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

A

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

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

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

Displays an about popup for BioLegato.

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

Runs the command.

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

Makes the window visible so all of the variables may be set.

actionPerformed(ActionEvent) - Method in class org.biolegato.core.menu.variables.EZChooser

Handles selection changes of the radio buttons.

actionPerformed(ActionEvent) - Method in class org.biolegato.core.menu.variables.EZCommandButton

actionPerformed(ActionEvent) - Method in class org.biolegato.core.menu.variables.EZFileChooser

Handle the choose file button

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

Runs the command.

actionPerformed(ActionEvent) - Method in class org.biolegato.core.pcdmenu.PCDMenuItem

actionPerformed(ActionEvent) - Method in class org.biolegato.core.pcdmenu.widgets.Chooser

Handles selection changes of the radio buttons.

actionPerformed(ActionEvent) - Method in class org.biolegato.core.pcdmenu.widgets.FileChooser

Handle the choose file button

ActionThread - Class in org.biolegato.core.menu

Class used for making abstract actions which launch threads.

ActionThread(String, Runnable) - Constructor for class org.biolegato.core.menu.ActionThread

Creates a new instance of ActionThread.

addEscapes(String) - Static method in error org.biolegato.core.pcdmenu.parser.TokenMgrError

Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string

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

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

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

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

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

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

addPropertiesListener(String, PropertiesListener) - Static method in class org.biolegato.core.main.BLMain

Adds a properties listener to the properties object.

addPropertiesListener(String, PropertiesListener) - Method in class org.biolegato.core.properties.BLProperties

Adds a listener for property changes NOTE: this method allows filtering based on which property changed

addWidget(String, Widget) - Method in class org.biolegato.core.pcdmenu.PCDMenuItem

addWidget(String, Widget) - Method in class org.biolegato.core.pcdmenu.TabWidget

addWidget(String, Widget) - Method in interface org.biolegato.core.pcdmenu.WidgetContainer

adjustBeginLineColumn(int, int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

adjustBeginLineColumn(int, int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

ArchList() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses a list of supported system architectures in a PCD file The list is then compared with the current system architecture to see if it is supported by the PCD command.

ArchName() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Matches an architecture name and returns whether it is supported by the current architecture.

assertIndent(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Asserts indentation level (calls token_source.testIndent)

B

backup(int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Backup a number of characters.

backup(int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Backup a number of characters.

beginColumn - Variable in class org.biolegato.core.pcdmenu.parser.Token

The column number of the first character of this Token.

beginLine - Variable in class org.biolegato.core.pcdmenu.parser.Token

The line number of the first character of this Token.

BeginToken() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Start.

BeginToken() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Start.

BLMain - Class in org.biolegato.core.main

The main program and generic function class.

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

BLMain.ARCH - Enum in org.biolegato.core.main

BLMain.OS - Enum in org.biolegato.core.main

BLProperties - Class in org.biolegato.core.properties

Stores the properties for BioLegato.

BLProperties() - Constructor for class org.biolegato.core.properties.BLProperties

Create a new BLProperties instance

Bool() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses a boolean token into a java boolean

bufcolumn - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

bufcolumn - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

buffer - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

buffer - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

bufline - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

bufline - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

bufpos - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Position in buffer.

bufpos - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

Position in buffer.

buttonFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any button field

C

choice_list - Variable in class org.biolegato.core.menu.variables.EZChoiceList

The combobox contianing the data.

choice_list - Variable in class org.biolegato.core.pcdmenu.widgets.ChoiceList

The combobox contianing the data.

ChoiceList - Class in org.biolegato.core.pcdmenu.widgets

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

ChoiceList(String, Map<String, String>, String) - Constructor for class org.biolegato.core.pcdmenu.widgets.ChoiceList

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

choices - Variable in class org.biolegato.core.menu.variables.EZChoiceList

The list of choices

choices - Variable in class org.biolegato.core.menu.variables.EZComboBox

The list of choices

choices - Variable in class org.biolegato.core.pcdmenu.widgets.ListWidget

The list of choices

Chooser - Class in org.biolegato.core.pcdmenu.widgets

Wrapper class for a group of radiobuttons.

