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

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pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.dataset.ESTInfoWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.dataset.SummaryWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.job.ClusterWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.job.HeuristicsWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.job.JobInfoWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.job.MSTWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.job.SubmitJobWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.job.VerifyWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.server.ServerAddingEntryWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.server.ServerInfoWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.core.server.ServerTypeWizardPage

This method is called just before this page is to be displayed.

pageChanged(WizardDialog, int, int) - Method in class org.peace_tools.generic.GenericWizardPage

Method to setup this page just before it is displayed.

pageChanged(WizardDialog, int, int) - Method in interface org.peace_tools.generic.WizardPage

This method is invoked on a wizard page just before it is going to be displayed.

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.dataset.ESTInfoWizardPage

Method to intercept page change and trigger FASTA validation.

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.job.ClusterWizardPage

This method validates the cluster file set for in this page.

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.job.FiltersWizardPage

Method to veto a page change if filter string is invalid.

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.job.JobInfoWizardPage

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.job.MSTWizardPage

This method validates the MST file set for in this page.

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.server.ServerAddingEntryWizardPage

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.server.ServerInfoWizardPage

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.core.server.ServerTypeWizardPage

pageChanging(WizardDialog, int, int) - Method in class org.peace_tools.generic.GenericWizardPage

Method to veto a page change (if needed).

pageChanging(WizardDialog, int, int) - Method in interface org.peace_tools.generic.WizardPage

This method is invoked to indicate indicate to the currently visible page that the user is moving away from the current page by clicking either on the "Previous" or the "Next" button.

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

A custom panel that is used to hold all the pages of this wizard.

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

The array list containing the set of pages to be displayed by this wizard in the same sequence as they are to be displayed.

paint(Graphics) - Method in class org.peace_tools.views.CustomTableCellRenderer

paint(Graphics, int, ESTEntry) - Method in class org.peace_tools.views.overlap.OverlapPanel

Helper method to paint a given fragment using a given graphics handle.

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

Paints the border for the specified component with the specified position and size.

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

This method overrides the default method in the parent class.

paintComponent(Graphics) - Method in class org.peace_tools.generic.CustomPanel

Paint the background image as and when necessary This method is automatically invoked by the core Java AWT runtime engine whenever the background for the CustomPanel needs to be repainted.

paintComponent(Graphics) - Method in class org.peace_tools.views.ClusterSummaryView.TickLine

This method overrides the default paint method to fill the area with black.

paintComponent(Graphics) - Method in class org.peace_tools.views.overlap.ClusterList

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

Override the default paint method for this panel to render fragments.

paintComponent(Graphics) - Method in class org.peace_tools.views.overlap.Ruler

paintHorizRule(Graphics) - Method in class org.peace_tools.views.overlap.Ruler

Helper method to paint the horizontal ruler.

paintIcon(Component, Graphics, int, int) - Method in class org.peace_tools.views.overlap.ClusterListCellRenderer.CustomIcon

paintVerticalRule(Graphics) - Method in class org.peace_tools.views.overlap.Ruler

Helper method to paint the horizontal ruler.

Pair - Class in org.peace_tools.generic

A simple class to encapsulate a pair that is used to describe pairs of values that are stored in other data structures.

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

The constructor merely initializes the pair encapsulated by this object.

pam - Variable in class org.peace_tools.views.overlap.OverlapView

The PreAlignmentModel that provides the necessary information for rendering the core information required for this view.

pane - Variable in class org.peace_tools.generic.dndTabs.DnDTabButton

The tab pane which which this tab button is logically associated.

panel - Variable in class org.peace_tools.views.overlap.OverlapView

The overlap panel that actual renders the fragments for us.

Param - Class in org.peace_tools.workspace

A simple class to encapsulate a pair that is used to describe parameters.

Param(String, String) - Constructor for class org.peace_tools.workspace.Param

The constructor merely initializes the pair encapsulated by this object.

parameters - Variable in class org.peace_tools.workspace.Filter

The list of parameters that are simply managed as a name-value pair within this class.

parameters - Variable in class org.peace_tools.workspace.Heuristic

The list of parameters that are simply managed as a name-value pair within this class.

parent - Variable in class org.peace_tools.core.session.ServerSession

The parent component that visually owns this server session.

parent - Variable in class org.peace_tools.data.ClusterNode

The parent cluster for this MSTcluster.

parent - Variable in class org.peace_tools.data.MSTNode

The parent node for this MSTNode.

parseFilterChain(Element) - Static method in class org.peace_tools.workspace.Job

Helper method to unmarshall the filter list into an in-memory array list.

parseHeuristicChain(Element) - Static method in class org.peace_tools.workspace.Job

Helper method to unmarshall the heuristic list into an in-memory array list.

parseLevel(String) - Method in class org.peace_tools.generic.Log

Parses a string containing a valid logging level and sets the level appropriately.

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

Field to read/display the password ID.

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

This is a transient field that is never persisted (for security purposes).

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

The absolute path to the file referenced by this file attribute.

path - Variable in class org.peace_tools.generic.dndTabs.DnDTabPos

Vector to maintain path from center pane to the desired position of a tab.

path - Variable in class org.peace_tools.workspace.DataSet

The complete path to the actual EST file on the local machine.

