UserLog

Obtain reference to the globally unique instance of the UserLog.

getLogEntries() - Method in class org.peace_tools.generic.ProgrammerLog

Obtain the set of log entries contained in the user logs.

getLogEntries() - Method in class org.peace_tools.generic.UserLog

Obtain the set of log entries contained in the user logs.

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

Obtain the instance of the main frame class that owns this wizard.

getMaxCol() - Method in class org.peace_tools.data.OverlapModel

Obtain the last column where a nucleotide is present.

getMaxRow() - Method in class org.peace_tools.data.OverlapModel

Determine the maximum number of rows in this overlap model.

getMaxRunTime() - Method in class org.peace_tools.workspace.Job

Obtain the total time to be requested for this job.

getMemory() - Method in class org.peace_tools.workspace.Job

Obtain the memory to be requested for this job.

getMenuHelper(AbstractMenuHelper.HelperType) - Method in class org.peace_tools.core.MainFrame

Obtain a menu helper for a given helper type.

getMenuItem(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.AbstractMenuHelper

Obtain a main menu item for the given action type.

getMenuItem(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.FileMenuHelper

getMenuItem(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.HelpMenuHelper

getMenuItem(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.JobMenuHelper

getMenuItem(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.ServerMenuHelper

getMenuItem(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.ViewMenuHelper

getMetadata() - Method in class org.peace_tools.data.ClusterFile

Obtain the meta data associated with this cluster file.

getMetric() - Method in class org.peace_tools.data.MSTNode

Returns the metric value set for this node.

getMonitor(Job) - Static method in class org.peace_tools.core.JobMonitor

Method to obtain an existing monitor thread for this job.

getMonitor() - Method in class org.peace_tools.workspace.Job

Obtain the job monitoring thread (if any)

getMST() - Method in class org.peace_tools.data.MSTTreeModel

Obtain the raw MST file data associated with this model.

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

Obtain the MST entry created and added by this wizard.

getMSTData(String, Component) - Method in class org.peace_tools.data.DataStore

Method to load/get a given cluster file.

getMSTData(String) - Method in class org.peace_tools.workspace.DataSet

Obtain the MSTData entry for a given job ID.

getMSTData(String) - Method in class org.peace_tools.workspace.Workspace

Obtain the MSTData entry for a given job ID.

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

Obtain the path to the MST file entered by the user.

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

Helper method to obtain the MST file specified by the user.

getMSTID() - Method in class org.peace_tools.workspace.MSTClusterData

Obtain the work space wide unique identifier set for this MST data set.

getMSTList() - Method in class org.peace_tools.workspace.DataSet

Obtain the list of MST data files encapsulated by this data set.

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

Obtain the name associated with this cluster (if any) This method must be used to obtain the name associated with this cluster.

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

The name associated to identify this ESTList.

getName() - Method in class org.peace_tools.generic.Pair

The name set for this parameter.

getName() - Method in class org.peace_tools.workspace.Filter

Obtain the type of filter represented by this class.

getName() - Method in class org.peace_tools.workspace.Heuristic

Obtain the name of the heuristic associated with this class.

getName() - Method in class org.peace_tools.workspace.Param

The name set for this parameter.

getName() - Method in class org.peace_tools.workspace.Server

Returns the server's domain name (or IP address) set for for this server entry.

getNodes() - Method in class org.peace_tools.workspace.Job

Obtain the number of nodes that were requested for running this job.

getOperation() - Method in class org.peace_tools.workspace.WorkspaceEvent

Determine the type of operation reported by this event.

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

Determine the type of OS that this session is connected to.

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

Determine the type of OS that this session is connected to.

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

Determine the type of OS that this session is connected to.

getPage() - Method in class org.peace_tools.generic.GenericWizardPage

Method to return the component for this wizard page.

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

Obtain wizard page associated with the given index.

getPage() - Method in interface org.peace_tools.generic.WizardPage

Obtain the actual component associated with this wizard page.

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

Obtain the page pane to which wizard pages must be added.

