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BioPCD parser v1.1.0 API
A B C D E F G I J K L M N O P Q R S T U V W 

A

AbstractFileChooser - Class in org.biopcd.widgets
A wrapper class used to abstract file selection within command windows.
AbstractFileChooser(String, int, String) - Constructor for class org.biopcd.widgets.AbstractFileChooser
Creates a new instance of the abstract class file/directory chooser widget.
AbstractFileChooser(String, String, String, int, String) - Constructor for class org.biopcd.widgets.AbstractFileChooser
Creates a new instance of the abstract class file/directory chooser widget.
Act(int, Map<String, Widget>) - Method in class org.biopcd.parser.PCD
Generates a parameter component according to the PCD file's <T_ACT> production(s).
actionPerformed(ActionEvent) - Method in class org.biopcd.parser.CommandThread
Runs the command.
actionPerformed(ActionEvent) - Method in class org.biopcd.parser.RunWindow
Displays the command parameter window.
actionPerformed(ActionEvent) - Method in class org.biopcd.widgets.Chooser
Handles selection changes of the radio buttons.
addEscapes(String) - Static method in error org.biopcd.parser.TokenMgrError
Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string
addTab(String, Map<String, Widget>) - Method in class org.biopcd.widgets.TabbedWidget
Adds a new tab to the tabbed widget
adjustBeginLineColumn(int, int) - Method in class org.biopcd.parser.SimpleCharStream
Method to adjust line and column numbers for the start of a token.
ArchList() - Method in class org.biopcd.parser.PCD
Parses a list of supported system architectures in a PCD file
ArchName() - Method in class org.biopcd.parser.PCD
Matches an architecture name and returns the appropriate SystemToken.ARCH value.
archs - Variable in class org.biopcd.parser.SystemToken
The system architectures associated with the operating system.
assertIndent(int) - Method in class org.biopcd.parser.PCD
Asserts indentation level (calls token_source.testIndent)
ASTAct - Class in org.biopcd.parser
 
ASTAct(int) - Constructor for class org.biopcd.parser.ASTAct
 
ASTAct(PCD, int) - Constructor for class org.biopcd.parser.ASTAct
 
ASTArchList - Class in org.biopcd.parser
 
ASTArchList(int) - Constructor for class org.biopcd.parser.ASTArchList
 
ASTArchList(PCD, int) - Constructor for class org.biopcd.parser.ASTArchList
 
ASTArchName - Class in org.biopcd.parser
 
ASTArchName(int) - Constructor for class org.biopcd.parser.ASTArchName
 
ASTArchName(PCD, int) - Constructor for class org.biopcd.parser.ASTArchName
 
ASTBody - Class in org.biopcd.parser
 
ASTBody(int) - Constructor for class org.biopcd.parser.ASTBody
 
ASTBody(PCD, int) - Constructor for class org.biopcd.parser.ASTBody
 
ASTBool - Class in org.biopcd.parser
 
ASTBool(int) - Constructor for class org.biopcd.parser.ASTBool
 
ASTBool(PCD, int) - Constructor for class org.biopcd.parser.ASTBool
 
ASTbuttonFields - Class in org.biopcd.parser
 
ASTbuttonFields(int) - Constructor for class org.biopcd.parser.ASTbuttonFields
 
ASTbuttonFields(PCD, int) - Constructor for class org.biopcd.parser.ASTbuttonFields
 
ASTContent - Class in org.biopcd.parser
 
ASTContent(int) - Constructor for class org.biopcd.parser.ASTContent
 
ASTContent(PCD, int) - Constructor for class org.biopcd.parser.ASTContent
 
ASTDecimal - Class in org.biopcd.parser
 
ASTDecimal(int) - Constructor for class org.biopcd.parser.ASTDecimal
 
ASTDecimal(PCD, int) - Constructor for class org.biopcd.parser.ASTDecimal
 
ASTdecimalFields - Class in org.biopcd.parser
 
ASTdecimalFields(int) - Constructor for class org.biopcd.parser.ASTdecimalFields
 
ASTdecimalFields(PCD, int) - Constructor for class org.biopcd.parser.ASTdecimalFields
 
ASTdirFields - Class in org.biopcd.parser
 
ASTdirFields(int) - Constructor for class org.biopcd.parser.ASTdirFields
 
ASTdirFields(PCD, int) - Constructor for class org.biopcd.parser.ASTdirFields
 
ASTfileFields - Class in org.biopcd.parser
 
ASTfileFields(int) - Constructor for class org.biopcd.parser.ASTfileFields
 
ASTfileFields(PCD, int) - Constructor for class org.biopcd.parser.ASTfileFields
 
ASTFileFormat - Class in org.biopcd.parser
 
ASTFileFormat(int) - Constructor for class org.biopcd.parser.ASTFileFormat
 
ASTFileFormat(PCD, int) - Constructor for class org.biopcd.parser.ASTFileFormat
 
ASTFullSQLQuery - Class in org.biopcd.parser
 
ASTFullSQLQuery(int) - Constructor for class org.biopcd.parser.ASTFullSQLQuery
 
ASTFullSQLQuery(PCD, int) - Constructor for class org.biopcd.parser.ASTFullSQLQuery
 
ASTIdent - Class in org.biopcd.parser
 
ASTIdent(int) - Constructor for class org.biopcd.parser.ASTIdent
 
ASTIdent(PCD, int) - Constructor for class org.biopcd.parser.ASTIdent
 
ASTlistFields - Class in org.biopcd.parser
 
ASTlistFields(int) - Constructor for class org.biopcd.parser.ASTlistFields
 
ASTlistFields(PCD, int) - Constructor for class org.biopcd.parser.ASTlistFields
 
ASTNumber - Class in org.biopcd.parser
 
ASTNumber(int) - Constructor for class org.biopcd.parser.ASTNumber
 
ASTNumber(PCD, int) - Constructor for class org.biopcd.parser.ASTNumber
 
ASTnumberFields - Class in org.biopcd.parser
 
ASTnumberFields(int) - Constructor for class org.biopcd.parser.ASTnumberFields
 
ASTnumberFields(PCD, int) - Constructor for class org.biopcd.parser.ASTnumberFields
 
ASTPanel - Class in org.biopcd.parser
 
ASTPanel(int) - Constructor for class org.biopcd.parser.ASTPanel
 
ASTPanel(PCD, int) - Constructor for class org.biopcd.parser.ASTPanel
 
ASTParam - Class in org.biopcd.parser
 
ASTParam(int) - Constructor for class org.biopcd.parser.ASTParam
 
ASTParam(PCD, int) - Constructor for class org.biopcd.parser.ASTParam
 
ASTParseDBConnect - Class in org.biopcd.parser
 
ASTParseDBConnect(int) - Constructor for class org.biopcd.parser.ASTParseDBConnect
 
ASTParseDBConnect(PCD, int) - Constructor for class org.biopcd.parser.ASTParseDBConnect
 