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

The path to the directory on the server (may it be local or remote) where the files corresponding to this job are stored.

path - Variable in class org.peace_tools.workspace.MSTClusterData

The path to the actual MST file (on the local machine) that is referred by this entry.

path - Variable in class org.peace_tools.workspace.MSTData

The path to the actual MST file (on the local machine) that is referred by this entry.

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

The default prefix that is added to the path of the files to be loaded by the various methods in this class.

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

The pre-compiled pattern corresponding to this regular expression.

PEACE - Class in org.peace_tools.core

The top-level class for the PEACE GUI application.

PEACE() - Constructor for class org.peace_tools.core.PEACE

The constructor.

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

Reference to the main PEACE class.

PEACE_NS - Static variable in class org.peace_tools.workspace.DOMHelper

This string defines the name space for the XML elements created by the utility methods.

PEACEInstaller - Class in org.peace_tools.core

PEACEInstaller(Server) - Constructor for class org.peace_tools.core.PEACEInstaller

The constructor lays out the main components in this tab.

permanent - Variable in class org.peace_tools.generic.dndTabs.DnDTabbedPane

A boolean variable that indicates if this tab is permanent and should not be deleted even if it is empty.

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

Field to read/display the polling time.

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

The delay between successive checks for job status on the server.

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

The pop up that contains the cluster list to be displayed to the user.

popupMenu - Variable in class org.peace_tools.views.DataSetFileListView

This is a pop-up menu that is displayed whenever the user clicks the left mouse button on a table entry.

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

This is a pop-up menu that is displayed whenever the user clicks the left mouse button on a menu item.

popupMenu - Variable in class org.peace_tools.views.JobListView

The pop up menu that is displayed when the user left-clicks on an item in the job list view.

popupMenu - Variable in class org.peace_tools.views.ServerListView

The pop up menu that is displayed when the user left-clicks on an item in the server list view.

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

The "Prev" button that is displayed at the bottom of the wizard in a separate panel.

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

This reference is used to track the object used to hold the list of DBClassifiers in the work space.

prevClusterList - Variable in class org.peace_tools.data.ESTList

This reference is used to track the object used to hold the list of DBClassifiers in the work space.

prevIcon - Variable in class org.peace_tools.generic.dndTabs.DnDTabPos

The icon (if any) to be used for the tab.

prevName - Variable in class org.peace_tools.generic.dndTabs.DnDTabPos

The name for the tab when its position is restored.

prevSize - Variable in class org.peace_tools.generic.dndTabs.DnDTabPos

The preferred width / height of the tab.

print(PrintStream) - Method in class org.peace_tools.data.ClusterFile

Method to print the cluster in a simple text-based format.

print(PrintStream, ClusterNode, String) - Method in class org.peace_tools.data.ClusterNode

Method to recursively print the information that is stored in this cluster.

print(PrintStream) - Method in class org.peace_tools.data.MST

Method to print the MST in a simple text-based format.

print(PrintStream, MSTNode, String) - Method in class org.peace_tools.data.MSTNode

Method to recursively print the information that is stored in this node.

ProgrammerLog - Class in org.peace_tools.generic

Top-level logging class for creating programmer logs.

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

The default (and only) constructor.

programmerLog - Static variable in class org.peace_tools.generic.ProgrammerLog

The globally unique instance of the UserLog.

ProgrammerLogPane - Class in org.peace_tools.views

This log pane customizes the features of the LogPane to display the programmer logs in a free form manner.

ProgrammerLogPane() - Constructor for class org.peace_tools.views.ProgrammerLogPane

A constructor for the ProgrammerLogPane.

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

The progress bar that is placed in indeterminate mode when deleting remote entries and directories.

progressBar - Variable in class org.peace_tools.core.FileCopyDialog

The progress bar that is displayed at the bottom of the dialog box to indicate the progress made in copying files.

progressBar - Variable in class org.peace_tools.core.PEACEInstaller

A roving progress bar to show the user we are doing some work.

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

A roving progress bar to show the user we are doing some work.

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

A roving progress bar to show the user we are doing some work.

progressBar - Variable in class org.peace_tools.core.ServerConnectionTester

The roving (indeterminate mode) progress bar to illustrate that some work is being done (and to ensure that the GUI is not hanging).

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

The progress bar that is placed in indeterminate mode to indicate to the user that the job data is being download.

progressBar - Variable in class org.peace_tools.views.JobListView.JobStatusRenderer

The progress bar is used when the job is in running status to indicate the amount of progress made thus far.

progressInfo - Variable in class org.peace_tools.core.FileCopyDialog

Label displayed on top of the progress bar indicating the file being currently copied.

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

A transient (not persisted) progress information about the job.

PropertiesTreeMaker - Class in org.peace_tools.views

A helper (utility) class to assemble various properties about Jobs, MST file, and Cluster file in the form of a JTree.

PropertiesTreeMaker() - Constructor for class org.peace_tools.views.PropertiesTreeMaker

The default and only constructor.

purpose - Variable in class org.peace_tools.core.session.LocalServerSession

A simple textual information indicating the purpose for this session.

purpose - Variable in class org.peace_tools.core.session.RemoteServerSession

A simple textual information indicating the purpose for this session.

PURPOSE_MSG - Static variable in class org.peace_tools.core.JobMonitor

A static formatable purpose message that is filled in and used as the purpose for the server session initiated by this job monitor.

PURPOSE_MSG - Static variable in class org.peace_tools.core.ServerConnectionTester

A simple message that is formatted (to fill in server name) and set as the purpose for the session/connection.