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

Method to obtain the top-level GUI container for this installer.

getParameters() - Method in class org.peace_tools.workspace.Filter

Obtain the full list of parameters passed to this filter.

getParameters() - Method in class org.peace_tools.workspace.Heuristic

Obtain the full list of parameters passed to this heuristic.

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

Helper method to check and get password from the user.

getPassword() - Method in class org.peace_tools.workspace.Server

Return the password to be used for logging on to a remote server.

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

The path to the file represented by this object.

getPath(Object) - Method in class org.peace_tools.data.DataSetTreeModel

This is a helper method to determine path to a given entry.

getPath() - Method in class org.peace_tools.workspace.DataSet

Obtain the complete file name and path where the actual EST file is located.

getPath() - Method in class org.peace_tools.workspace.Job

Obtain the system generated directory where the output files for this job are stored on the server.

getPath() - Method in class org.peace_tools.workspace.MSTClusterData

Obtain the complete file name and path where the actual cluster file is located.

getPath() - Method in class org.peace_tools.workspace.MSTData

Obtain the complete file name and path where the actual MST file is located.

getPattern() - Method in class org.peace_tools.workspace.DBClassifier

This method must be used to obtain the pre-compiled pattern associated with this classifier.

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

Obtain platform-specific job configuration information.

getPollTime() - Method in class org.peace_tools.workspace.Server

Obtain the delay between successive polling efforts for this server.

getPosition(Component, DnDTabbedPane.Location[]) - Method in class org.peace_tools.generic.dndTabs.DnDTabPos

Traverse saved position information as much as possible.

getPreferredSize() - Method in class org.peace_tools.generic.CustomPanel

Provide feedback on the preferred size of this panel This method overrides the default implementation of the getPreferredSize() method in the super class.

getProgressInfo() - Method in class org.peace_tools.workspace.Job

Obtain the current progress information status for this job.

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

Obtain the purpose set for this session.

getRegExp() - Method in class org.peace_tools.workspace.DBClassifier

Obtain the raw regular expression set for this classifier.

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

Obtain the type of information being rendered for each fragment.

getRoot() - Method in class org.peace_tools.data.ClusterFile

Obtain the top-level root cluster for this cluster file.

getRoot() - Method in class org.peace_tools.data.ClusterTreeTableModel

Obtain the top-level root node.

getRoot() - Method in class org.peace_tools.data.DataSetTreeModel

Obtain the root of the data set tree.

getRoot() - Method in class org.peace_tools.data.MST

Obtain the root node of this MST.

getRoot() - Method in class org.peace_tools.data.MSTTreeModel

Obtain the root of the data set tree.

getRow(Object) - Method in class org.peace_tools.data.DataSetTableModel

Obtain the row for a given entry in this list.

getRow(int) - Method in class org.peace_tools.data.OverlapModel

Obtain the list of EST entries on a given row in the model.

getRow(int, int, int, ArrayList<Long>) - Static method in class org.peace_tools.data.OverlapModel

This is a helper method that is used to determine the row on which a fragment can be accommodated.

getRowCount() - Method in class org.peace_tools.data.DataSetTableModel

Method to return the number of rows to be displayed in the table.

getRowCount() - Method in class org.peace_tools.data.ESTTableModel

Method to return the number of rows to be displayed in the table.

getRowCount() - Method in class org.peace_tools.data.JobListTableModel

Method to return the number of rows to be displayed in the Job table.

getRowCount() - Method in class org.peace_tools.data.ServerListTableModel

Method to return the number of rows to be displayed in the Server table.

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

Obtain the current row scaling factor being used.

getRunTime() - Method in class org.peace_tools.workspace.JobBase

Obtain the wall clock run time for this job.

getSelectedItem() - Method in class org.peace_tools.data.OverlapModel

Obtain the currently displayed cluster in the combo box.

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

Helper method to obtain selected server ID.

getSequence() - Method in class org.peace_tools.data.EST

Obtain the actual sequence of base pairs for this EST.

