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

This is a refactored (to keep code clutter to a minimum in the actionPerformed() method) method that is called only from the actionPerformed() method whenever the user clicks on the "OK" button in the workspace tab.

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

This instance variable is used to contain the type of status change being reported via this event.

org.peace_tools - package org.peace_tools

Provides all the packages and classes associated with PEACE GUI, including files necessary to install the C++ clustering engine on local and remote servers.

org.peace_tools.core - package org.peace_tools.core

Contains the core classes that coordinate the activities of various classes and wizards.

org.peace_tools.core.dataset - package org.peace_tools.core.dataset

Contains the classes associated with the data set wizard.

org.peace_tools.core.job - package org.peace_tools.core.job

Contains the classes associated with the job wizard.

org.peace_tools.core.server - package org.peace_tools.core.server

Contains the classes associated with the server wizard.

org.peace_tools.core.session - package org.peace_tools.core.session

Contains the classes associated with providing a session on a local or remote server.

org.peace_tools.data - package org.peace_tools.data

Contains the classes that provide data for the various views in the GUI.

org.peace_tools.generic - package org.peace_tools.generic

Provides a generic set of application-independent classes for performing standard GUI operations.

org.peace_tools.generic.dndTabs - package org.peace_tools.generic.dndTabs

Provides generic functionality to organize GUI as dockable tabs.

org.peace_tools.views - package org.peace_tools.views

Contains the classes that provide views for the various data objects in the GUI.

org.peace_tools.views.overlap - package org.peace_tools.views.overlap

Contains the classes that provide a custom overlap view of clusters.

org.peace_tools.workspace - package org.peace_tools.workspace

Contains the classes that provide persistent storage of work space configuration.

orientation - Variable in class org.peace_tools.views.overlap.Ruler

The orientation being used for this ruler.

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

The last known OS type for the remote server.

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

The styled document that is used to display the output from the installation process is different colors.

outputs - Variable in class org.peace_tools.views.JobDetailsView

The styled documents that is used to display the output from the job information.

OverlapModel - Class in org.peace_tools.data

A custom data model to provide pre-alignment information using MST and clustering data.

OverlapModel(ClusterFile, ESTList, MSTClusterData) - Constructor for class org.peace_tools.data.OverlapModel

The constructor.

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

The OverlapModel that provides the necessary information for rendering the core information required by this panel.

overlapModel - Variable in class org.peace_tools.views.overlap.OverlapPanel

The OverlapModel that provides the necessary information for rendering the core information required by this panel.

OverlapPanel - Class in org.peace_tools.views.overlap

The overlap panel that displays the actual overlap image.

OverlapPanel(OverlapModel, ClusterColorMapper, double, double) - Constructor for class org.peace_tools.views.overlap.OverlapPanel

The only constructor.

OverlapView - Class in org.peace_tools.views.overlap

A pre-alignment overlap view of fragments organized based on clusters.

OverlapView(MainFrame, OverlapModel, ClusterFile) - Constructor for class org.peace_tools.views.overlap.OverlapView

The default constructor.

OVERVIEW_MSG - Static variable in class org.peace_tools.core.dataset.DataSetWizard

A static overview message that is displayed in the first overview page displayed by this wizard to the user.

OVERVIEW_MSG - Static variable in class org.peace_tools.core.job.JobWizard

A static overview message that is displayed in the first overview page displayed by this wizard to the user.

OverviewMsg - Static variable in class org.peace_tools.core.server.ServerWizard

A static overview message that is displayed in the first overview page displayed by this wizard to the user.

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

The final top-level component that logically owns this cluster list.