A B C D E F G H I L M N O P R S T V W

A

ABOUT_MENUITEM - Static variable in class org.biolegato.main.BLMain

The menu item for BioLegato's "About..."

actionPerformed(ActionEvent) - Method in class org.biolegato.menu.Chooser

Handles selection changes of the radio buttons.

actionPerformed(ActionEvent) - Method in class org.biolegato.menu.CommandThread

Runs the command.

actionPerformed(ActionEvent) - Method in class org.biolegato.menu.FileChooser

Handle the choose file button

actionPerformed(ActionEvent) - Method in class org.biolegato.menu.RunWindow

addMenuHeading(String) - Static method in class org.biolegato.main.BLMain

Adds a menu heading (JMenu) to our menu (BLMenu).

addMenuHeading(int, String) - Static method in class org.biolegato.main.BLMain

Adds a menu heading (JMenu) to our menu (BLMenu).

addMenuItem(int, String, JMenuItem) - Static method in class org.biolegato.main.BLMain

Adds a menu item (JMenuItem) to a menu heading (JMenu) within the window (ProgramWindow)

addMenuItem(String, JMenuItem) - Static method in class org.biolegato.main.BLMain

Adds a menu item (JMenuItem) to a menu heading (JMenu) within the window (ProgramWindow)

B

BLMain - Class in org.biolegato.main

The main program and generic function class.

BLMain() - Constructor for class org.biolegato.main.BLMain

BLMain.ARCH - Enum in org.biolegato.main

BLMain.OS - Enum in org.biolegato.main

buttons - Variable in class org.biolegato.menu.RunWindow

List of buttons for the window.

C

choice_list - Variable in class org.biolegato.menu.ChoiceList

The list containing the data.

ChoiceList - Class in org.biolegato.menu

A wrapper class used to abstract choice lists within command windows.

ChoiceList(String, String[], String[], int) - Constructor for class org.biolegato.menu.ChoiceList

Creates a new instance of GDEComboBox (represents "choice_list" in GDE menu files).

Chooser - Class in org.biolegato.menu

Wrapper class for a group of radiobuttons.

Chooser(String, String[], String[], int) - Constructor for class org.biolegato.menu.Chooser

Creates a new instance of EZChooser.

close() - Method in class org.biolegato.menu.ChoiceList

Closes the open object

close() - Method in class org.biolegato.menu.Chooser

close() - Method in class org.biolegato.menu.ComboBoxWidget

close() - Method in class org.biolegato.menu.NumberWidget

close() - Method in class org.biolegato.menu.TempFile

Releases any files currently in use by this class

close() - Method in class org.biolegato.menu.TextWidget

close() - Method in interface org.biolegato.menu.Widget

Notifies the variable that the program has now completed successfully, and it can perform any closing operations

CLOSE_ACTION - Variable in class org.biolegato.menu.RunWindow

Action for command buttons to close the window.

combobox - Variable in class org.biolegato.menu.ComboBoxWidget

The combobox contianing the data

comboboxUI - Variable in class org.biolegato.menu.ComboBoxWidget

The UI to enable scrolling of the JComboBox.

ComboBoxWidget - Class in org.biolegato.menu

A wrapper class used to abstract combo boxes within command windows.

ComboBoxWidget(String, String[], String[], int) - Constructor for class org.biolegato.menu.ComboBoxWidget

Creates a new instance of EZComboBox (represents "choice_list" in GDE menu files).

CommandButton - Class in org.biolegato.menu

Creates a JButton, which when clicked runs internal API functions or external commands

CommandButton(Map<String, Widget>, String, String, boolean) - Constructor for class org.biolegato.menu.CommandButton

Creates a new instance of CommandButton

CommandThread - Class in org.biolegato.menu

Class used for making abstract actions which launch threads.

CommandThread(String) - Constructor for class org.biolegato.menu.CommandThread

Creates a new instance of CommandThread.