Chooser(String, Map<String, String>, String) - Constructor for class org.biolegato.core.pcdmenu.widgets.Chooser

Creates a new instance of EZChooser.

chooserFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any chooser object

clear() - Method in class org.biolegato.core.main.OrderedHash

close() - Method in class org.biolegato.core.menu.variables.EZCommandButton

close() - Method in class org.biolegato.core.menu.variables.EZTempFile

Releases any files currently in use by this class

close() - Method in interface org.biolegato.core.menu.variables.EZVariable

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

close() - Method in class org.biolegato.core.menu.variables.EZWidgetVariable

Finalizes the current variable.

close() - Method in class org.biolegato.core.pcdmenu.CommandButton

close() - Method in class org.biolegato.core.pcdmenu.TabWidget

close() - Method in class org.biolegato.core.pcdmenu.TempFile

Releases any files currently in use by this class

close() - Method in class org.biolegato.core.pcdmenu.widgets.ChoiceList

Closes the open object

close() - Method in class org.biolegato.core.pcdmenu.widgets.Chooser

close() - Method in class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

close() - Method in class org.biolegato.core.pcdmenu.widgets.DecimalWidget

close() - Method in class org.biolegato.core.pcdmenu.widgets.NumberWidget

close() - Method in class org.biolegato.core.pcdmenu.widgets.TextWidget

close() - Method in interface org.biolegato.core.pcdmenu.widgets.Widget

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

closeWindow() - Method in class org.biolegato.core.menu.EZRunWindow

column - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

column - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

combobox - Variable in class org.biolegato.core.menu.variables.EZComboBox

The combobox contianing the data

combobox - Variable in class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

The combobox contianing the data

comboboxUI - Variable in class org.biolegato.core.menu.variables.EZComboBox

The UI to enable scrolling of the JComboBox.

comboboxUI - Variable in class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

The UI to enable scrolling of the JComboBox.

ComboBoxWidget - Class in org.biolegato.core.pcdmenu.widgets

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

ComboBoxWidget(String, Map<String, String>, String) - Constructor for class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

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

comboFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any combobox object

COMMA - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

CommandButton - Class in org.biolegato.core.pcdmenu

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

CommandButton(String, String, boolean) - Constructor for class org.biolegato.core.pcdmenu.CommandButton

Creates a new instance of CommandButton

CommandThread - Class in org.biolegato.core.pcdmenu

Class used for making abstract actions which launch threads.

CommandThread(String) - Constructor for class org.biolegato.core.pcdmenu.CommandThread

Creates a new instance of CommandThread.

CommandThread(String, OrderedHash<String, Widget>) - Constructor for class org.biolegato.core.pcdmenu.CommandThread

Creates a new instance of CommandThread.

COMMENT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

ContentValue() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

create() - Method in class org.biolegato.core.plugins.PluginWrapper

Creates a new object the plugin class.

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

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

createGDEButton(String, String, boolean) - Static method in class org.biolegato.core.menu.GDEMenuParser

createVariable(Map) - Method in class org.biolegato.core.menu.EZRunWindow

Used to create BioLegato variables.

curChar - Variable in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

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

Stores the current machine architecture

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

Stores the current operating system

currentToken - Variable in exception org.biolegato.core.pcdmenu.parser.ParseException

This is the last token that has been consumed successfully.

D

DATA - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

Lexical state.

DataCanvas - Interface in org.biolegato.core.plugintypes

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

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

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

debugStream - Variable in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Debug output.

Decimal() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses a decimal number from a PCD file into a Java double

DECIMAL - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

decimalFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any decimal field

DecimalWidget - Class in org.biolegato.core.pcdmenu.widgets

Wraps a widget(s) for selecting numeric values.

DecimalWidget(String, double, double, double) - Constructor for class org.biolegato.core.pcdmenu.widgets.DecimalWidget

Creates a new instance of DecimalWidget

DEFAULT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

Lexical state.

DEFAULT_FONT - Static variable in class org.biolegato.core.main.BLMain

The default font for BioLegato

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

Check out: http://lopica.sourceforge.net/os.html

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

Check out: http://lopica.sourceforge.net/os.html

DIGITS - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

disable_tracing() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Disable tracing.

display() - Method in class org.biolegato.core.pcdmenu.CommandButton

display() - Method in class org.biolegato.core.pcdmenu.TabWidget

display() - Method in class org.biolegato.core.pcdmenu.TempFile

display() - Method in class org.biolegato.core.pcdmenu.widgets.ChoiceList

Displays the choice list

display() - Method in class org.biolegato.core.pcdmenu.widgets.Chooser

display() - Method in class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

display() - Method in class org.biolegato.core.pcdmenu.widgets.DecimalWidget

display() - Method in class org.biolegato.core.pcdmenu.widgets.FileChooser

display() - Method in class org.biolegato.core.pcdmenu.widgets.NumberWidget

display() - Method in class org.biolegato.core.pcdmenu.widgets.TextWidget

display() - Method in interface org.biolegato.core.pcdmenu.widgets.Widget

Displays the current object

Done() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reset buffer when finished.

