NAME

       EMBOSS::GUI - provide web-based access to EMBOSS

AUTHOR

       Luke McCarthy <lukem@gene.pbi.nrc.ca>

SYNOPSIS

         use EMBOSS::GUI;

         $emboss = EMBOSS::GUI->new();

         $emboss->intro_page;
         $emboss->about_page;
         $emboss->menu_page;
         $emboss->app_page;
         $emboss->help_page;
         $emboss->default_page;

DESCRIPTION

       EMBOSS::GUI provides a simple web-based interface to the EMBOSS suite of bioinformatics tools.  The
       distribution should have included a sample CGI script that wraps the module appropriately.

       Alternatively, EMBOSS::GUI can be used to gather information about the local EMBOSS installation.  Public
       methods for that purpose are described below:

       new(%args)
           Returns a new EMBOSS::GUI object.

           %args is a hash of optional named arguments.  The following arguments are %recognized:

           html => $object
               Specifies an alternative HTML renderer object to use when generating the web interface.  See
               EMBOSS::GUI::XHTML for the methods the replacement object must implement.

       go()
           Process CGI arguments and display the corresponding page.

       intro_page()
           Generates an introductory page describing EMBOSS and the GUI.

       about_page()
           Generates a page describing the local EMBOSS configuration, including the version and filesystem
           location of each perl module required by the GUI.

       menu_page()
           Generates the main menu page.

       app_page()
           Generates the application-specific input page or runs an EMBOSS application and generates the output
           page.

       help_page()
           Generates the application-specific manual page.

       output_page()
           Generates the application output page, or a placeholder page if the application is still running.

       default_page()
           Generates a default page according to the current configuration.

       frameset_page()
           Generates a page that sets up the menu and main content frames.

       apps()
           Returns a list of available EMBOSS applications.  Each element of the list is a reference to an array
           containing the name and description of an application.

       groups()
           Returns a list of application groups.  Each element of the list is a reference to an array containing
           the name of the group and a list of applications belonging to that group (each application is in turn
           a reference to an array as described in apps() above.)  Note that an individual application can
           appear in multiple groups.

       is_excluded($subject)
           Returns true if the subject is being excluded from public display, false otherwise.

           $subject is the name of an application or application group as it appears in the output from
           wossname.

       databases()
           Returns a list of available databases.  Each element of the list is the name of a database, suitable
           for use in a USA.

BUGS

       None that I know of...

COPYRIGHT

       Copyright (c) 2004 Luke McCarthy.  All rights reserved.  This program is free software.  You may copy or
       redistribute it under the same terms as Perl itself.