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

The icon that is displayed in this dialog box to the left.

icon - Variable in class org.peace_tools.generic.IconTreeNode

The icon to be used for this mutable tree node.

ICON_SIZE - Static variable in class org.peace_tools.views.overlap.ClusterListCellRenderer

The size of the square to be used to display the color being used for rendering the cluster.

IconNames - Static variable in class org.peace_tools.core.FileMenuHelper

The icon file names for each menu item created by this helper.

IconNames - Static variable in class org.peace_tools.core.HelpMenuHelper

The icon file names for each menu title created by this helper.

IconNames - Static variable in class org.peace_tools.core.ServerMenuHelper

The icon file names for each menu title created by this helper.

IconNames - Static variable in class org.peace_tools.core.ViewMenuHelper

The icon file names for each menu title created by this helper.

IconTreeNode - Class in org.peace_tools.generic

A simple tree node that also permits an icon to be set.

IconTreeNode(Object, Icon) - Constructor for class org.peace_tools.generic.IconTreeNode

Constructor to create a tree node with an icon.

id - Variable in class org.peace_tools.data.EST

The unique ID for this EST.

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

The unique generated data set ID value for this data.

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

The unique generated ID value for this entry.

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

The unique generated data set ID value for this data.

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

A unique identifier for this Server entry.

info - Variable in class org.peace_tools.data.EST

The name and other information associated with the EST.

INFO_ERR_MSG - Static variable in class org.peace_tools.views.JobDetailsView

A formattable string that is formatted and displayed to the user as an error message.

INFO_ERR_MSG - Static variable in class org.peace_tools.views.ServerJobsView

A formattable string that is formatted and displayed to the user as an error message.

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

A simple standard message to be displayed at the bottom of this page.

INFO_MSG - Static variable in class org.peace_tools.core.job.AnalyzerWizardPage

A generic informational message that is displayed at the top of this wizard page to provide some additional information to the user.

INFO_MSG - Static variable in class org.peace_tools.core.job.FiltersWizardPage

A generic informational message that is displayed at the top of this wizard page to provide some additional information to the user.

INFO_MSG - Static variable in class org.peace_tools.core.job.HeuristicsWizardPage

A generic informational message that is displayed at the top of this wizard page to provide some additional information to the user.

INFO_MSG - Static variable in class org.peace_tools.core.job.JobInfoWizardPage

A generic informational message that is displayed at the top of this wizard page to provide some additional information to the user.

INFO_MSG - Static variable in class org.peace_tools.core.job.SubmitJobWizardPage

A generic informational message that is displayed at the top of this wizard page to provide some contextual information to the user.

INFO_MSG - Static variable in class org.peace_tools.core.job.VerifyWizardPage

A generic informational message that is displayed at the top of this wizard page to provide some contextual information to the user.

INFO_MSG - Static variable in class org.peace_tools.core.server.ServerAddingEntryWizardPage

A simple standard message to be displayed at the bottom of this page.

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

A simple message that is formatted (to fill in server name) and displayed to the user informing him of the progress being made.

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

Field to be displayed to the user in this wizard pane.

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

Field to be displayed to the user in this wizard pane.

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

This array contains three informational labels containing the information in ClusterWizardPage.THRESHOLD_INFO, ClusterWizardPage.TWO_PASS_INFO, and ClusterWizardPage.CLU_INFO respectively in that order.

insertUpdate(DocumentEvent) - Method in class org.peace_tools.core.PEACEInstaller

Implementation for method in DocumentListener to scroll to end of the document.

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

Field to read/display the install path where PEACE is (or has been) installed on the given server.

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

The location on the Server where PEACE is installed and the necessary runtime components of PEACE are located.

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

Returns a byte array containing the two's-complement representation of the integer.
The byte array will be in big-endian byte-order with a fixes length of 4 (the least significant byte is in the 4th element).

Example:
intToByteArray(258) will return { 0, 0, 1, 2 },
BigInteger.valueOf(258).toByteArray() returns { 1, 2 }.

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

Convenience method to interrupt a job monitor thread.

INVALID_CLR_MSG - Static variable in class org.peace_tools.core.job.ClusterWizardPage

A generic informational message that is displayed to the user if the selected MST file is invalid.

INVALID_ENTRY - Static variable in class org.peace_tools.core.job.JobInfoWizardPage

A simple message to be displayed to the user when the user selects a data set that currently does not have a valid FASTA file associated with it.

INVALID_FASTA_MSG - Static variable in class org.peace_tools.core.dataset.ESTInfoWizardPage

Just a simple error message that is displayed when connection to the remote host could not be successfully established.

INVALID_MST_MSG - Static variable in class org.peace_tools.core.job.MSTWizardPage

A generic informational message that is displayed to the user if the selected MST file is invalid.

isBorderOpaque() - Method in class org.peace_tools.generic.CustomBorder

Returns whether or not the border is opaque.

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

Determine if the cell in this column is editable for the passed node.

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

Interface method to determine if an entry in the JTable is editable.

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

Interface method to determine if an entry in the JTable is editable.

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

Interface method to determine if an entry in the JTable is editable.

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

Interface method to determine if an entry in the JTable is editable.

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

Override default method in parent class to correctly handle mouse button clicks.

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

Determine if the clusters are current with work space classifiers.

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

Determine if the EST list is current with work space classifiers.

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

This method is a part of the Transferable interface.

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

Determine if this entry is a directory.

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

Flag to indicate if this f/w analyzer provides distance metrics (rather than similarity) for identifying similar ESTs.

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

Determine if this f/w analyzer uses a distance metric or a similarity metric.

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

Convenience method to determine if job has completed.

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

Determine if this classifier is enabled.

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

Determine if this node represents a EST entry in the cluster tree.

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

Determine if this entry is a regular file.

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

Indicate all labels are in HTML.

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

Determine if this cluster is a leaf cluster that has no child clusters or EST entries.

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

Determine if a given node in the tree is a leaf node.

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

Method to determine if a given entry is a leaf object.

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

Determine if this node is a leaf node that has no child nodes.

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

Method to determine if a given entry is a leaf object.

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

Determine if base masking is enabled or disabled.

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

This method may be used to determine if this tabbed pane should be permanently present or not.

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

Method to determine if this Server entry represents a local or a remote server.

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

Determine if this cluster node is the root cluster.

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

Determine if this node is the root node.

isTreeView - Variable in class org.peace_tools.views.DataSetPopupMenu

Instance variable that tracks if this pop-up menu is being used with a tree view or with a table view.

isVisible() - Method in class org.peace_tools.generic.dndTabs.DnDTabPos

Determine the visibility information in this tab.

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

Determine if logs are actually being written to a log file.