org.biolegato.core.main
Class BLMain

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      org.biolegato.core.main.BLMain

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public final class BLMain
extends javax.swing.JFrame

The main program and generic function class.

This class is used to generate the main window, do all startup processing, and run the program. This class also contains most of the utility functions.

Version:

0.5.8 1-Sept-2009

Author:

Graham Alvare, Brian Fristensky

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JFrame

javax.swing.JFrame.AccessibleJFrame

Nested classes/interfaces inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

protected Sequence[]	clipboard Global clipboard used for copy, cut, and paste
static java.lang.String	CURRENT_DIR This constant is set to the path of where biolegato was run The value of this constant determined at runtime.
static java.awt.Font	DEFAULT_FONT The default font for BioLegato
static int	DOUBLE_CLICK_TIME The amount of time between clicks to be considered a double click.
protected SeqDoc	mainSeqDoc The main data container for BioLegato.
static java.lang.String	NAME This constant stores the program's name
static java.lang.String	PROGRAM_DIR This constant is set to the path of BioLegato.jar The value of this constant determined at runtime.
protected BLProperties	properties Stores the properties for BioLegato.
static long	serialVersionUID This constant is used for Serialization
static java.lang.String	VERSION This constant is used to keep track of version changes.

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

BLMain(java.lang.String[] args)
Creates a new instance of ProgramWindow.

Method Summary

void	aboutPopup() Displays an about popup for BioLegato.
void	addData(Sequence[] dataAdd) Adds the data to the canvas.
javax.swing.JMenu	addMenuHeading(int order, java.lang.String name) Adds a menu heading (JMenu) to our menu (BLMenu).
javax.swing.JMenu	addMenuHeading(java.lang.String name) Adds a menu heading (JMenu) to our menu (BLMenu).
void	addMenuItem(java.lang.String headingName, javax.swing.JMenuItem menuItem) Adds a menu item (JMenuItem) to a menu heading (JMenu) within the window (ProgramWindow)
void	addPropertiesListener(java.lang.String key, PropertiesListener listener) Adds a properties listener to the properties object.
static void	error(java.lang.String message) Sends an error message to BioLegato's standard err.
static void	error(java.lang.String message, java.lang.String location) Sends an error message to BioLegato's standard err.
Sequence[]	getAllData() Returns the complete contents of the data in the canvas.
Sequence[]	getClipboard() Obtains the current contents of the clipboard.
Sequence[]	getData() Returns the current/selected data in the canvas.
java.lang.String	getProperty(java.lang.String property) Retrieves individual settings for BioLegato.
SeqDoc	getSeqDoc() Returns the root sequence document for BioLegato.
static void	main(java.lang.String[] args) Starts up BioLegato.
static void	message(java.lang.String message) Sends a message to BioLegato's standard out.
static void	message(java.lang.String message, java.lang.String location) Sends a message to BioLegato's standard out.
static java.lang.String	readStream(java.io.BufferedReader reader) Reads the complete contents of a BufferedReader into a string.
java.lang.Process	safeExecute(java.lang.String cmd) Ensures that the command will be executed properly as a shell command
void	setClipboard(Sequence[] copy) Changes the current contents of the clipboard.
void	setProperty(java.lang.String key, java.lang.String value) Changes properties for BioLegato.
void	shellCommand(java.lang.String cmd, java.lang.String data) Runs simple shell commands.
static void	warning(java.lang.String message) Sends an warning message to BioLegato's standard err.
static void	warning(java.lang.String message, java.lang.String location) Sends an warning message to BioLegato's standard err.

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Frame

addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

properties

protected BLProperties properties

Stores the properties for BioLegato. See BLProperties for a list of properties intrinsic to BioLegato.

mainSeqDoc

protected SeqDoc mainSeqDoc

The main data container for BioLegato. This stores all data and sequences used by the program.

clipboard

protected Sequence[] clipboard

Global clipboard used for copy, cut, and paste

NAME

public static final java.lang.String NAME

This constant stores the program's name

See Also:

Constant Field Values

PROGRAM_DIR

public static final java.lang.String PROGRAM_DIR

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

CURRENT_DIR

public static final java.lang.String CURRENT_DIR

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

VERSION

public static final java.lang.String VERSION

This constant is used to keep track of version changes.

See Also:

Constant Field Values

DEFAULT_FONT

public static final java.awt.Font DEFAULT_FONT

The default font for BioLegato

DOUBLE_CLICK_TIME

public static final int DOUBLE_CLICK_TIME

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

See Also:

Constant Field Values

serialVersionUID

public static final long serialVersionUID

This constant is used for Serialization

See Also:

Constant Field Values

Constructor Detail

BLMain

public BLMain(java.lang.String[] args)

Creates a new instance of ProgramWindow.

Parameters:

args - the command line arguments for BioLegato.