Done() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reset buffer when finished.

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

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

DOUBLEQ - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

E

elements() - Method in class org.biolegato.core.main.OrderedHash

enable_tracing() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Enable tracing.

endColumn - Variable in class org.biolegato.core.pcdmenu.parser.Token

The column number of the last character of this Token.

endLine - Variable in class org.biolegato.core.pcdmenu.parser.Token

The line number of the last character of this Token.

entrySet() - Method in class org.biolegato.core.main.OrderedHash

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

Replaces $VARIABLE name with environment variables.

EOF - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

End of File.

eol - Variable in exception org.biolegato.core.pcdmenu.parser.ParseException

The end of line string for this machine.

EOL - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

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

Sends an error message to BioLegato's standard err.

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

Sends an error message to BioLegato's standard err.

ExecMenuItem - Class in org.biolegato.core.pcdmenu

ExecMenuItem(String, String, String, String) - Constructor for class org.biolegato.core.pcdmenu.ExecMenuItem

Creates a new instance of ExecMenuItem

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

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

ExpandBuff(boolean) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

ExpandBuff(boolean) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

expectedTokenSequences - Variable in exception org.biolegato.core.pcdmenu.parser.ParseException

Each entry in this array is an array of integers.

EZChoiceList - Class in org.biolegato.core.menu.variables

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

EZChoiceList(Map) - Constructor for class org.biolegato.core.menu.variables.EZChoiceList

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

EZChooser - Class in org.biolegato.core.menu.variables

Wrapper class for a group of radiobuttons.

EZChooser(Map<String, Object>) - Constructor for class org.biolegato.core.menu.variables.EZChooser

Creates a new instance of EZChooser.

EZComboBox - Class in org.biolegato.core.menu.variables

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

EZComboBox(Map) - Constructor for class org.biolegato.core.menu.variables.EZComboBox

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

EZCommandButton - Class in org.biolegato.core.menu.variables

EZCommandButton(EZRunWindow, Map) - Constructor for class org.biolegato.core.menu.variables.EZCommandButton

Creates a new instance of EZCommandButton

EZFileChooser - Class in org.biolegato.core.menu.variables

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

EZFileChooser(Map) - Constructor for class org.biolegato.core.menu.variables.EZFileChooser

Creates a new instance of GDETempFile.

EZMenuItem - Class in org.biolegato.core.menu

The window used for setting options to run a menu command.

EZMenuItem(Map<String, Object>) - Constructor for class org.biolegato.core.menu.EZMenuItem

Creates a new instance of a run window.

EZRunWindow - Class in org.biolegato.core.menu

EZRunWindow(Map<String, Object>) - Constructor for class org.biolegato.core.menu.EZRunWindow

Creates a new instance of EZRunWindow

EZSlider - Class in org.biolegato.core.menu.variables

Wraps a widget(s) for selecting numeric values.

EZSlider(Map) - Constructor for class org.biolegato.core.menu.variables.EZSlider

Creates a new instance of EZSlider

EZTempFile - Class in org.biolegato.core.menu.variables

Stores information about the file fields used by the command

EZTempFile(Map) - Constructor for class org.biolegato.core.menu.variables.EZTempFile

Creates a new instance of EZTempFile.

EZTextField - Class in org.biolegato.core.menu.variables

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

EZTextField(Map) - Constructor for class org.biolegato.core.menu.variables.EZTextField

Creates a new instance of EZTextField

EZVariable - Interface in org.biolegato.core.menu.variables

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

EZWidgetVariable - Class in org.biolegato.core.menu.variables

A superclass used to abstract variables for creating command windows.

EZWidgetVariable(Map) - Constructor for class org.biolegato.core.menu.variables.EZWidgetVariable

Creates a new instance of EZVariable (used to add the name to the variable).

F

FileChooser - Class in org.biolegato.core.pcdmenu.widgets

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

FileChooser(String, String) - Constructor for class org.biolegato.core.pcdmenu.widgets.FileChooser

Creates a new instance of GDETempFile.

FillBuff() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

FillBuff() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

G

GDEMakeMenus - Class in org.biolegato.core.menu

GDEMenu is used to read and parse GDE menu files into into BioLegato

GDEMakeMenus() - Constructor for class org.biolegato.core.menu.GDEMakeMenus

GDEMenu - Class in org.biolegato.core.menu

GDEMenu is used to read and parse GDE menu files into into BioLegato

GDEMenu() - Constructor for class org.biolegato.core.menu.GDEMenu

GDEMenuParser - Class in org.biolegato.core.menu

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

Creates a new instance of GDEMenuParser

generateParseException() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Generate ParseException.

getBeginColumn() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Get token beginning column number.

getBeginColumn() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Get token beginning column number.

getBeginLine() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Get token beginning line number.

getBeginLine() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Get token beginning line number.