ASTparseFullMenu - Class in org.biopcd.parser
 
ASTparseFullMenu(int) - Constructor for class org.biopcd.parser.ASTparseFullMenu
 
ASTparseFullMenu(PCD, int) - Constructor for class org.biopcd.parser.ASTparseFullMenu
 
ASTparseMenuItem - Class in org.biopcd.parser
 
ASTparseMenuItem(int) - Constructor for class org.biopcd.parser.ASTparseMenuItem
 
ASTparseMenuItem(PCD, int) - Constructor for class org.biopcd.parser.ASTparseMenuItem
 
ASTSystemName - Class in org.biopcd.parser
 
ASTSystemName(int) - Constructor for class org.biopcd.parser.ASTSystemName
 
ASTSystemName(PCD, int) - Constructor for class org.biopcd.parser.ASTSystemName
 
ASTTab - Class in org.biopcd.parser
 
ASTTab(int) - Constructor for class org.biopcd.parser.ASTTab
 
ASTTab(PCD, int) - Constructor for class org.biopcd.parser.ASTTab
 
ASTtempfileFields - Class in org.biopcd.parser
 
ASTtempfileFields(int) - Constructor for class org.biopcd.parser.ASTtempfileFields
 
ASTtempfileFields(PCD, int) - Constructor for class org.biopcd.parser.ASTtempfileFields
 
ASTText - Class in org.biopcd.parser
 
ASTText(int) - Constructor for class org.biopcd.parser.ASTText
 
ASTText(PCD, int) - Constructor for class org.biopcd.parser.ASTText
 
ASTtextAreaFields - Class in org.biopcd.parser
 
ASTtextAreaFields(int) - Constructor for class org.biopcd.parser.ASTtextAreaFields
 
ASTtextAreaFields(PCD, int) - Constructor for class org.biopcd.parser.ASTtextAreaFields
 
ASTtextFields - Class in org.biopcd.parser
 
ASTtextFields(int) - Constructor for class org.biopcd.parser.ASTtextFields
 
ASTtextFields(PCD, int) - Constructor for class org.biopcd.parser.ASTtextFields
 

B

backup(int) - Method in class org.biopcd.parser.SimpleCharStream
Backup a number of characters.
beginColumn - Variable in class org.biopcd.parser.Token
The column number of the first character of this Token.
beginLine - Variable in class org.biopcd.parser.Token
The line number of the first character of this Token.
BeginToken() - Method in class org.biopcd.parser.SimpleCharStream
Start.
BLANK_STRING_ARRAY - Static variable in class org.biopcd.widgets.ListWidget
This array is used for the template toArray method for lists i.e.
Body(int, PCDIO) - Method in class org.biopcd.parser.PCD
Parses PCD menu item content
Bool() - Method in class org.biopcd.parser.PCD
Parses a boolean token into a java boolean
bufcolumn - Variable in class org.biopcd.parser.SimpleCharStream
 
buffer - Variable in class org.biopcd.parser.SimpleCharStream
 
bufline - Variable in class org.biopcd.parser.SimpleCharStream
 
bufpos - Variable in class org.biopcd.parser.SimpleCharStream
Position in buffer.
buttonFields(int, String) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any button field

C

children - Variable in class org.biopcd.parser.SimpleNode
 
childrenAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.SimpleNode
Accept the visitor.
choice_list - Variable in class org.biopcd.widgets.ChoiceList
The list containing the data.
ChoiceList - Class in org.biopcd.widgets
A wrapper class used to abstract choice lists within command windows.
ChoiceList(String) - Constructor for class org.biopcd.widgets.ChoiceList
Creates a new instance of a choice list widget (this specific constructor is used by the PCD editor ONLY!).
ChoiceList(String, String, PCDSQL, int) - Constructor for class org.biopcd.widgets.ChoiceList
Creates a new instance of choice list widget.
ChoiceList(String, String, String[], String[], int) - Constructor for class org.biopcd.widgets.ChoiceList
Creates a new instance of ChoiceList (represents "choice_list" in GDE menu files).
Chooser - Class in org.biopcd.widgets
Wrapper class for a group of radiobuttons.
Chooser(String) - Constructor for class org.biopcd.widgets.Chooser
Creates a new instance of a chooser widget (used by PCD edit ONLY!).
Chooser(String, String, PCDSQL, int) - Constructor for class org.biopcd.widgets.Chooser
Creates a new instance of chooser widget.
Chooser(String, String, String[], String[], int) - Constructor for class org.biopcd.widgets.Chooser
Creates a new instance of a chooser widget.
clearNodeScope(Node) - Method in class org.biopcd.parser.JJTPCDState
 
close() - Method in class org.biopcd.parser.RunWindow
Action for command buttons to close the window.
close() - Method in class org.biopcd.sql.JDBCDBConnection
Close the database connection represented by this object.
close() - Method in interface org.biopcd.widgets.CloseableWindow
Action for command buttons to close the window.
close - Variable in class org.biopcd.widgets.CommandButton
Whether the button closes the main window when clicked.
close() - Method in class org.biopcd.widgets.WidgetInstance
Notifies the variable that the program has now completed successfully.
CloseableWindow - Interface in org.biopcd.widgets
This class provides a common interface for all RunnableWindows (and other windows) which may be closed.
closeNodeScope(Node, int) - Method in class org.biopcd.parser.JJTPCDState
 
closeNodeScope(Node, boolean) - Method in class org.biopcd.parser.JJTPCDState
 
cnames - Variable in class org.biopcd.widgets.ListWidget
The list of choice names
COEL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
column - Variable in class org.biopcd.parser.SimpleCharStream
 
combobox - Variable in class org.biopcd.widgets.ComboBoxWidget
The combo box object to display
COMBOBOX_UI - Variable in class org.biopcd.widgets.ComboBoxWidget
The UI to enable scrolling of the JComboBox.
ComboBoxWidget - Class in org.biopcd.widgets
A wrapper class used to abstract combo boxes within command windows.
ComboBoxWidget(String) - Constructor for class org.biopcd.widgets.ComboBoxWidget
Creates a new instance of a combo box widget (this specific constructor is used by the PCD editor ONLY!).
ComboBoxWidget(String, String, PCDSQL, int) - Constructor for class org.biopcd.widgets.ComboBoxWidget
Creates a new instance of combo box widget.
ComboBoxWidget(String, String, String[], String[], int) - Constructor for class org.biopcd.widgets.ComboBoxWidget
Creates a new instance of a combo box parameter widget (represents "choice_list" in GDE menu files).
COMMA - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
command - Variable in class org.biopcd.widgets.CommandButton
The command to run when the button is clicked.
CommandButton - Class in org.biopcd.widgets
Creates a JButton, which when clicked runs internal API functions or external commands
CommandButton(String) - Constructor for class org.biopcd.widgets.CommandButton
Creates a new instance of a choice list widget (this specific constructor is used by the PCD editor ONLY!).
CommandButton(String, Map<String, Widget>, String, String, boolean) - Constructor for class org.biopcd.widgets.CommandButton
Creates a new instance of CommandButton
CommandThread - Class in org.biopcd.parser
Class used for making abstract actions which launch threads.
CommandThread(String) - Constructor for class org.biopcd.parser.CommandThread
Creates a new instance of CommandThread.
CommandThread(String, Map<String, Widget>) - Constructor for class org.biopcd.parser.CommandThread
Creates a new instance of CommandThread.
COMMENT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
connect() - Method in class org.biopcd.sql.JDBCDBConnection
Connect to the database.
Content(int, Map<String, Widget>, PCDIO) - Method in class org.biopcd.parser.PCD
Parses PCD file content
copyInclude(String, String, BufferedWriter) - Static method in class org.biopcd.parser.PreProcess
Parses out the name of an include file from an @include directive, and writes the contents of that file to the output blmenu file.
createTransferable(JComponent) - Method in class org.biopcd.widgets.WidgetTransferHandler
This creates the Transferable object.
curChar - Variable in class org.biopcd.parser.PCDTokenManager
 
