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B C D E G H I K L M N O R S T U V W

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B

BASE_PORT - Static variable in class edu.stanford.genetics.treeview.app.Daemon

 

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C

closeAllWindows() - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

loops over the list of windows the TreeViewApp has collected through the WindowListener interface.

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D

DAEMON_RUNNING - Static variable in class edu.stanford.genetics.treeview.app.Daemon

 

DEBUG - Static variable in class edu.stanford.genetics.treeview.app.Daemon

 

Daemon - class edu.stanford.genetics.treeview.app.Daemon.

A daemon is a thread that waits for request and forward to a RequestHandler in this case, the TreeViewApp The intention of this : If an instance of the program is running, it shall starts a daemon which waits for requests.

Daemon(Daemon.RequestHandler) - Constructor for class edu.stanford.genetics.treeview.app.Daemon

 

Daemon.RequestHandler - interface edu.stanford.genetics.treeview.app.Daemon.RequestHandler.

 

Daemon.SimpleClient - class edu.stanford.genetics.treeview.app.Daemon.SimpleClient.

 

Daemon.SimpleClient() - Constructor for class edu.stanford.genetics.treeview.app.Daemon.SimpleClient

 

daemon - Static variable in class edu.stanford.genetics.treeview.app.TreeViewAppX

 

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E

edu.stanford.genetics.treeview.app - package edu.stanford.genetics.treeview.app

 

endProgram() - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

Stores the globalconfig, closes all windows, and then exits.

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G

getGlobalConfig() - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

returns an XmlConfig representing global configuration variables

getTreeViewFrame(boolean) - Method in class edu.stanford.genetics.treeview.app.TreeViewAppX

 

getUpdateUrl() - Static method in class edu.stanford.genetics.treeview.app.TreeViewApp

Getter for updateUrl, a string representing a website where you can download newer versions.

getVersionTag() - Static method in class edu.stanford.genetics.treeview.app.LinkedViewApp

 

getVersionTag() - Static method in class edu.stanford.genetics.treeview.app.TreeViewApp

The release-level version tag for the whole application.

globalConfig - Variable in class edu.stanford.genetics.treeview.app.TreeViewApp

holds global config

globalConfigName() - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

Get a per-user file in which to store global config info.

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H

handleRequest(String[]) - Method in interface edu.stanford.genetics.treeview.app.Daemon.RequestHandler

 

handleRequest(String[]) - Method in class edu.stanford.genetics.treeview.app.TreeViewAppX

 

handler - Variable in class edu.stanford.genetics.treeview.app.Daemon

 

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I

initSocket() - Method in class edu.stanford.genetics.treeview.app.Daemon

 

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K

KnnViewApp - class edu.stanford.genetics.treeview.app.KnnViewApp.

This class defines the knnview application.

KnnViewApp() - Constructor for class edu.stanford.genetics.treeview.app.KnnViewApp

Constructor for the KnnViewApp object

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L

LinkedViewApp - class edu.stanford.genetics.treeview.app.LinkedViewApp.

Main class of LinkedView application.

LinkedViewApp() - Constructor for class edu.stanford.genetics.treeview.app.LinkedViewApp

Constructor for the LinkedViewApp object

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M

main(String[]) - Static method in class edu.stanford.genetics.treeview.app.KnnViewApp

Starts KnnView application with an empty window.

main(String[]) - Static method in class edu.stanford.genetics.treeview.app.LinkedViewApp

 

main(String[]) - Static method in class edu.stanford.genetics.treeview.app.TreeViewApp

Main method for TreeView application.

main(String[]) - Static method in class edu.stanford.genetics.treeview.app.TreeViewAppX

 

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N

NUM_OF_PORTS - Static variable in class edu.stanford.genetics.treeview.app.Daemon

 

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O

openNew() - Method in class edu.stanford.genetics.treeview.app.KnnViewApp

opens a TreeViewFrame window

openNew(FileSet) - Method in class edu.stanford.genetics.treeview.app.KnnViewApp

Open a new window with the given fileset loaded in it.

openNew() - Method in class edu.stanford.genetics.treeview.app.LinkedViewApp

 

openNew(FileSet) - Method in class edu.stanford.genetics.treeview.app.LinkedViewApp

 

openNew() - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

opens a ViewFrame window

openNew(FileSet) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

opens a new ViewFrame window displaying the specified FileSet

openNew(String[]) - Method in class edu.stanford.genetics.treeview.app.TreeViewAppX

opens a TreeViewFrame window

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R

REQUST_TIME_OUT - Static variable in class edu.stanford.genetics.treeview.app.Daemon

 

rebuildWindowMenus() - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

rebuilds all the window menus.

run() - Method in class edu.stanford.genetics.treeview.app.Daemon

 

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S

sendRequest(String[]) - Method in class edu.stanford.genetics.treeview.app.Daemon.SimpleClient

 

sendRequest(int, String[]) - Static method in class edu.stanford.genetics.treeview.app.Daemon.SimpleClient

 

serverSocket - Variable in class edu.stanford.genetics.treeview.app.Daemon

 

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T

TreeViewApp - class edu.stanford.genetics.treeview.app.TreeViewApp.

This class defines the treeview application.

TreeViewApp() - Constructor for class edu.stanford.genetics.treeview.app.TreeViewApp

Constructor for the TreeViewApp object.

TreeViewApp(XmlConfig) - Constructor for class edu.stanford.genetics.treeview.app.TreeViewApp

Constructor for the TreeViewApp object takes configuration from the passed in XmlConfig.

TreeViewAppX - class edu.stanford.genetics.treeview.app.TreeViewAppX.

This class defines the treeview application.

TreeViewAppX() - Constructor for class edu.stanford.genetics.treeview.app.TreeViewAppX

 

toString(String[]) - Static method in class edu.stanford.genetics.treeview.app.Daemon

 

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U

USE_DAEMON - Static variable in class edu.stanford.genetics.treeview.app.TreeViewAppX

 

updateUrl - Static variable in class edu.stanford.genetics.treeview.app.TreeViewApp

 

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V

versionTag - Static variable in class edu.stanford.genetics.treeview.app.TreeViewApp

Description of the Field

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W

windowActivated(WindowEvent) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

 

windowClosed(WindowEvent) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

A WindowListener, which allows other windows to react to another window being closed.

windowClosing(WindowEvent) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

 

windowDeactivated(WindowEvent) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

 

windowDeiconified(WindowEvent) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

 

windowIconified(WindowEvent) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

 

windowOpened(WindowEvent) - Method in class edu.stanford.genetics.treeview.app.TreeViewApp

A WindowListener, which allows other windows to react to another window being opened.

windows - Variable in class edu.stanford.genetics.treeview.app.TreeViewApp

holds all open windows

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B C D E G H I K L M N O R S T U V W

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