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

Obtain the current server entry that is being edited via this server wizard.

getServer(int) - Method in class org.peace_tools.data.ServerListTableModel

This is a convenience method to obtain the server entry.

getServer(String) - Method in class org.peace_tools.workspace.ServerList

Obtain reference to a Server object, given its work space wide unique server ID.

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

Helper method to compute the full path to the EST data file on the server.

getServerID() - Method in class org.peace_tools.workspace.JobBase

Obtain the work space wide unique identifier set for the server on which this job is scheduled to run (or was run).

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

Obtain the ServerList that encapsulates the list of Servers that have been configured in this workspace.

getServerName() - Method in class org.peace_tools.workspace.JobSummary

The server name that was obtained from the Server entry and stored in this summary when the JobSummary object was created.

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

Obtain the list of Server objects that are currently available in a work space.

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

The size of the file in bytes.

getSize() - Method in class org.peace_tools.data.OverlapModel

Obtain the number of entries to be displayed in the combo box.

getSize() - Method in class org.peace_tools.workspace.ClassifierList

Convenience method to determine the number of classifiers in this list.

getStartTimestamp() - Method in class org.peace_tools.workspace.Job

Obtain the timestamp indicating when the job actually started running on the server.

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

Helper method to translate a cluster Index to an absolute x-coordinate.

getStatus() - Method in class org.peace_tools.workspace.JobBase

Obtain the current status set for this job.

getStatus() - Method in class org.peace_tools.workspace.Server

Obtain the current status set for this server.

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

This is a helper method that can be used to obtain an input stream for a resource.

getStringValue(Document, String) - Static method in class org.peace_tools.workspace.DOMHelper

Utility method to obtain the value of a given element as a string.

getStringValue(Element, String) - Static method in class org.peace_tools.workspace.DOMHelper

Utility method to obtain the value of a given element as a string.

getStringValue(Element, String, boolean) - Static method in class org.peace_tools.workspace.DOMHelper

Utility method to obtain the value of a given element as a string.

getStringValue(NodeList, String, boolean) - Static method in class org.peace_tools.workspace.DOMHelper

Utility method to obtain the value of a given element as a String.

getSubTitle() - Method in class org.peace_tools.generic.GenericWizardPage

This method returns the sub-title set for this web page.

getSubTitle() - Method in interface org.peace_tools.generic.WizardPage

This method must be implemented to return a sub-title for this wizard page.

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

This method is a convenience method that can be used to obtain a String summarizing the filters setup for this job.

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

This is a helper method that is invoked from the last wizard page (SubmitJobWizardPage) to obtain summary data.

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

Obtain the name of the server that the user has selected.

getSummary() - Method in class org.peace_tools.workspace.Filter

Provides a multi-line information about this filter.

getSummary() - Method in class org.peace_tools.workspace.Heuristic

Provides a multi-line information about this heuristic.

getSummary(String) - Method in class org.peace_tools.workspace.MSTClusterData

Provides a textual multi-line summary for this element.

getSummary(String) - Method in class org.peace_tools.workspace.MSTData

Provides a textual multi-line summary for this element.

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.peace_tools.views.DBClassifierEditor.ColorEditor

Custom implementation for obtaining cell editor component.

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.peace_tools.views.CustomTableCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.peace_tools.views.DataSetFileListView.ServerNameStatusRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.peace_tools.views.DBClassifierEditor.ColorRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.peace_tools.views.JobListView.JobNameStatusRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.peace_tools.views.JobListView.JobStatusRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.peace_tools.views.ServerListView.ServerNameStatusRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.peace_tools.views.UserLogPane.StatusTimeStamp

getThreshold() - Method in class org.peace_tools.workspace.MSTClusterData

The threshold value used for cluster generating.

getTitle() - Method in class org.peace_tools.generic.GenericWizardPage

This method returns the title set for this wizard page.

getTitle() - Method in interface org.peace_tools.generic.WizardPage

This method must be implemented to return a title for this wizard page.