CURRENT_ARCH - Static variable in class org.biopcd.parser.PCD
Stores the current machine architecture
CURRENT_OS - Static variable in class org.biopcd.parser.PCD
Stores the current operating system
currentToken - Variable in exception org.biopcd.parser.ParseException
This is the last token that has been consumed successfully.

D

DATA - Static variable in interface org.biopcd.parser.PCDConstants
Lexical state.
debug - Static variable in class org.biopcd.parser.PCD
Whether to operate in debug mode
debugStream - Variable in class org.biopcd.parser.PCDTokenManager
Debug output.
Decimal() - Method in class org.biopcd.parser.PCD
Parses a decimal number from a PCD file into a Java double
DECIMAL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
decimalFields(int, String) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any decimal field
DEFAULT - Static variable in interface org.biopcd.parser.PCDConstants
Lexical state.
DEFAULT_BUFF_SIZE - Static variable in class org.biopcd.parser.StreamCopier
The default buffer size for copying streams
detectARCH() - Static method in enum org.biopcd.parser.PCD.ARCH
Detects the current system architecture Check out: http://lopica.sourceforge.net/os.html
detectOS() - Static method in enum org.biopcd.parser.PCD.OS
Detects the current operating system Check out: http://lopica.sourceforge.net/os.html
DIGITS - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
dir - Variable in class org.biopcd.parser.PCDObject
The parent directory that the menu item was read from (optional)
DirectoryChooser - Class in org.biopcd.widgets
A wrapper class used for directory selection within command windows.
DirectoryChooser(String) - Constructor for class org.biopcd.widgets.DirectoryChooser
Creates a new instance of a directory chooser widget (this specific constructor is used by the PCD editor ONLY!).
DirectoryChooser(String, String, String) - Constructor for class org.biopcd.widgets.DirectoryChooser
Creates a new instance of a file chooser widget.
dirFields(int, String) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any directory chooser
disable_tracing() - Method in class org.biopcd.parser.PCD
Disable tracing.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.AbstractFileChooser
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.ChoiceList
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.Chooser
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.ComboBoxWidget
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.CommandButton
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.NumberWidget
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.PanelWidget
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.TabbedWidget
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.TempFile
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.TextAreaWidget
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in class org.biopcd.widgets.TextWidget
Displays the current widget within the container 'dest'.
display(Container, CloseableWindow) - Method in interface org.biopcd.widgets.Widget
Displays the current widget within the container 'dest'.
displayEdit(JFrame) - Method in class org.biopcd.widgets.NumberWidget
Displays the current widget in an editor panel.
displayEdit(JFrame) - Method in class org.biopcd.widgets.PanelWidget
Displays the current widget in an editor panel.
displayEdit(JFrame) - Method in class org.biopcd.widgets.SimpleWidget
Displays the current widget in an editor panel.
displayEdit(JFrame) - Method in class org.biopcd.widgets.TabbedWidget
Displays the current widget in an editor panel.
displayEdit(JFrame) - Method in class org.biopcd.widgets.TempFile
Displays the current widget in an editor panel.
displayEdit(JFrame) - Method in interface org.biopcd.widgets.Widget
Displays the current widget in an editor panel.
DOLLAR - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
Done() - Method in class org.biopcd.parser.SimpleCharStream
Reset buffer when finished.
DOUBLEQ - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
dragMouseMoved(DragSourceDragEvent) - Method in class org.biopcd.widgets.WidgetTransferHandler
 
drop() - Method in class org.biopcd.widgets.WidgetGenerator
Generate a new widget to drop in the destination window.
dump(String) - Method in class org.biopcd.parser.SimpleNode
 

E

edit(Component, Container) - Method in class org.biopcd.widgets.PanelWidget
Populates a container with the component objects necessary for editing the current widget
edit(Component, Container) - Method in class org.biopcd.widgets.TabbedWidget
Populates a container with the component objects necessary for editing the current widget
editImage(JLabel, JPanel) - Static method in class org.biopcd.widgets.SimpleWidget
Utility method to generate the image object representing the current content of the widget.
editWindow(Container) - Method in class org.biopcd.widgets.CommandButton
Populates a container with the component objects necessary for editing the current widget's properties.
editWindow(Container) - Method in class org.biopcd.widgets.ListWidget
Populates a container with the component objects necessary for editing the current widget's properties.
editWindow(Container) - Method in class org.biopcd.widgets.NumberWidget
Populates a container with the component objects necessary for editing the current widget's properties.
editWindow(Container) - Method in class org.biopcd.widgets.SimpleWidget
Populates a container with the component objects necessary for editing the current widget's properties.
editWindow(Container) - Method in class org.biopcd.widgets.TempFile
Populates a container with the component objects necessary for editing the current widget's properties.
editWindow(Container) - Method in class org.biopcd.widgets.TextAreaWidget
Populates a container with the component objects necessary for editing the current widget's properties.
editWindow(Container) - Method in class org.biopcd.widgets.TextWidget
Populates a container with the component objects necessary for editing the current widget's properties.
enable_tracing() - Method in class org.biopcd.parser.PCD
Enable tracing.
endColumn - Variable in class org.biopcd.parser.Token
The column number of the last character of this Token.
endLine - Variable in class org.biopcd.parser.Token
The line number of the last character of this Token.
ENVVAR - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
EOF - Static variable in interface org.biopcd.parser.PCDConstants
End of File.
eol - Variable in exception org.biopcd.parser.ParseException
The end of line string for this machine.
EOL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
equals(Object) - Method in class org.biopcd.parser.SystemToken
Tests for equality.
exec - Variable in class org.biopcd.parser.PCDObject
If the exec parameter in a PCD file is set, this variable will also be set.
ExpandBuff(boolean) - Method in class org.biopcd.parser.SimpleCharStream
 
expectedTokenSequences - Variable in exception org.biopcd.parser.ParseException
Each entry in this array is an array of integers.