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

Returns the current/selected data in the canvas.

getColumn() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Deprecated.

getColumn() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Deprecated.

getCurrentPWD() - Static method in class org.biolegato.core.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"

getEndColumn() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Get token end column number.

getEndColumn() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Get token end column number.

getEndLine() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Get token end line number.

getEndLine() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Get token end line number.

GetImage() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Get token literal value.

GetImage() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Get token literal value.

getIndent() - Method in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Returns the current indentation level

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

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

getKey(int) - Method in class org.biolegato.core.main.OrderedHash

getKey() - Method in class org.biolegato.core.main.OrderedHash.MapEntry

getKeyCount() - Method in class org.biolegato.core.main.OrderedHash

getLine() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Deprecated.

getLine() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Deprecated.

getMessage() - Method in error org.biolegato.core.pcdmenu.parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getName() - Method in class org.biolegato.core.menu.variables.EZCommandButton

getName() - Method in class org.biolegato.core.menu.variables.EZTempFile

Returns the name of the variable.

getName() - Method in class org.biolegato.core.plugins.PluginWrapper

Returns the class's name.

getNewDefault() - Method in class org.biolegato.core.menu.variables.EZChoiceList

This function is used to maintain user variable settings from window to window.

getNewDefault() - Method in class org.biolegato.core.menu.variables.EZChooser

This function is used to maintain user variable settings from window to window.

getNewDefault() - Method in class org.biolegato.core.menu.variables.EZComboBox

This function is used to maintain user variable settings from window to window.

getNewDefault() - Method in class org.biolegato.core.menu.variables.EZWidgetVariable

This function is used to maintain user variable settings from window to window.

getNewDefault() - Method in class org.biolegato.core.pcdmenu.widgets.ChoiceList

This function is used to maintain user variable settings from window to window.

getNewDefault() - Method in class org.biolegato.core.pcdmenu.widgets.Chooser

This function is used to maintain user variable settings from window to window.

getNewDefault() - Method in class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

This function is used to maintain user variable settings from window to window.

getNextToken() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Get the next Token.

getNextToken() - Method in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Get the next Token.

getPlugin(String) - Method in class org.biolegato.core.plugins.PluginLoader

Retrieves a plugin by name.

getPluginHash() - Method in class org.biolegato.core.plugins.PluginLoader

Maintains a list with all of the plugins loaded by BioLegato.

getPlugins(Class<?>) - Static method in class org.biolegato.core.main.BLMain

Returns a list with all of the plugins loaded by BioLegato that are instances of the class type indicated.

getPlugins(Class<?>) - Method in class org.biolegato.core.plugins.PluginLoader

Returns a list with all of the plugins loaded by BioLegato that are instances of the class type indicated.

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

Returns the properties object associated with this instance of BioLegato

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

Retrieves individual settings for BioLegato.

getProperty(String) - Method in class org.biolegato.core.properties.BLProperties

Obtains a property from the BLProperties object.

GetSuffix(int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Get the suffix.

GetSuffix(int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Get the suffix.

getTabName() - Method in interface org.biolegato.core.plugintypes.DataCanvas

Returns the name of the canvas.

getTabSize(int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

getTabSize(int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

getToken(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Get the specific Token.

getType() - Static method in class org.biolegato.core.menu.variables.EZChoiceList

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.menu.variables.EZChooser

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.menu.variables.EZComboBox

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.menu.variables.EZFileChooser

Returns the type name

getType() - Static method in class org.biolegato.core.menu.variables.EZSlider

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.menu.variables.EZTempFile

Returns the type name

getType() - Static method in class org.biolegato.core.menu.variables.EZTextField

Returns the name of this type of variable

getType() - Static method in class org.biolegato.core.menu.variables.EZWidgetVariable

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.pcdmenu.TempFile

Returns the type name

getType() - Static method in class org.biolegato.core.pcdmenu.widgets.ChoiceList

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.pcdmenu.widgets.Chooser

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

Returns the name of this type of variable.

getType() - Static method in class org.biolegato.core.pcdmenu.widgets.DecimalWidget

Returns the name of this type of variable.

getValue() - Method in class org.biolegato.core.main.OrderedHash.MapEntry

getValue() - Method in class org.biolegato.core.menu.variables.EZChoiceList

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.menu.variables.EZChooser

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.menu.variables.EZComboBox

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.menu.variables.EZCommandButton

getValue() - Method in class org.biolegato.core.menu.variables.EZSlider

Returns the current value of the variable.

