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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EDGE_PANEL_SIZE - Static variable in class org.peace_tools.generic.dndTabs.DnDTabbedPane

This constant determines the default size that is used for panels that are docked to the edges (top, left, bottom, right) of a given DnDTabPanel.

editingCanceled(ChangeEvent) - Method in class org.peace_tools.views.DBClassifierEditor

editingStopped(ChangeEvent) - Method in class org.peace_tools.views.DBClassifierEditor

emphasize(JComponent) - Method in class org.peace_tools.core.ViewFactory

A helper method to create thread to make a tab blink to emphasize its presence.

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

Flag to indicate if this classifier is enabled and must be used to classify ESTs.

enableHTMLText(String, boolean) - Static method in class org.peace_tools.generic.Utilities

Utility method to modify HTML text to look enabled or disabled.

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

Check box to indicate if the Low Complexity (LC) filter must be enabled for this job.

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

Check box to indicate if the length filter must be enabled for this job.

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

Check box to indicate if the t/v heuristic is to be used for this job.

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

Check box to indicate if the u/v sample heuristic is to be used for this job.

encode(Log.LogLevel) - Static method in class org.peace_tools.generic.Log

Utility method to convert a log level to a single character value.

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

This instance variable tracks the currently selected work space entry.

entryType - Variable in class org.peace_tools.workspace.WorkspaceEvent

This instance variable is used to contain the type of the entry regarding which a status change is being reported.

ERROR_ICON - Static variable in class org.peace_tools.views.PropertiesTreeMaker

A static constant to refer to the error icon position in the PropertiesTreeMaker.CustomIcons array.

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

An error message that is formatted (to fill in server name) and displayed to the user informing him about the problem that occurred when attempting to connect to the server.

ErrorMsg - Static variable in class org.peace_tools.core.server.ServerInfoWizardPage

Just a simple error message that is displayed when install on a server/remote host could not be successfully verified.

ErrorMsg - Static variable in class org.peace_tools.core.server.ServerTypeWizardPage

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

EST - Class in org.peace_tools.data

EST(int, String, String) - Constructor for class org.peace_tools.data.EST

EST Constructor.

est - Variable in class org.peace_tools.data.ESTEntry

The EST node for this ESTEntry.

ESTEntry - Class in org.peace_tools.data

A class that represents a single EST entry in PreAlignmentModel.

ESTEntry(EST, int, int) - Constructor for class org.peace_tools.data.ESTEntry

Constructor to create an object.

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

The list of EST entry objects encapsulated by this data model.

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

A table (A sparse 2-dimensional array) of ESTEntries.

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

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

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

The aggregate classification information associated with this EST.

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

The zero-based index of the EST that a given MST node represents.

ESTInfoWizardPage - Class in org.peace_tools.core.dataset

This class serves as the second interactive page in a the Data Set Wizard.

ESTInfoWizardPage(DataSetWizard, DataSet, boolean) - Constructor for class org.peace_tools.core.dataset.ESTInfoWizardPage

The constructor.

estList - Variable in class org.peace_tools.core.dataset.DataSetWizard

The list of ESTs associated with this data set.

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

Reference to the EST file that contains the cluster data to be adapted and interfaced by this model.

ESTList - Class in org.peace_tools.data

Class to encapsulate a list of ESTs.

ESTList(String) - Constructor for class org.peace_tools.data.ESTList

Create an empty list of ESTs tagged with a given name.

estList - Variable in class org.peace_tools.data.ESTTableModel

Reference to the list of fragments that is actually exposed by this table model.

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

The list of ESTs for which this MST was constructed.

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

Reference to the EST file that contains the fragment data that is to be adapted and presented by this model.

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

The set of ESTs that the clusters correspond to.

ESTRenderer - Static variable in class org.peace_tools.views.ESTTableView

A simple/custom cell renderer that displays data using a monospaced font.

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

This instance variable contains the list of ESTs encapsulated in this ESTList class.

ESTTableModel - Class in org.peace_tools.data

A bridge class between FASTA entries in a FASTA file and a JTable.

ESTTableModel(ESTList) - Constructor for class org.peace_tools.data.ESTTableModel

The default constructor.

ESTTableView - Class in org.peace_tools.views

The table model that provides a graphical display of fragments in a FASTA file.

ESTTableView(ESTTableModel, MainFrame) - Constructor for class org.peace_tools.views.ESTTableView

The default constructor.

exec(String, String[]) - Method in class org.peace_tools.core.session.LocalServerSession

This method can be used to run a brief command that produces succinct output.

exec(String, DefaultStyledDocument) - Method in class org.peace_tools.core.session.LocalServerSession

This method can be used to run a long running command that may produce verbose output.

exec(String, String[]) - Method in class org.peace_tools.core.session.RemoteServerSession

This method can be used to run a brief command that produces succinct output.

exec(String, DefaultStyledDocument) - Method in class org.peace_tools.core.session.RemoteServerSession

This method can be used to run a long running command that may produce verbose output.

exec(String, String[]) - Method in class org.peace_tools.core.session.ServerSession

This method can be used to run a brief command that produces succinct output.

exec(String, DefaultStyledDocument) - Method in class org.peace_tools.core.session.ServerSession

This method can be used to run a long running command that may produce verbose output.

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

Bit value indicating if this entry is executable.

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

Determine if this entry exists.