F

FileChooser - Class in org.biopcd.widgets
A wrapper class used to abstract file selection within command windows.
FileChooser(String) - Constructor for class org.biopcd.widgets.FileChooser
Creates a new instance of a file chooser widget (this specific constructor is used by the PCD editor ONLY!).
FileChooser(String, String, String) - Constructor for class org.biopcd.widgets.FileChooser
Creates a new instance of a file chooser widget.
fileFields(int, String) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any file chooser
FileFormat() - Method in class org.biopcd.parser.PCD
Parses file formats supported by BioPCD
FillBuff() - Method in class org.biopcd.parser.SimpleCharStream
 
FLAVOUR - Static variable in class org.biopcd.widgets.WidgetGenerator
The data flavour (of the widget generator) used for drag-and-drop.
FullSQLQuery() - Method in class org.biopcd.parser.PCD
Parses an SQL database production

G

generateParseException() - Method in class org.biopcd.parser.PCD
Generate ParseException.
getBeginColumn() - Method in class org.biopcd.parser.SimpleCharStream
Get token beginning column number.
getBeginLine() - Method in class org.biopcd.parser.SimpleCharStream
Get token beginning line number.
getColumn() - Method in class org.biopcd.parser.SimpleCharStream
Deprecated.
getCurrentPWD() - Static method in class org.biopcd.parser.PCD
Gets the present working directory "PWD" for all PCD widgets (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.biopcd.parser.SimpleCharStream
Get token end column number.
getEndLine() - Method in class org.biopcd.parser.SimpleCharStream
Get token end line number.
GetImage() - Method in class org.biopcd.parser.SimpleCharStream
Get token literal value.
getIndent() - Method in class org.biopcd.parser.PCDTokenManager
Returns the current indentation level
getInstance() - Method in class org.biopcd.widgets.ChoiceList
Creates a new widget instance of the widget A widget instance is an object that stores the value of a widget past after the widget has been closed.
getInstance() - Method in class org.biopcd.widgets.Chooser
Creates a new widget instance of the widget A widget instance is an object that stores the value of a widget past after the widget has been closed.
getInstance() - Method in class org.biopcd.widgets.ComboBoxWidget
Creates a new widget instance of the widget A widget instance is an object that stores the value of a widget past after the widget has been closed.
getInstance() - Method in class org.biopcd.widgets.CommandButton
Creates a new widget instance of the widget
getInstance() - Method in class org.biopcd.widgets.ListWidget
Creates a new widget instance of the widget
getInstance() - Method in class org.biopcd.widgets.NumberWidget
Creates a new widget instance of the widget A widget instance is an object that stores the value of a widget past after the widget has been closed.
getInstance() - Method in class org.biopcd.widgets.PanelWidget
Creates a new widget instance of the widget
getInstance() - Method in class org.biopcd.widgets.TabbedWidget
Creates a new widget instance of the widget
getInstance() - Method in class org.biopcd.widgets.TempFile
Creates a new widget instance of the widget
getInstance() - Method in class org.biopcd.widgets.TextAreaWidget
Creates a new widget instance of the widget A widget instance is an object that stores the value of a widget past after the widget has been closed.
getInstance() - Method in class org.biopcd.widgets.TextWidget
Creates a new widget instance of the widget.
getInstance() - Method in interface org.biopcd.widgets.Widget
Creates a new widget instance of the widget
getJFrame() - Method in class org.biopcd.parser.RunWindow
This method returns a Component object, such as a JFrame or JDialog object, which can be used as a parent window object for modal child windows.
getJFrame() - Method in interface org.biopcd.widgets.CloseableWindow
This method returns a Component object, such as a JFrame or JDialog object, which can be used as a parent window object for modal child windows.
getLine() - Method in class org.biopcd.parser.SimpleCharStream
Deprecated.
getMessage() - Method in error org.biopcd.parser.TokenMgrError
You can also modify the body of this method to customize your error messages.
getNextToken() - Method in class org.biopcd.parser.PCD
Get the next Token.
getNextToken() - Method in class org.biopcd.parser.PCD.PCDMetaTokenManager
 
getNextToken() - Method in class org.biopcd.parser.PCDTokenManager
Get the next Token.
getSourceActions(JComponent) - Method in class org.biopcd.widgets.WidgetTransferHandler
This is queried to see whether the component can be copied, moved, both or neither.
GetSuffix(int) - Method in class org.biopcd.parser.SimpleCharStream
Get the suffix.
getTabSize(int) - Method in class org.biopcd.parser.SimpleCharStream
 
getToken(int) - Method in class org.biopcd.parser.PCD
Get the specific Token.
getTransferData(DataFlavor) - Method in class org.biopcd.widgets.WidgetGenerator
One of three methods defined by the Transferable interface.
getTransferDataFlavors() - Method in class org.biopcd.widgets.WidgetGenerator
One of three methods defined by the Transferable interface.
getValue() - Method in class org.biopcd.parser.Token
An optional attribute value of the Token.
getValue() - Method in class org.biopcd.widgets.WidgetInstance
Returns the value stored by the WidgetInstance object.

I

icon - Variable in class org.biopcd.parser.PCDObject
The menu item icon for the current PCD file program
ID - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
id - Variable in class org.biopcd.parser.SimpleNode
 
Ident() - Method in class org.biopcd.parser.PCD
Parses an identifier token from a PCD file into a Java String
image - Variable in class org.biopcd.parser.Token
The string image of the token.
inBuf - Variable in class org.biopcd.parser.SimpleCharStream
 
includePCD(File) - Static method in class org.biopcd.parser.PreProcess
Inserts PCD code from a file into the blmenu.
INDENT_SIZE - Static variable in class org.biopcd.parser.PCDTokenManager
Used to store the size of an indent in spaces This is necessary for calculations within the Java program
index - Variable in class org.biopcd.widgets.ListWidget
Stores the current value selected by the chooser.
input_stream - Variable in class org.biopcd.parser.PCDTokenManager
 
inputStream - Variable in class org.biopcd.parser.SimpleCharStream
 
isDataFlavorSupported(DataFlavor) - Method in class org.biopcd.widgets.WidgetGenerator
One of three methods defined by the Transferable interface.
isSystemSupported() - Method in class org.biopcd.parser.PCDObject
Calculates whether this PCD menu is supported on the current system-architecture configuration.
isUNIX() - Method in enum org.biopcd.parser.PCD.OS
Returns true is the current operating system is UNIX-based.
isWindows() - Method in enum org.biopcd.parser.PCD.OS
Returns true is the current operating system is Windows-based.

