NAME
    Bio Legato - A customizable GUI for running programs

VERSION
    Version 0.7.0

SYNOPSIS
    biolegato [options] [files]

DESCRIPTION
    BioLegato is a customizable GUI for running programs.
    Its initial intent is to be a replacement for GDE; however
    with its large plugin API, it may be customized to run more
    than just CLI programs.

    With the versitility of BioLegato's plugin interface, it
    supports a wide range of file formats which may be added to
    at any time through addition of plugins.

OPTIONS
  NOTE: All command line parameters are case insensitive
        and may optionally begin with -, --, or / to prevent
        confusion with filenames

    help,h,?
        Displays usage information for BioLegato
    manpage,man
        Displays the manpage entry for BioLegato (this screen)
    optionlist
        Displays the list of options for using BioLegato
    version,v
        Displays the version information for BioLegato
    pipe,p,in
        Inserts input from standard input into the canvas
    debug
        Enables BioLegato's debug mode
    plugins
        Displays a list of loaded plugins
    properties
        Displays a list of BioLegato's properties

USAGE EXAMPLES
    biolegato

    biolegato insequence.gb

    biolegato --debug
    biolegato /debug
    biolegato -debug

    biolegato --plugins --properties --debug

    biolegato --plugins /properties -debug insequence.gb

ENVIRONMENT VARIABLES
    BioLegato searches for the following environment variables.  If they don't exist BioLegato sets them to defaults.

      Variable             Default value
        BIOLEGATO_HOME       <the path of the current working directory>

PROPERTIES
    BioLegato supports the followind properties:

      Property             Description
        debug                determines whether or not to display debug information
        plugins              sets the plugin directory
        temp                 sets the temporary files directory
        font.size            determines the default font size for objects in BioLegato
        font.type            determines the default font type for objects in BioLegato
        shell.name           determines the shell to execute
        shell.parameter      determines the parameter for directing the shell to execute a command
        pwd.properties       determines whether or not to read the properties file located in the current working directory
        user.properties      determines whether or not to read the user's propery files (located in the user's home directory
        user.plugins         determines whether or not to read the user's plugin files (located in the user's home directory
        default.canvas       determines the default canvas to show on startup
        default.fileformat   determines the default file format for open/save dialogs
        GDE.menu             determines whether or not to read the GDE menu files (backwards compatibility mode)
        GDE.help.viewer      determines which file to feed the help file to
        GDE.help.path        the location to search for the help files
        undo                 whether or not to enable undo support
        undo.size            whether or not to enable undo support

    This properties class will read properties files from the directory containing BioLegato, the user directory and finally
    the directory BioLegato was launched from.  Please note that you can disable reading of properties files
    from the user directory via. "user.properties"; likewise you can disable reading properties files in the directory BioLegato
    was launched from via. "pwd.properties"
    NOTE: for path properties BioLegato will replace all $'s with the appropriate environment variables if set.

SUPPORTED PLUGINS
    Currently BioLegato supports the following main types of Plugins:

        Canvases
           extends the class: org.biolegato.core.plugintypes.DataCanvas
        File formats
           extends the class: org.biolegato.core.plugintypes.DataFormat
        Menu types
           extends the class: org.biolegato.core.plugintypes.MenuType
        Properties
           extends the class: org.biolegato.core.plugintypes.PropertiesExtension

    For more information about plugins, please consult the BioLegato API

FILES
    biolegato
        Script to run BioLegato
    biolegato.jar
        BioLegato's core java code
    changelog.txt
        BioLegato's revision history
    plugins/GDE_Menu.jar        Provides backward compatibility with GDE menus
    plugins/GDE_anvas.jar        Provides GDE style multiple alignment canvas
    plugins/GDEFile.class        Provides internal file support for GDE files
    plugins/GDEFlatFile.class        Provides internal file support for GDE flatfiles
    plugins/GenBankFile2008.class        Provides internal file support for GenBank files (2008 standard copliant)
    plugins/FastA.class        Provides internal file support for FastA files

FILE FORMATS
    All file formats in BioLegato are supported through plugins.
    Below is a list of file formats supported by a default
    installation of BioLegato (with all standard plugins):

        BioLegato flatfiles
        FastA files
        GDE flatfiles
        GDE format files
        GenBank files (2008 standard compliant)

BUGS
    There are currently no known bugs in this version of BioLegato

    Please report all bugs to: Graham Alvare <alvare@cc.umanitoba.ca>
AUTHORS
    Dr. Brian Fristensky
    Department of Plant Science
    University of Manitoba
    Winnipeg, MB  Canada R3T 2N2

    Email: frist@cc.umanitoba.ca
    Web: http://home.cc.umanitoba.ca/~frist

    Graham Alvare
    Department of Plant Science
    University of Manitoba
    Winnipeg, MB  Canada R3T 2N2

    Email: alvare@cc.umanitoba.ca
    Web: http://home.cc.umanitoba.ca/~alvare