CommandThread(String, Map<String, Widget>) - Constructor for class org.biolegato.menu.CommandThread

Creates a new instance of CommandThread.

create() - Method in class org.biolegato.main.PluginWrapper

Creates a new object the plugin class.

create(Class[], Object[]) - Method in class org.biolegato.main.PluginWrapper

Creates a new object the wrapped plugin class (returns null if unsuccessful).

CURRENT_ARCH - Static variable in class org.biolegato.main.BLMain

Stores the current machine architecture

CURRENT_DIR - Static variable in class org.biolegato.main.BLMain

This constant is set to the path of where biolegato was run The value of this constant determined at runtime.

CURRENT_OS - Static variable in class org.biolegato.main.BLMain

Stores the current operating system

D

DataCanvas - Interface in org.biolegato.main

All subclasses are expected to implement a displayable canvas for BioLegato.

debug - Static variable in class org.biolegato.main.BLMain

Stores information regarding the usage of the debug command NOTE: This should always be accessed using Main.debug

DEFAULT_PROPERTIES - Static variable in class org.biolegato.main.BLMain

Stores the properties for BioLegato.

detectARCH() - Static method in enum org.biolegato.main.BLMain.ARCH

Detects the current system architecture Check out: http://lopica.sourceforge.net/os.html

detectOS() - Static method in enum org.biolegato.main.BLMain.OS

Detects the current operating system Check out: http://lopica.sourceforge.net/os.html

display() - Method in interface org.biolegato.main.DataCanvas

Displays the main pane of the data canvas

display(Container) - Method in class org.biolegato.menu.ChoiceList

Displays the choice list

display(Container) - Method in class org.biolegato.menu.Chooser

Displays the chooser widget

display(Container) - Method in class org.biolegato.menu.ComboBoxWidget

Displays the combobox widget

display(Container, RunWindow) - Method in class org.biolegato.menu.CommandButton

display(Container) - Method in class org.biolegato.menu.FileChooser

Displays the file chooser widget

display(Container) - Method in class org.biolegato.menu.NumberWidget

Displays the number widget

display(Container) - Method in class org.biolegato.menu.TempFile

Displays the current widget

display(Container) - Method in class org.biolegato.menu.TextWidget

Displays the text widget

display(Container) - Method in interface org.biolegato.menu.Widget

Displays the current object

DOUBLE_CLICK_TIME - Static variable in class org.biolegato.main.BLMain

The amount of time between clicks to be considered a double click.

E

EMPTY_STRING - Static variable in class org.biolegato.main.BLMain

This constant stores an empty string (to avoid recreation)

envreplace(String) - Static method in class org.biolegato.main.BLMain

Replaces $VARIABLE name with environment variables.

error(String, String) - Static method in class org.biolegato.main.BLMain

Sends an error message to BioLegato's standard err.

EXIT_MENUITEM - Static variable in class org.biolegato.main.BLMain

The menu item for BioLegato's "Exit..."

F

FileChooser - Class in org.biolegato.menu

A wrapper class used to abstract file selection within command windows.

FileChooser(String, String) - Constructor for class org.biolegato.menu.FileChooser

Creates a new instance of GDETempFile.

G

GDEMenuParser - Class in org.biolegato.menu

GDEMenuParser() - Constructor for class org.biolegato.menu.GDEMenuParser

GDEMenuParser.WidgetType - Enum in org.biolegato.menu

getCanvas() - Static method in class org.biolegato.main.BLMain

Returns the current/selected data in the canvas.

getCurrentPWD() - Static method in class org.biolegato.main.BLMain

Gets the present working directory "PWD" for BioLegato (this does NOT change CURRENT_DIR!) This value can be used to cache which directory file dialog boxes should use as their "current working directory"

getJFrame() - Static method in class org.biolegato.main.BLMain

Provides access for other classes to the main program window JFrame object.