J

JDBCDBConnection - Class in org.biopcd.sql
(EXPERIMENTAL!) Stores PCD connection data.
JDBCDBConnection(String, String, boolean) - Constructor for class org.biopcd.sql.JDBCDBConnection
Creates a new PCD SQL connection object.
JDBCDBConnection(String, String, String, String) - Constructor for class org.biopcd.sql.JDBCDBConnection
Creates a new PCD SQL connection object.
jj_nt - Variable in class org.biopcd.parser.PCD
Next token.
jjFillToken() - Method in class org.biopcd.parser.PCDTokenManager
 
jjnewLexState - Static variable in class org.biopcd.parser.PCDTokenManager
Lex State array.
jjstrLiteralImages - Static variable in class org.biopcd.parser.PCDTokenManager
Token literal values.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTAct
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTArchList
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTArchName
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTBody
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTBool
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTbuttonFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTContent
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTDecimal
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTdecimalFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTdirFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTfileFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTFileFormat
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTFullSQLQuery
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTIdent
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTlistFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTNumber
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTnumberFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTPanel
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTParam
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTParseDBConnect
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTparseFullMenu
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTparseMenuItem
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTSystemName
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTTab
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTtempfileFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTText
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTtextAreaFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.ASTtextFields
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in interface org.biopcd.parser.Node
Accept the visitor.
jjtAccept(PCDVisitor, Object) - Method in class org.biopcd.parser.SimpleNode
Accept the visitor.
JJTACT - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
jjtAddChild(Node, int) - Method in interface org.biopcd.parser.Node
This method tells the node to add its argument to the node's list of children.
jjtAddChild(Node, int) - Method in class org.biopcd.parser.SimpleNode
 
JJTARCHLIST - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTARCHNAME - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTBODY - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTBOOL - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTBUTTONFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
jjtClose() - Method in interface org.biopcd.parser.Node
This method is called after all the child nodes have been added.
jjtClose() - Method in class org.biopcd.parser.SimpleNode
 
JJTCONTENT - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTDECIMAL - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTDECIMALFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTDIRFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTFILEFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTFILEFORMAT - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTFULLSQLQUERY - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
jjtGetChild(int) - Method in interface org.biopcd.parser.Node
This method returns a child node.
jjtGetChild(int) - Method in class org.biopcd.parser.SimpleNode
 
jjtGetNumChildren() - Method in interface org.biopcd.parser.Node
Return the number of children the node has.
jjtGetNumChildren() - Method in class org.biopcd.parser.SimpleNode
 
jjtGetParent() - Method in interface org.biopcd.parser.Node
 
jjtGetParent() - Method in class org.biopcd.parser.SimpleNode
 
jjtGetValue() - Method in class org.biopcd.parser.SimpleNode
 
JJTIDENT - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTLISTFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
jjtNodeName - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTNUMBER - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTNUMBERFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
jjtOpen() - Method in interface org.biopcd.parser.Node
This method is called after the node has been made the current node.
jjtOpen() - Method in class org.biopcd.parser.SimpleNode
 
JJTPANEL - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTPARAM - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTPARSEDBCONNECT - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTPARSEFULLMENU - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTPARSEMENUITEM - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTPCDState - Class in org.biopcd.parser
 
JJTPCDState() - Constructor for class org.biopcd.parser.JJTPCDState
 
jjtree - Variable in class org.biopcd.parser.PCD
 
jjtSetParent(Node) - Method in interface org.biopcd.parser.Node
This pair of methods are used to inform the node of its parent.
jjtSetParent(Node) - Method in class org.biopcd.parser.SimpleNode
 
jjtSetValue(Object) - Method in class org.biopcd.parser.SimpleNode
 
JJTSYSTEMNAME - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTTAB - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTTEMPFILEFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTTEXT - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTTEXTAREAFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTTEXTFIELDS - Static variable in interface org.biopcd.parser.PCDTreeConstants
 
JJTVOID - Static variable in interface org.biopcd.parser.PCDTreeConstants
 

K

kind - Variable in class org.biopcd.parser.Token
An integer that describes the kind of this token.

L

label - Variable in class org.biopcd.widgets.CommandButton
the text to display for the button.
label - Variable in class org.biopcd.widgets.ListWidget
The label to associate with the list widget
label - Variable in class org.biopcd.widgets.NumberWidget
The label for the widget
label - Variable in class org.biopcd.widgets.TextAreaWidget
the label for the text field
label - Variable in class org.biopcd.widgets.TextWidget
the label for the text field
LexicalError(boolean, int, int, int, String, char) - Static method in error org.biopcd.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.biopcd.parser.PCDTokenManager
Lexer state names.
line - Variable in class org.biopcd.parser.SimpleCharStream
 
listFields(int, String, PCD.ListType) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any list object
ListWidget - Class in org.biopcd.widgets
A wrapper class used to abstract combo boxes and lists within command windows.
ListWidget(String) - Constructor for class org.biopcd.widgets.ListWidget
Creates a new instance of the abstract class list widget.
ListWidget(String, String, PCDSQL, int) - Constructor for class org.biopcd.widgets.ListWidget
Creates a new instance of the abstract class list widget.
ListWidget(String, String, String[], String[], int) - Constructor for class org.biopcd.widgets.ListWidget
Creates a new instance of the abstract class list widget.
loadPCDFile(File, PCDIO) - Static method in class org.biopcd.parser.PCD
Parses a PCD file into its corresponding PCDObject.
loadPCDPath(File, Map<String, Map<String, PCDObject>>, PCDIO, JFrame) - Static method in class org.biopcd.parser.PCD
Loads a path of PCD files into BioLegato
loadPCDStream(Reader, File, PCDIO) - Static method in class org.biopcd.parser.PCD
Parses a PCD input stream into its corresponding PCDObject

M

mainFrame - Variable in class org.biopcd.widgets.WidgetGenerator
The parent window containing the widget generator.
maxNextCharInd - Variable in class org.biopcd.parser.SimpleCharStream
 

N

name - Variable in class org.biopcd.parser.PCDObject
The menu item name for the current PCD file program
name - Variable in class org.biopcd.widgets.SimpleWidget
The PCD variable name (this name can be referenced in the command using the % symbol; for example, if the name value was set to "A", the value of this widget could be accessed by using %A% (lower or upper-case) within the PCD menu command string.
nameCount - Static variable in class org.biopcd.widgets.WidgetGenerator
A name counter used to help ensure that each dropped widget has a unique default name.
newToken(int, String) - Static method in class org.biopcd.parser.Token
Returns a new Token object, by default.
newToken(int) - Static method in class org.biopcd.parser.Token
 
next - Variable in class org.biopcd.parser.Token
A reference to the next regular (non-special) token from the input stream.
nl() - Method in class org.biopcd.parser.PCD
Matches new line characters including preceding whitespace
NL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
Node - Interface in org.biopcd.parser
 
nodeArity() - Method in class org.biopcd.parser.JJTPCDState
 
nodeCreated() - Method in class org.biopcd.parser.JJTPCDState
 
Number() - Method in class org.biopcd.parser.PCD
Parses a non-decimal number from a PCD file into a Java integer
NUMBER - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
numberFields(int, String) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any number field.
NumberWidget - Class in org.biopcd.widgets
Wraps component(s) for selecting numeric values.
NumberWidget(String) - Constructor for class org.biopcd.widgets.NumberWidget
Creates a new instance of a number chooser widget (this specific constructor is used by the PCD editor ONLY!).
NumberWidget(String, String, int, int, int) - Constructor for class org.biopcd.widgets.NumberWidget
Creates a new instance of a number chooser widget (or simply, number widget)

O

openNodeScope(Node) - Method in class org.biopcd.parser.JJTPCDState
 
org.biopcd.parser - package org.biopcd.parser
 
org.biopcd.sql - package org.biopcd.sql
 
org.biopcd.widgets - package org.biopcd.widgets
 
os - Variable in class org.biopcd.parser.SystemToken
The operating system represented by the system token.