getValue() - Method in class org.biolegato.core.menu.variables.EZTempFile

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.core.menu.variables.EZTextField

Returns the value of the variable.

getValue() - Method in interface org.biolegato.core.menu.variables.EZVariable

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.menu.variables.EZWidgetVariable

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.pcdmenu.CommandButton

getValue() - Method in class org.biolegato.core.pcdmenu.parser.Token

An optional attribute value of the Token.

getValue() - Method in class org.biolegato.core.pcdmenu.TabWidget

getValue() - Method in class org.biolegato.core.pcdmenu.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.core.pcdmenu.widgets.ChoiceList

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.pcdmenu.widgets.Chooser

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.pcdmenu.widgets.ComboBoxWidget

Returns the value of the variable.

getValue() - Method in class org.biolegato.core.pcdmenu.widgets.DecimalWidget

Returns the current value of the variable.

getValue() - Method in class org.biolegato.core.pcdmenu.widgets.NumberWidget

Returns the current value of the variable.

getValue() - Method in class org.biolegato.core.pcdmenu.widgets.TextWidget

Returns the value of the variable.

getValue() - Method in interface org.biolegato.core.pcdmenu.widgets.Widget

Returns the value of the variable.

getVariableHash() - Method in class org.biolegato.core.menu.EZRunWindow

H

hasMoreElements() - Method in class org.biolegato.core.main.OrderedHash.EnumeratingItterator

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

Stores the user's home directory

I

ID - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

Ident() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses an identifier token from a PCD file into a Java String

image - Variable in class org.biolegato.core.pcdmenu.parser.Token

The string image of the token.

inBuf - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

inBuf - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

IND - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

INDENT_SIZE - Static variable in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Used to store the size of an indent in spaces This is necessary for calculations within the Java program

inorsp(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses an optional indent (this is useful for values that can be spaced or indented onto a new line (e.g.

input_stream - Variable in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

inputStream - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

inputStream - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

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

Used to test instanceof for the plugin class.

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

Tests if a character is a digit or not.

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

isWidget() - Method in class org.biolegato.core.menu.variables.EZTempFile

Returns the widget status of the variable (i.e., is the variable displayable)

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

J

jj_nt - Variable in class org.biolegato.core.pcdmenu.parser.PCDFile

Next token.

jjFillToken() - Method in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

jjnewLexState - Static variable in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Lex State array.

jjstrLiteralImages - Static variable in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Token literal values.

K

keys() - Method in class org.biolegato.core.main.OrderedHash

keySet() - Method in class org.biolegato.core.main.OrderedHash

kind - Variable in class org.biolegato.core.pcdmenu.parser.Token

An integer that describes the kind of this token.

L

label - Variable in class org.biolegato.core.pcdmenu.widgets.ListWidget

The label to associate with the list widget

LexicalError(boolean, int, int, int, String, char) - Static method in error org.biolegato.core.pcdmenu.parser.TokenMgrError

Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.

lexStateNames - Static variable in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Lexer state names.

line - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

line - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

listFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any list object

ListWidget - Class in org.biolegato.core.pcdmenu.widgets

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

ListWidget(String, Map<String, String>, String) - Constructor for class org.biolegato.core.pcdmenu.widgets.ListWidget

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

loadMenu() - Static method in class org.biolegato.core.menu.GDEMakeMenus

Reads in the makemenus GDE menus.

loadMenu() - Static method in class org.biolegato.core.menu.GDEMenu

Reads in the default .GDEMenus files.

loadMenu() - Static method in class org.biolegato.core.pcdmenu.PCDMenu

Reads in the default .GDEMenus files.

M

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

Starts up BioLegato.

maxNextCharInd - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

maxNextCharInd - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

MenuWindow - Class in org.biolegato.core.pcdmenu

MenuWindow(String, OrderedHash<String, Widget>) - Constructor for class org.biolegato.core.pcdmenu.MenuWindow

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

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

Sends a message to BioLegato's standard out.

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

Sends a message to BioLegato's standard out.

N

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

This constant stores the program's name

name - Variable in class org.biolegato.core.menu.EZMenuItem

The name of the command to run

newToken(int, String) - Static method in class org.biolegato.core.pcdmenu.parser.Token

Returns a new Token object, by default.

newToken(int) - Static method in class org.biolegato.core.pcdmenu.parser.Token

next - Variable in class org.biolegato.core.pcdmenu.parser.Token

A reference to the next regular (non-special) token from the input stream.

nextElement() - Method in class org.biolegato.core.main.OrderedHash.EnumeratingItterator

NL - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

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

Tests if a character is a digit or not.