Method Detail

safeExecute

public java.lang.Process safeExecute(java.lang.String cmd)

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

This function generates a command list for execution. The command list will contain the appropriate shell for the current operating system, followed by the "execution-argument", (whatever flag is required to tell the shell that the rest of the commandline should be executed by the shell), followed by the command to execute (the variable cmd)

Operating system values obtained from http://lopica.sourceforge.net/os.html

Parameters:

cmd - the command string to execute

Returns:

if successful a Process object for the executed command.

shellCommand

public void shellCommand(java.lang.String cmd,
                         java.lang.String data)

Runs simple shell commands. Reroutes all output to the console.

Parameters:

cmd - the command string to run

data - the data to use as standard input (System.in)

setProperty

public void setProperty(java.lang.String key,
                        java.lang.String value)

Changes properties for BioLegato.

Parameters:

key - the property to change.

value - the new value for the property.

getProperty

public java.lang.String getProperty(java.lang.String property)

Retrieves individual settings for BioLegato. This is used to obtain values of properties in BioLeagato

Parameters:

property - the property key to retrieve the value for

Returns:

the property value corresponding to the key parameter

setClipboard

public void setClipboard(Sequence[] copy)

Changes the current contents of the clipboard.

Parameters:

copy - the new content for the clipboard.

getClipboard

public Sequence[] getClipboard()

Obtains the current contents of the clipboard.

Returns:

the current contents of the clipboard.

getSeqDoc

public SeqDoc getSeqDoc()

Returns the root sequence document for BioLegato.

Returns:

the root sequence document.

getData

public Sequence[] getData()
                   throws javax.swing.text.BadLocationException

Returns the current/selected data in the canvas.

Returns:

the current data for usage by commands

Throws:

javax.swing.text.BadLocationException - any exceiptions related to obtaining the data

getAllData

public Sequence[] getAllData()
                      throws javax.swing.text.BadLocationException

Returns the complete contents of the data in the canvas.

Returns:

the complete contents of the data in the canvas

Throws:

javax.swing.text.BadLocationException - any location exceptions thrown by the underlying Document class

addData

public void addData(Sequence[] dataAdd)
             throws javax.swing.text.BadLocationException

Adds the data to the canvas.

Parameters:

dataAdd - the data to add to the canvas.

Throws:

javax.swing.text.BadLocationException - any exceptions thrown by the underlying document class

addMenuHeading

public javax.swing.JMenu addMenuHeading(java.lang.String name)

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

Parameters:

name - the name of the menu heading

Returns:

either the JMenu which was added or the JMenu that corresponds to the existing menu heading.

addMenuHeading

public javax.swing.JMenu addMenuHeading(int order,
                                        java.lang.String name)

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

Parameters:

order - the position to place the menu tag

name - the name of the menu heading

Returns:

either the JMenu which was added or the JMenu that corresponds to the existing menu heading.

addMenuItem

public void addMenuItem(java.lang.String headingName,
                        javax.swing.JMenuItem menuItem)

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

If the heading which was entered does not exist, this function will create it; hence why addMenuHeading returns the heading corresponding to the name entered if a menu heading with that name already exists.

Parameters:

headingName - is the name of the menu heading to add the menu item to.

menuItem - is the menu item to add to the heading.

aboutPopup

public void aboutPopup()

Displays an about popup for BioLegato.

addPropertiesListener

public void addPropertiesListener(java.lang.String key,
                                  PropertiesListener listener)

Adds a properties listener to the properties object.

Parameters:

key - the key of the properties to listen to.

listener - the listener to add to the object.

main

public static void main(java.lang.String[] args)

Starts up BioLegato.

Parameters:

args - the command line arguments.

error

public static void error(java.lang.String message)

Sends an error message to BioLegato's standard err. Alias for error(message, null);

Parameters:

message - the error message to send.

error

public static void error(java.lang.String message,
                         java.lang.String location)

Sends an error message to BioLegato's standard err.

Parameters:

message - the error message to send.

location - the location the error occurred.

warning

public static void warning(java.lang.String message)

Sends an warning message to BioLegato's standard err. Alias for warning(message, null);

Parameters:

message - the warning message to send.

warning

public static void warning(java.lang.String message,
                           java.lang.String location)

Sends an warning message to BioLegato's standard err.

Parameters:

message - the warning message to send.

location - the location the error occurred.

message

public static void message(java.lang.String message)

Sends a message to BioLegato's standard out. Alias for message(message, null);

Parameters:

message - the message to send.

message

public static void message(java.lang.String message,
                           java.lang.String location)

Sends a message to BioLegato's standard out.

Parameters:

message - the message to send.

location - the location the message was sent from.

readStream

public static java.lang.String readStream(java.io.BufferedReader reader)
                                   throws java.io.IOException

Reads the complete contents of a BufferedReader into a string.

Parameters:

reader - the BufferedReader to read.

Returns:

the contents of the BufferedReader.

Throws:

java.io.IOException - throws any exceptions from the read operation.