P

Panel(int, Map<String, Widget>, PCDIO) - Method in class org.biopcd.parser.PCD
Generates a non-tabbed panel based on reading the panel tag from the PCD file.
PanelWidget - Class in org.biopcd.widgets
A panel widget enables a PCD menu to have panels with sub-widgets.
PanelWidget() - Constructor for class org.biopcd.widgets.PanelWidget
Creates a new empty instance of a panel widget (this specific constructor is used by the PCD editor ONLY!).
PanelWidget(Map<String, Widget>) - Constructor for class org.biopcd.widgets.PanelWidget
Creates a new instance of a panel widget
Param(int, Map<String, Widget>, PCDIO) - Method in class org.biopcd.parser.PCD
Generates a parameter component according to the PCD file's <T_PARAM> production(s).
parent - Variable in class org.biopcd.parser.SimpleNode
 
ParseDBConnect() - Method in class org.biopcd.parser.PCD
Parses an SQL database production
ParseException - Exception in org.biopcd.parser
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception org.biopcd.parser.ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception org.biopcd.parser.ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception org.biopcd.parser.ParseException
Constructor with message.
parseFullMenu(Map<String, Map<String, PCDObject>>, int, File, PCDIO, JFrame) - Method in class org.biopcd.parser.PCD
Parses a PCD menu.
parseMenuItem(int, File, PCDIO) - Method in class org.biopcd.parser.PCD
Parses a PCD menu item.
parser - Variable in class org.biopcd.parser.SimpleNode
 
PCD - Class in org.biopcd.parser
A class used to parse PCD files into BioLegato.
PCD(InputStream) - Constructor for class org.biopcd.parser.PCD
Constructor with InputStream.
PCD(InputStream, String) - Constructor for class org.biopcd.parser.PCD
Constructor with InputStream and supplied encoding
PCD(Reader) - Constructor for class org.biopcd.parser.PCD
Constructor.
PCD(PCDTokenManager) - Constructor for class org.biopcd.parser.PCD
Constructor with generated Token Manager.
PCD.ARCH - Enum in org.biopcd.parser
An enumeration representing all of the system architectures detectable by BioLegato.
PCD.ListType - Enum in org.biopcd.parser
An enumeration to store which type of list to create using list parameters.
PCD.OS - Enum in org.biopcd.parser
An enumeration representing all of the operating systems detectable by BioLegato.
PCD.PCDMetaTokenManager - Class in org.biopcd.parser
 
PCDConstants - Interface in org.biopcd.parser
Token literal values and constants.
PCDIO - Interface in org.biopcd.parser
PCD I/O Canvas.
PCDObject - Class in org.biopcd.parser
Objects representing an entire PCD menu.
PCDObject(File, String, String, String, String, Set<SystemToken>, Map<String, Widget>) - Constructor for class org.biopcd.parser.PCDObject
Creates a new PCD object.
pcdOut(int, Appendable) - Method in class org.biopcd.sql.JDBCDBConnection
Writes the BioPCD representation of the PCD SQL command
pcdOut(int, Appendable) - Method in class org.biopcd.sql.PCDSQL
Writes the BioPCD representation of the PCD SQL command
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.ChoiceList
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.Chooser
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.ComboBoxWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.CommandButton
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.DirectoryChooser
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.FileChooser
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable, String) - Method in class org.biopcd.widgets.ListWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.NumberWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.PanelWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.SimpleWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.TabbedWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.TempFile
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.TextAreaWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable, String) - Method in class org.biopcd.widgets.TextAreaWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in class org.biopcd.widgets.TextWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable, String) - Method in class org.biopcd.widgets.TextWidget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
pcdOut(int, Appendable) - Method in interface org.biopcd.widgets.Widget
Writes the BioPCD representation of the menu widget to a writer object (see BioLegato's BioPCD editor for more details)
PCDSQL - Class in org.biopcd.sql
(EXPERIMENTAL!) A class to store SQL queries read in by PCD.
PCDSQL(JDBCDBConnection, String, boolean) - Constructor for class org.biopcd.sql.PCDSQL
Creates a new PCD SQL query object.
PCDTokenManager - Class in org.biopcd.parser
Token Manager.
PCDTokenManager(SimpleCharStream) - Constructor for class org.biopcd.parser.PCDTokenManager
Constructor.
PCDTokenManager(SimpleCharStream, int) - Constructor for class org.biopcd.parser.PCDTokenManager
Constructor.
PCDTreeConstants - Interface in org.biopcd.parser
 
PCDVisitor - Interface in org.biopcd.parser
 
peekNode() - Method in class org.biopcd.parser.JJTPCDState
 
popNode() - Method in class org.biopcd.parser.JJTPCDState
 
PreProcess - Class in org.biopcd.parser
This package is for code to pre-process a blmenu file, prior to parsing PCD.
PreProcess() - Constructor for class org.biopcd.parser.PreProcess
 
prevCharIsCR - Variable in class org.biopcd.parser.SimpleCharStream
 
prevCharIsLF - Variable in class org.biopcd.parser.SimpleCharStream
 
pushNode(Node) - Method in class org.biopcd.parser.JJTPCDState
 

Q

query() - Method in class org.biopcd.sql.PCDSQL
 
quote(String) - Static method in class org.biopcd.parser.CommandThread
Quotes a string, so it will not be modified by replaceArguments