Number() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses a non-decimal number from a PCD file into a Java integer

NUMBER - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

numberFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any number field

NumberWidget - Class in org.biolegato.core.pcdmenu.widgets

Wraps a widget(s) for selecting numeric values.

NumberWidget(String, int, int, int) - Constructor for class org.biolegato.core.pcdmenu.widgets.NumberWidget

Creates a new instance of EZSlider

O

OrderedHash<K,V> - Class in org.biolegato.core.main

OrderedHash() - Constructor for class org.biolegato.core.main.OrderedHash

Creates a new instance of OrderedHash

OrderedHash(Map) - Constructor for class org.biolegato.core.main.OrderedHash

OrderedHash.EnumeratingItterator<T> - Class in org.biolegato.core.main

OrderedHash.EnumeratingItterator(Iterator<T>) - Constructor for class org.biolegato.core.main.OrderedHash.EnumeratingItterator

OrderedHash.MapEntry<H,I> - Class in org.biolegato.core.main

OrderedHash.MapEntry(H, I) - Constructor for class org.biolegato.core.main.OrderedHash.MapEntry

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

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

org.biolegato.core.menu.variables - package org.biolegato.core.menu.variables

org.biolegato.core.pcdmenu - package org.biolegato.core.pcdmenu

org.biolegato.core.pcdmenu.parser - package org.biolegato.core.pcdmenu.parser

org.biolegato.core.pcdmenu.widgets - package org.biolegato.core.pcdmenu.widgets

org.biolegato.core.plugins - package org.biolegato.core.plugins

org.biolegato.core.plugintypes - package org.biolegato.core.plugintypes

org.biolegato.core.properties - package org.biolegato.core.properties

original - Variable in class org.biolegato.core.menu.variables.EZWidgetVariable

P

Param(int, WidgetContainer) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Generates a parameter component according to the PCD file's production(s).

Parse() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses PCD files The format for a PCD file is: [ Optional Blank Space ] [ PCD Options ] Tabs and Parameters

ParseException - Exception in org.biolegato.core.pcdmenu.parser

This exception is thrown when parse errors are encountered.

ParseException(Token, int[][], String[]) - Constructor for exception org.biolegato.core.pcdmenu.parser.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

ParseException() - Constructor for exception org.biolegato.core.pcdmenu.parser.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for exception org.biolegato.core.pcdmenu.parser.ParseException

Constructor with message.

PCDFile - Class in org.biolegato.core.pcdmenu.parser

PCDFile(InputStream) - Constructor for class org.biolegato.core.pcdmenu.parser.PCDFile

Constructor with InputStream.

PCDFile(InputStream, String) - Constructor for class org.biolegato.core.pcdmenu.parser.PCDFile

Constructor with InputStream and supplied encoding

PCDFile(Reader) - Constructor for class org.biolegato.core.pcdmenu.parser.PCDFile

Constructor.

PCDFile(PCDFileTokenManager) - Constructor for class org.biolegato.core.pcdmenu.parser.PCDFile

Constructor with generated Token Manager.

PCDFileConstants - Interface in org.biolegato.core.pcdmenu.parser

Token literal values and constants.

PCDFileTokenManager - Class in org.biolegato.core.pcdmenu.parser

Token Manager.

PCDFileTokenManager(SimpleCharStream) - Constructor for class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Constructor.

PCDFileTokenManager(SimpleCharStream, int) - Constructor for class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Constructor.

PCDMenu - Class in org.biolegato.core.pcdmenu

PCDMenu() - Constructor for class org.biolegato.core.pcdmenu.PCDMenu

PCDMenuItem - Class in org.biolegato.core.pcdmenu

PCDMenuItem(String, String, String) - Constructor for class org.biolegato.core.pcdmenu.PCDMenuItem

PCDOption() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses a list of supported PCD options Currently supported options: Option name Description name the name of the PCD command tip the tool-tip text for the PCD command icon the path of the PCD command's icon file system a list of supported system configurations for the PCD command

PluginLoader - Class in org.biolegato.core.plugins

This class is used to handle plugins.

PluginLoader(String) - Constructor for class org.biolegato.core.plugins.PluginLoader

Loads an the plugins into BioLegato.

PluginWrapper - Class in org.biolegato.core.plugins

This class is used to wrap plugins.