getName() - Method in interface org.biolegato.main.DataCanvas

Returns the name of the canvas.

getName() - Method in class org.biolegato.main.PluginWrapper

Returns the class's name.

getProperty(String) - Static method in class org.biolegato.main.BLMain

Retrieves individual settings for BioLegato.

getValue() - Method in class org.biolegato.menu.ChoiceList

Returns the value of the variable.

getValue() - Method in class org.biolegato.menu.Chooser

Returns the value of the variable.

getValue() - Method in class org.biolegato.menu.ComboBoxWidget

Returns the value of the variable.

getValue() - Method in class org.biolegato.menu.NumberWidget

Returns the current value of the variable.

getValue() - Method in class org.biolegato.menu.TempFile

Gets the current filename corresponding to this variable If the file does not exists, then this function creates a file to use for IO and writes any initial contents

getValue() - Method in class org.biolegato.menu.TextWidget

Returns the value of the variable.

getValue() - Method in interface org.biolegato.menu.Widget

Returns the value of the variable.

H

HOME_DIR - Static variable in class org.biolegato.main.BLMain

Stores the user's home directory

I

index - Variable in class org.biolegato.menu.ListWidget

Stores the current value selected by the chooser.

isA(Class<?>) - Method in class org.biolegato.main.PluginWrapper

Used to test inheritance for the plugin class.

isDigit(char) - Static method in class org.biolegato.main.BLMain

Tests if a character is a digit or not.

isUNIX() - Method in enum org.biolegato.main.BLMain.OS

isWindows() - Method in enum org.biolegato.main.BLMain.OS

L

label - Variable in class org.biolegato.menu.ListWidget

The label to associate with the list widget

ListWidget - Class in org.biolegato.menu

A wrapper class used to abstract combo boxes within command windows.

ListWidget(String, String[], String[], int) - Constructor for class org.biolegato.menu.ListWidget

Creates a new instance of EZComboBox (represents "choice_list" in GDE menu files).

loadClass(Map<String, PluginWrapper>, URL, String) - Static method in class org.biolegato.main.PluginLoader

Loads a class and its subclasses for a given url.

loadGDEMenus() - Static method in class org.biolegato.menu.GDEMenuParser

Reads in the default .GDEMenus files.

loadJar(Map<String, PluginWrapper>, File) - Static method in class org.biolegato.main.PluginLoader

Loads all plugin classes within a jar file.

loadMakemenus() - Static method in class org.biolegato.menu.GDEMenuParser

Reads in the makemenus GDE menus.

loadPlugins(Map<String, PluginWrapper>, String) - Static method in class org.biolegato.main.PluginLoader

Loads an the plugins into BioLegato.

M

main(String[]) - Static method in class org.biolegato.main.BLMain

Starts up BioLegato.

message(String, String) - Static method in class org.biolegato.main.BLMain

Sends a message to BioLegato's standard out.

N

NAME - Static variable in class org.biolegato.main.BLMain

This constant stores the program's name

names - Variable in class org.biolegato.menu.ListWidget

The list of choice names

numberDigits(int) - Static method in class org.biolegato.main.BLMain

Divide and conquer algorithm to calculate the number of digits for a given number

NumberWidget - Class in org.biolegato.menu

Wraps a widget(s) for selecting numeric values.

NumberWidget(String, int, int, int) - Constructor for class org.biolegato.menu.NumberWidget

Creates a new instance of EZSlider

O

org.biolegato.main - package org.biolegato.main

org.biolegato.menu - package org.biolegato.menu

P

PluginLoader - Class in org.biolegato.main

This class is used to handle plugins.

PluginLoader() - Constructor for class org.biolegato.main.PluginLoader

PluginWrapper - Class in org.biolegato.main

This class is used to wrap plugins.

PluginWrapper(String, Class<?>) - Constructor for class org.biolegato.main.PluginWrapper

Creates a new instance of the plugin wrapper class.