R

readChar() - Method in class org.biopcd.parser.SimpleCharStream
Read a character.
readFile(String, Reader, boolean, boolean) - Method in interface org.biopcd.parser.PCDIO
Reads data into the canvas.
recursiveDraw(Component, Graphics) - Static method in class org.biopcd.widgets.SimpleWidget
Utility method to recursively draw every subcomponent in a Component object onto a graphics object.
ReInit(InputStream) - Method in class org.biopcd.parser.PCD
Reinitialise.
ReInit(InputStream, String) - Method in class org.biopcd.parser.PCD
Reinitialise.
ReInit(Reader) - Method in class org.biopcd.parser.PCD
Reinitialise.
ReInit(PCDTokenManager) - Method in class org.biopcd.parser.PCD
Reinitialise.
ReInit(SimpleCharStream) - Method in class org.biopcd.parser.PCDTokenManager
Reinitialise parser.
ReInit(SimpleCharStream, int) - Method in class org.biopcd.parser.PCDTokenManager
Reinitialise parser.
ReInit(Reader, int, int, int) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(Reader, int, int) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(Reader) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int, int) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, String) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int) - Method in class org.biopcd.parser.SimpleCharStream
Reinitialise.
replaceArguments(String, Map<String, WidgetInstance>) - Method in class org.biopcd.parser.CommandThread
Replaces the variables in the command string with their corresponding values.
reset() - Method in class org.biopcd.parser.JJTPCDState
 
rootNode() - Method in class org.biopcd.parser.JJTPCDState
 
run() - Method in class org.biopcd.parser.CommandThread
Used for running the command.
run() - Method in class org.biopcd.parser.StreamCopier
This run method does the copying of the source stream to the destination.
RunWindow - Class in org.biopcd.parser
The run window is used within the menu system to display options for running programs
RunWindow(String, Map<String, Widget>, JFrame, Image) - Constructor for class org.biopcd.parser.RunWindow
Creates a new instance of RunWindow
runWindow - Variable in class org.biopcd.parser.RunWindow
The current window

S

setCurrentPWD(File) - Static method in class org.biopcd.parser.PCD
Sets the present working directory "PWD" for all PCD widgets (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.biopcd.parser.PCDTokenManager
Set debug output.
setTabSize(int) - Method in class org.biopcd.parser.SimpleCharStream
 
setValue(String) - Method in class org.biopcd.widgets.ChoiceList
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.Chooser
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.ComboBoxWidget
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.CommandButton
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.ListWidget
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.NumberWidget
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.PanelWidget
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.TabbedWidget
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.TempFile
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.TextAreaWidget
Changes the current value for the widget.
setValue(String) - Method in class org.biopcd.widgets.TextWidget
Changes the current value for the widget.
setValue(String) - Method in interface org.biopcd.widgets.Widget
Changes the current value for the widget.
shellCommand(String, String) - Static method in class org.biopcd.parser.CommandThread
Runs simple shell commands.
SIGN - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
SimpleCharStream - Class in org.biopcd.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.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(Reader) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream) - Constructor for class org.biopcd.parser.SimpleCharStream
Constructor.
SimpleNode - Class in org.biopcd.parser
 
SimpleNode(int) - Constructor for class org.biopcd.parser.SimpleNode
 
SimpleNode(PCD, int) - Constructor for class org.biopcd.parser.SimpleNode
 
SimpleWidget - Class in org.biopcd.widgets
An abstract class to relate widget variables and invisible variables (such as temporary files).
SimpleWidget(String) - Constructor for class org.biopcd.widgets.SimpleWidget
Creates a new instance of the abstract class SimpleWidget
SP - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
specialToken - Variable in class org.biopcd.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.biopcd.widgets.NumberWidget
Handles synchronization between the slider and the spinner.
staticFlag - Static variable in class org.biopcd.parser.SimpleCharStream
Whether parser is static.
StreamCopier - Class in org.biopcd.parser
Stream copier copies the contents of one stream to another.
StreamCopier(int, InputStream, OutputStream) - Constructor for class org.biopcd.parser.StreamCopier
Creates a new instance of the stream copier object
strindent(String, int) - Static method in class org.biopcd.parser.PreProcess
This method indents a string with blanks.
substituteEnvVars(String) - Static method in class org.biopcd.parser.PreProcess
Substitute environment variables in file paths.
substituteEnvVars(String, Map<String, ?>) - Static method in class org.biopcd.parser.PreProcess
Handle "hello ${var}", "${var:default}", find var in replaceMap replace value.
SwitchTo(int) - Method in class org.biopcd.parser.PCDTokenManager
Switch to specified lex state.
SystemName() - Method in class org.biopcd.parser.PCD
Parses a list of supported operating systems in a PCD file
systems - Variable in class org.biopcd.parser.PCDObject
Stores which systems the current PCD file is supported on
SystemToken - Class in org.biopcd.parser
Tokenizes operating system and architecture types for comparison.
SystemToken(SystemToken.OS, Set<SystemToken.ARCH>) - Constructor for class org.biopcd.parser.SystemToken
Creates a new operating system/architectures token.
SystemToken.ARCH - Enum in org.biopcd.parser
Enumeration to represent all of the system architectures selectable by PCD
SystemToken.OS - Enum in org.biopcd.parser
Enumeration to represent all of the operating systems selectable by PCD

T

T_ACT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_ALL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_AMD64 - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_AND - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_BUTTON - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CANVAS - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CHECK - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CHOICES - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CHOOSER - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CLOSE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CMDNAME - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_COMBOBOX - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CONTENT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_CSV - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_DATABASE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_DECIMAL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_DEFAULT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_DIR - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_DIRECTION - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_EXEC - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_FALSE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_FASTA - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_FILE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_FLAT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_FORMAT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_GDE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_GENBANK - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_HSQLDB - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_ICON - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_IF - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_IN - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_ITEM - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_JDBC - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_LABEL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_LINUX - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_LIST - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_LOGIN - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_MASK - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_MAX - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_MENU - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_MIN - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_MYSQL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_NUMBER - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_OR - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_OSX - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_OUT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_OVERWRITE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_PANEL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_PARAM - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_PROMPT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_QUERY - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_RAW - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_SAVE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_SELECTION - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_SHELL - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_SOLARIS - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_SPARC - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_SYS - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TAB - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TABSET - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TEMPFILE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TEXT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TEXTAREA - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_THEN - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TIP - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TRUE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TSV - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_TYPE - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_UNIX - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_WINDOWS - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_X86 - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
T_XOR - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
Tab(int, Map<String, Widget>, PCDIO) - Method in class org.biopcd.parser.PCD
Generates a tabbed pane based on reading the tab tag from the PCD file.
TAB - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
TabbedWidget - Class in org.biopcd.widgets
A tabbed widget enables a PCD menu to have tabs with sub-widgets.
TabbedWidget() - Constructor for class org.biopcd.widgets.TabbedWidget
Creates a new instance of a tabbed widget
tabSize - Variable in class org.biopcd.parser.SimpleCharStream
 