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

Creates a new instance of the plugin wrapper class.

prevCharIsCR - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

prevCharIsCR - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

prevCharIsLF - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

prevCharIsLF - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

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

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

PropertiesListener - Interface in org.biolegato.core.properties

Handler/listener interface for properties changes.

propertiesUpdate(String, String) - Method in interface org.biolegato.core.properties.PropertiesListener

Receives properties update information from BioLegato

put(K, V) - Method in class org.biolegato.core.main.OrderedHash

putAll(Map<? extends K, ? extends V>) - Method in class org.biolegato.core.main.OrderedHash

R

readChar() - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Read a character.

readChar() - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Read a character.

readDirectory(File) - Static method in class org.biolegato.core.pcdmenu.PCDMenu

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

Reads a file into the canvas

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

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

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

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

readStream(BufferedReader) - Static method in class org.biolegato.core.main.BLMain

Reads the complete contents of a BufferedReader into a string.

ReInit(InputStream) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Reinitialise.

ReInit(InputStream, String) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Reinitialise.

ReInit(Reader) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Reinitialise.

ReInit(PCDFileTokenManager) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Reinitialise.

ReInit(SimpleCharStream) - Method in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Reinitialise parser.

ReInit(SimpleCharStream, int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Reinitialise parser.

ReInit(Reader, int, int, int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(Reader, int, int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(Reader) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(InputStream, String, int, int, int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(InputStream, int, int, int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(InputStream, String) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(InputStream) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(InputStream, String, int, int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(InputStream, int, int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Reinitialise.

ReInit(Reader, int, int, int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(Reader, int, int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(Reader) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(InputStream, String, int, int, int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(InputStream, int, int, int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(InputStream, String) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(InputStream) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(InputStream, String, int, int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

ReInit(InputStream, int, int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

Reinitialise.

remove(Object) - Method in class org.biolegato.core.main.OrderedHash

replaceArguments(String) - Method in class org.biolegato.core.menu.variables.EZCommandButton

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

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

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

run() - Method in class org.biolegato.core.menu.variables.EZCommandButton

Used for running the command.

run() - Method in class org.biolegato.core.pcdmenu.CommandThread

Used for running the command.

runWindow - Variable in class org.biolegato.core.menu.EZRunWindow

The current window

S

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

Ensures that the command will be executed properly as a shell command

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

This constant is used for Serialization

setCurrentPWD(File) - Static method in class org.biolegato.core.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"

setDebugStream(PrintStream) - Method in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Set debug output.

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

Changes properties for BioLegato.

setProperty(String, String) - Method in class org.biolegato.core.properties.BLProperties

Changes a property within the BLProperties object

setTabSize(int) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

setTabSize(int) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

setValue(I) - Method in class org.biolegato.core.main.OrderedHash.MapEntry

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

Runs simple shell commands.

showPropertiesWindow(JFrame) - Method in class org.biolegato.core.properties.BLProperties

Displays the properties window for this instance of BioLegato

SimpleCharStream - Class in org.biolegato.core.pcdmenu.parser

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).

SimpleCharStream(Reader, int, int, int) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(Reader, int, int) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(Reader) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, int, int, int) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String, int, int) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, int, int) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream(InputStream) - Constructor for class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Constructor.

SimpleCharStream - Class in org.biolegato.core.pcdmenu

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).

SimpleCharStream(Reader, int, int, int) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(Reader, int, int) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(Reader) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, int, int, int) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String, int, int) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, int, int) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(InputStream, String) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

SimpleCharStream(InputStream) - Constructor for class org.biolegato.core.pcdmenu.SimpleCharStream

Constructor.

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

Invokes a static method from the plugin.

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

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

SP - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

specialToken - Variable in class org.biolegato.core.pcdmenu.parser.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

stateChanged(ChangeEvent) - Method in class org.biolegato.core.menu.variables.EZSlider

Handles synchronization between the slider and the spinner.

stateChanged(ChangeEvent) - Method in class org.biolegato.core.pcdmenu.widgets.DecimalWidget

Receives the new value on spinner changes

stateChanged(ChangeEvent) - Method in class org.biolegato.core.pcdmenu.widgets.NumberWidget

Handles synchronization between the slider and the spinner.

staticFlag - Static variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

Whether parser is static.

staticFlag - Static variable in class org.biolegato.core.pcdmenu.SimpleCharStream

Whether parser is static.

SwitchTo(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFileTokenManager

Switch to specified lex state.

SystemName() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses a list of supported operating systems in a PCD file The list is then compared with the current operating system to see if it is supported by the PCD command.

