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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handleDoubleClick(MouseEvent) - Method in class org.peace_tools.views.DataSetFileListView

Helper method to handle double click of the mouse on a list item.

handleDoubleClick(MouseEvent) - Method in class org.peace_tools.views.DataSetTreeView

Helper method to handle double click of the mouse on a tree item.

handleDoubleClick(MouseEvent) - Method in class org.peace_tools.views.JobListView

Helper method to handle double click of the mouse on a list item.

handleDoubleClick(MouseEvent) - Method in class org.peace_tools.views.ServerListView

Helper method to handle double click of the mouse on a list item.

handlePopup(MouseEvent) - Method in class org.peace_tools.views.DataSetFileListView

Helper method to left mouse click on a table item.

handlePopup(MouseEvent) - Method in class org.peace_tools.views.DataSetTreeView

Helper method to left mouse click on a tree item.

handlePopup(MouseEvent) - Method in class org.peace_tools.views.JobListView

Helper method to left mouse click on a table item.

handlePopup(MouseEvent) - Method in class org.peace_tools.views.ServerListView

Helper method to left mouse click on a table item.

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

Determine if all nodes in this MST have alignment information.

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

Utility method to determine if a given DOM element has an optional sub-element.

haveAlignmentInfo - Variable in class org.peace_tools.data.MST

Flag to indicate if the MST data contains initial, pre-assembly alignment metric that is useful to detect where overlaps between two adjacent (parent-child) fragments occur to obtain the given alignment metric.

HELP_ERROR - Static variable in class org.peace_tools.generic.HelpHandler

This message is displayed when the default system browser could not be launched to display help.

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

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

helperType - Variable in class org.peace_tools.core.AbstractMenuHelper

The type of helper that the derived class represents.

HelpHandler - Class in org.peace_tools.generic

A simple class to handle display of help URLs.

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

Private constructor to ensure this class is never instantiated.

HelpMenuHelper - Class in org.peace_tools.core

The help menu helper for the application.

HelpMenuHelper(MainFrame) - Constructor for class org.peace_tools.core.HelpMenuHelper

The constructor.

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

The URL to the online help page associated with this wizard.

Heuristic - Class in org.peace_tools.workspace

This class is meant to encapsulate the information and parameters for various heuristics used to accelerate clustering.

Heuristic(String) - Constructor for class org.peace_tools.workspace.Heuristic

The only constructor for this class.

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

This panel actually contains all the controls for setting up the necessary heuristics and their parameters required by certain analyzers.

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

The list of heuristics configured by the user for this job.

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

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

heuristicsSummary - Variable in class org.peace_tools.workspace.JobSummary

A string that contains summary of heuristics run as a part of the job used to generate the associated data.

HeuristicsWizardPage - Class in org.peace_tools.core.job

This class serves as an interactive page in a JobWizard.

HeuristicsWizardPage(JobWizard, AnalyzerWizardPage) - Constructor for class org.peace_tools.core.job.HeuristicsWizardPage

The constructor.

highlightBackground - Variable in class org.peace_tools.views.CustomTableCellRenderer

Flag to indicate if background for the base pairs in sequences must be colored differently for different base pairs.

highlightForeground - Variable in class org.peace_tools.views.CustomTableCellRenderer

Flag to indicate if base pairs in sequences must be highlighted.

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

The horizontal ruler that is displayed at the top of the overview panel.

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

Field to read/display the host name to the user.

hwp - Variable in class org.peace_tools.core.job.JobWizard

The analyzer wizard page contains the heuristic information to be used for constructing the MST for this job.

hyperlinkUpdate(HyperlinkEvent) - Method in class org.peace_tools.views.GenericHTMLView

Method to intercept hyper link clicks in HTML.