TempFile - Class in org.biopcd.widgets
Stores information about the file fields used by the command
TempFile(String) - Constructor for class org.biopcd.widgets.TempFile
Creates a new instance of a text widget (this specific constructor is used by the PCD editor ONLY!).
TempFile(String, PCDIO, boolean, boolean, boolean, boolean, String, boolean) - Constructor for class org.biopcd.widgets.TempFile
Creates a new instance of temporary file widgets.
tempfileFields(int, String, PCDIO) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any temporary file field
testIndent(int) - Method in class org.biopcd.parser.PCD
Tests indentation (NOTE: this calls the token manager)
Text() - Method in class org.biopcd.parser.PCD
Parses a text token from a PCD file into a Java String.
TEXT - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
textarea - Variable in class org.biopcd.widgets.TextAreaWidget
The text field for obtaining the data
textAreaFields(int, String) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any textarea
TextAreaWidget - Class in org.biopcd.widgets
A wrapper class used to abstract textareas within command windows.
TextAreaWidget(String) - Constructor for class org.biopcd.widgets.TextAreaWidget
Creates a new instance of a text widget (this specific constructor is used by the PCD editor ONLY!).
TextAreaWidget(String, String, String, boolean) - Constructor for class org.biopcd.widgets.TextAreaWidget
Creates a new instance of a text widget.
textfield - Variable in class org.biopcd.widgets.TextWidget
The text field for obtaining the data
textFields(int, String) - Method in class org.biopcd.parser.PCD
Parses all of the fields that should be part of any text field
textString(String) - Static method in class org.biopcd.parser.PCD
Parses a text string and converts environment variables to their corresponding values (e.g.
TextWidget - Class in org.biopcd.widgets
A wrapper class used to abstract text fields within command windows.
TextWidget(String) - Constructor for class org.biopcd.widgets.TextWidget
Creates a new instance of a text widget (this specific constructor is used by the PCD editor ONLY!).
TextWidget(String, String, String) - Constructor for class org.biopcd.widgets.TextWidget
Creates a new instance of a text widget.
token - Variable in class org.biopcd.parser.PCD
Current token.
Token - Class in org.biopcd.parser
Describes the input token stream.
Token() - Constructor for class org.biopcd.parser.Token
No-argument constructor
Token(int) - Constructor for class org.biopcd.parser.Token
Constructs a new token for the specified Image.
Token(int, String) - Constructor for class org.biopcd.parser.Token
Constructs a new token for the specified Image and Kind.
token_source - Variable in class org.biopcd.parser.PCD
Generated Token Manager.
tokenImage - Variable in exception org.biopcd.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.biopcd.parser.PCDConstants
Literal token values.
TokenMgrError - Error in org.biopcd.parser
Token Manager Error.
TokenMgrError() - Constructor for error org.biopcd.parser.TokenMgrError
No arg constructor.
TokenMgrError(String, int) - Constructor for error org.biopcd.parser.TokenMgrError
Constructor with message and reason.
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.biopcd.parser.TokenMgrError
Full Constructor.
tooltip - Variable in class org.biopcd.parser.PCDObject
The menu item tooltip text for the current PCD file program
toString() - Method in class org.biopcd.parser.SimpleNode
 
toString(String) - Method in class org.biopcd.parser.SimpleNode
 
toString() - Method in class org.biopcd.parser.Token
Returns the image.

U

unquote(String) - Static method in class org.biopcd.parser.CommandThread
Removes quotations added to a string by the 'quote' method
UpdateLineColumn(char) - Method in class org.biopcd.parser.SimpleCharStream
 

V

value - Variable in class org.biopcd.parser.SimpleNode
 
value - Variable in class org.biopcd.widgets.TextAreaWidget
the default value for the text field
value - Variable in class org.biopcd.widgets.TextWidget
the default value for the text field
valueOf(String) - Static method in enum org.biopcd.parser.PCD.ARCH
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopcd.parser.PCD.ListType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopcd.parser.PCD.OS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopcd.parser.SystemToken.ARCH
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopcd.parser.SystemToken.OS
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biopcd.parser.PCD.ARCH
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopcd.parser.PCD.ListType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopcd.parser.PCD.OS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopcd.parser.SystemToken.ARCH
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopcd.parser.SystemToken.OS
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.biopcd.widgets.ListWidget
The list of choice values
visit(SimpleNode, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTparseFullMenu, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTparseMenuItem, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTBody, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTContent, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTTab, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTPanel, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTAct, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTParam, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTbuttonFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTlistFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTtextFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTtextAreaFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTnumberFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTdecimalFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTfileFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTdirFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTtempfileFields, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTFileFormat, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTSystemName, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTArchList, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTArchName, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTParseDBConnect, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTFullSQLQuery, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTIdent, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTText, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTDecimal, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTNumber, Object) - Method in interface org.biopcd.parser.PCDVisitor
 
visit(ASTBool, Object) - Method in interface org.biopcd.parser.PCDVisitor
 

W

wclass - Variable in class org.biopcd.widgets.WidgetGenerator
The class the widget generator will generate new instances of when dropped.
Widget - Interface in org.biopcd.widgets
An interface to relate widget variables and invisible variables (such as temporary files).
WIDGET_ICON - Static variable in class org.biopcd.widgets.ChoiceList
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.Chooser
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.ComboBoxWidget
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.CommandButton
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.DirectoryChooser
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.FileChooser
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.NumberWidget
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.PanelWidget
The icon for the widget.
WIDGET_ICON - Static variable in class org.biopcd.widgets.TabbedWidget
The icon for the widget.
WIDGET_ICON - Static variable in class org.biopcd.widgets.TempFile
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.TextAreaWidget
The icon for the widget
WIDGET_ICON - Static variable in class org.biopcd.widgets.TextWidget
The icon for the widget
WidgetGenerator - Class in org.biopcd.widgets
Abstract interface to relate widget variables and invisible variables (such as temporary files) Acknowledgement - Bryan E.
WidgetGenerator(JFrame, Icon, String, Class) - Constructor for class org.biopcd.widgets.WidgetGenerator
Creates a new WidgetGenerator instance.
WidgetInstance - Class in org.biopcd.widgets
The corresponding widget instance, to store variable information until the current command is finished execution.
WidgetInstance(Object) - Constructor for class org.biopcd.widgets.WidgetInstance
Creates a new widget instance for storing variable information for the command (until command completion)
widgetList - Variable in class org.biopcd.parser.PCDObject
The widget list to use for running the current PCD command.
widgets - Variable in class org.biopcd.parser.RunWindow
List of widgets for the window.
widgets - Variable in class org.biopcd.widgets.CommandButton
The hash map containing all of the widgets to be used as parameters for the button.
WidgetTransferHandler - Class in org.biopcd.widgets
Widget transfer handler - used for dragging and dropping Widgets Acknowledgement - Bryan E.
WidgetTransferHandler() - Constructor for class org.biopcd.widgets.WidgetTransferHandler
Creates a new WidgetTransferHandler object.
writeFile(String, Appendable, boolean) - Method in interface org.biopcd.parser.PCDIO
Writes data out from the canvas.
WSP - Static variable in interface org.biopcd.parser.PCDConstants
RegularExpression Id.
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BioPCD parser v1.1.0 API

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