T

T_ALL - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_AMD64 - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_AND - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_BUTTON - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_CANVAS - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_CHECK - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_CHOICES - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_CHOOSER - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_CLOSE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_CMDNAME - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_COMBOBOX - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_CONTENT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_DECIMAL - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_DEFAULT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_FALSE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_FASTA - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_FILE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_FLAT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_FORMAT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_GDE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_GENBANK - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_ICON - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_IF - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_IN - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_LABEL - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_LINUX - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_LIST - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_MAX - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_MIN - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_NUMBER - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_OR - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_OSX - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_OUT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_OVERWRITE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_PARAM - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_RAW - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_SAVE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_SELECTION - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_SHELL - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_SOLARIS - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_SPARC - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_SYSTEM - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_TAB - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_TEMPFILE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_TEXT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_THEN - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_TIP - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_TRUE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_TYPE - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_UNIX - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_WINDOWS - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_X86 - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

T_XOR - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

Tab(int, WidgetContainer) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Generates a tabbed pane based on reading the tab tag from the PCD file.

TAB - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

tabSize - Variable in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

tabSize - Variable in class org.biolegato.core.pcdmenu.SimpleCharStream

TabWidget - Class in org.biolegato.core.pcdmenu

TabWidget() - Constructor for class org.biolegato.core.pcdmenu.TabWidget

Creates a new instance of the tab widget

TempFile - Class in org.biolegato.core.pcdmenu

Stores information about the file fields used by the command

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

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

tempfileFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any temporary file field

testIndent(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Tests indentation (NOTE: this calls the token manager)

testNumber(char[]) - Static method in class org.biolegato.core.main.BLMain

Checks if a character array is all digits.

Text() - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses a text token from a PCD file into a Java String

TEXT - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

RegularExpression Id.

textfield - Variable in class org.biolegato.core.menu.variables.EZTextField

The textfield for obtaining the data

textfield - Variable in class org.biolegato.core.pcdmenu.widgets.TextWidget

The textfield for obtaining the data

textFields(int) - Method in class org.biolegato.core.pcdmenu.parser.PCDFile

Parses all of the fields that should be part of any text field

TextWidget - Class in org.biolegato.core.pcdmenu.widgets

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

TextWidget(String, String) - Constructor for class org.biolegato.core.pcdmenu.widgets.TextWidget

Creates a new instance of TextWidget

token - Variable in class org.biolegato.core.pcdmenu.parser.PCDFile

Current token.

Token - Class in org.biolegato.core.pcdmenu.parser

Describes the input token stream.

Token() - Constructor for class org.biolegato.core.pcdmenu.parser.Token

No-argument constructor

Token(int) - Constructor for class org.biolegato.core.pcdmenu.parser.Token

Constructs a new token for the specified Image.

Token(int, String) - Constructor for class org.biolegato.core.pcdmenu.parser.Token

Constructs a new token for the specified Image and Kind.

token_source - Variable in class org.biolegato.core.pcdmenu.parser.PCDFile

Generated Token Manager.

tokenImage - Variable in exception org.biolegato.core.pcdmenu.parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

tokenImage - Static variable in interface org.biolegato.core.pcdmenu.parser.PCDFileConstants

Literal token values.

TokenMgrError - Error in org.biolegato.core.pcdmenu.parser

Token Manager Error.

TokenMgrError() - Constructor for error org.biolegato.core.pcdmenu.parser.TokenMgrError

No arg constructor.

TokenMgrError(String, int) - Constructor for error org.biolegato.core.pcdmenu.parser.TokenMgrError

Constructor with message and reason.

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.biolegato.core.pcdmenu.parser.TokenMgrError

Full Constructor.

toString() - Method in class org.biolegato.core.main.OrderedHash

toString() - Method in class org.biolegato.core.pcdmenu.parser.Token

Returns the image.

U

UpdateLineColumn(char) - Method in class org.biolegato.core.pcdmenu.parser.SimpleCharStream

UpdateLineColumn(char) - Method in class org.biolegato.core.pcdmenu.SimpleCharStream

V

value - Variable in class org.biolegato.core.pcdmenu.widgets.ListWidget

Stores the current value selected by the chooser.

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

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

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

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

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

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

values() - Method in class org.biolegato.core.main.OrderedHash

variableHash - Variable in class org.biolegato.core.menu.EZRunWindow

List of widgets for the window.

variableMapList - Variable in class org.biolegato.core.menu.EZRunWindow

Variable list - used for updating variable status

variables - Variable in class org.biolegato.core.menu.EZMenuItem

The list of variabes currently used by the window.

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

This constant is used to keep track of version changes.

W

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

Sends an warning message to BioLegato's standard err.

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

Sends an warning message to BioLegato's standard err.

Widget - Interface in org.biolegato.core.pcdmenu.widgets

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

WidgetContainer - Interface in org.biolegato.core.pcdmenu

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

Writes a file out from the canvas

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