getTool(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.AbstractMenuHelper

Obtain a tool bar button for the given action type.

getTool(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.FileMenuHelper

getTool(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.HelpMenuHelper

getTool(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.JobMenuHelper

getTool(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.ServerMenuHelper

getTool(AbstractMenuHelper.ActionType, boolean) - Method in class org.peace_tools.core.ViewMenuHelper

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

Obtain the toolbar associated with this frame.

getTooltipText(Object) - Method in class org.peace_tools.views.ClusterTreeTableView.DataSetRenderer

Provide an tool tip for the node.

getTransferData(DataFlavor) - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler.TransferableTab

This method is a part of the Transferable interface.

getTransferDataFlavors() - Method in class org.peace_tools.generic.dndTabs.DnDTabHandler.TransferableTab

This method is a part of the Transferable interface.

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.peace_tools.views.DataSetTreeView.DataSetRenderer

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.peace_tools.views.MSTFileView.DataSetRenderer

getTreeSelectionListener(JTree) - Method in class org.peace_tools.core.AbstractMenuHelper

The listener to be used in JTree to update tools & menu items.

getTreeSelectionListener(JTree) - Method in class org.peace_tools.core.FileMenuHelper

getTreeSelectionListener(JTree) - Method in class org.peace_tools.core.HelpMenuHelper

getTreeSelectionListener(JTree) - Method in class org.peace_tools.core.JobMenuHelper

getTreeSelectionListener(JTree) - Method in class org.peace_tools.core.ServerMenuHelper

getTreeSelectionListener(JTree) - Method in class org.peace_tools.core.ViewMenuHelper

getType() - Method in class org.peace_tools.workspace.FWAnalyzer

Determine the type of f/w analyzer that this object contains information about.

getType() - Method in class org.peace_tools.workspace.MSTData

The type of MST building approach supported by PEACE that was used to obtain the MST referred by this class.

getTypeCode(Object) - Method in class org.peace_tools.core.DeleteDialog

An internal method to returns a type code for a given work space entry.

getUserID() - Method in class org.peace_tools.workspace.Server

Obtain the user ID to be used for logging onto this server.

getValue() - Method in class org.peace_tools.generic.Pair

The value associated with this parameter.

getValue() - Method in class org.peace_tools.workspace.Param

The value associated with this parameter.

getValueAt(int, int) - Method in class org.peace_tools.data.DataSetTableModel

Obtain the value to be displayed at a given row and column.

getValueAt(int, int) - Method in class org.peace_tools.data.ESTTableModel

This method returns the subset of base pairs to be displayed in a given column for a given row.

getValueAt(int, int) - Method in class org.peace_tools.data.JobListTableModel

Obtain the value to be displayed at a given row and column.

getValueAt(int, int) - Method in class org.peace_tools.data.ServerListTableModel

Obtain the value to be displayed at a given row and column.

getValueFor(Object, int) - Method in class org.peace_tools.data.ClusterTreeTableModel

This method returns the subset of base pairs to be displayed in a given column for a given RowModel.

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

Obtain the view factory associated with this main frame.

getWordSize() - Method in class org.peace_tools.workspace.FWAnalyzer

The word size that was used to analyze EST sequences.

getWorkerThreads() - Static method in class org.peace_tools.core.MainFrame

Obtain the thread group that contains the job status monitoring threads.

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

Obtain the work space that was successfully selected by the user.

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

Method to provide consistent name for the PEACE workspace file name so that the file names are consistently used throughout.

getWsEntry() - Method in class org.peace_tools.data.ClusterTreeTableModel

Obtain the actual workspace entry whose data is contained in this model.

getWsEntry() - Method in class org.peace_tools.data.MSTTreeModel

Obtain the actual workspace entry whose data is contained in this model.

getWsEntry() - Method in class org.peace_tools.data.OverlapModel

Obtain the actual workspace entry whose data is contained in this model.

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

The panel that is used to draw the cluster graph.

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

The current version information of the software.