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.

perl v5.38.2                                       2024-02-25                                   EMBOSS::GUI(3pm)