PROGRAM_DIR - Static variable in class org.biolegato.main.BLMain

This constant is set to the path of BioLegato.jar The value of this constant determined at runtime.

R

readFile(String, File) - Method in interface org.biolegato.main.DataCanvas

Reads a file into the canvas

readGDEMenuFile(File) - Static method in class org.biolegato.menu.GDEMenuParser

This function loads a GDE formatted menu file into the program.

readGDEMenuFile(String, File) - Static method in class org.biolegato.menu.GDEMenuParser

This function loads a GDE formatted menu file into the program.

replaceArguments(String) - Method in class org.biolegato.menu.CommandThread

Replaces the variables in the command string with their corresponding values.

run() - Method in class org.biolegato.main.StreamCopier

run() - Method in class org.biolegato.menu.CommandThread

Used for running the command.

RunWindow - Class in org.biolegato.menu

RunWindow(String, List<CommandButton>, Map<String, Widget>) - Constructor for class org.biolegato.menu.RunWindow

Creates a new instance of RunWindow

runWindow - Variable in class org.biolegato.menu.RunWindow

The current window

S

serialVersionUID - Static variable in class org.biolegato.main.BLMain

This constant is used for Serialization

setCurrentPWD(File) - Static method in class org.biolegato.main.BLMain

Sets the present working directory "PWD" for BioLegato (this does NOT change CURRENT_DIR!) This value can be used to cache which directory file dialog boxes should use as their "current working directory"

shellCommand(String, String) - Static method in class org.biolegato.main.BLMain

Runs simple shell commands.

smethod(String) - Method in class org.biolegato.main.PluginWrapper

Invokes a static method from the plugin.

smethod(String, Class[], Object[]) - Method in class org.biolegato.main.PluginWrapper

Invokes a static method from the plugin (returns null if not successful).

stateChanged(ChangeEvent) - Method in class org.biolegato.menu.NumberWidget

Handles synchronization between the slider and the spinner.

StreamCopier - Class in org.biolegato.main

StreamCopier(int, InputStream, OutputStream) - Constructor for class org.biolegato.main.StreamCopier

T

TempFile - Class in org.biolegato.menu

Stores information about the file fields used by the command

TempFile(boolean, boolean, boolean, boolean, String) - Constructor for class org.biolegato.menu.TempFile

Creates a new instance of EZComboBox (represents "choice_list" in GDE menu files).

testNumber(String) - Static method in class org.biolegato.main.BLMain

Checks if a character array is all digits.

textfield - Variable in class org.biolegato.menu.TextWidget

The textfield for obtaining the data

TextWidget - Class in org.biolegato.menu

A wrapper class used to abstract text fields within command windows.

TextWidget(String, String) - Constructor for class org.biolegato.menu.TextWidget

Creates a new instance of TextWidget

toType(String) - Static method in enum org.biolegato.menu.GDEMenuParser.WidgetType

V

valueOf(String) - Static method in enum org.biolegato.main.BLMain.ARCH

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.main.BLMain.OS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.menu.GDEMenuParser.WidgetType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biolegato.main.BLMain.ARCH

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.main.BLMain.OS

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.menu.GDEMenuParser.WidgetType

Returns an array containing the constants of this enum type, in the order they're declared.

values - Variable in class org.biolegato.menu.ListWidget

The list of choice values

VERSION - Static variable in class org.biolegato.main.BLMain

This constant is used to keep track of version changes.

W

warning(String, String) - Static method in class org.biolegato.main.BLMain

Sends an warning message to BioLegato's standard err.

Widget - Interface in org.biolegato.menu

Abstract interface to relate widget variables and invisible variables (such as temporary files)

widgets - Variable in class org.biolegato.menu.RunWindow

List of widgets for the window.

writeFile(String, File) - Method in interface org.biolegato.main.DataCanvas

Writes a file out from the canvas

A B C D E F G H I L M N O P R S T V W