NAME

       EMBOSS::GUI::Conf - repository for EMBOSS::GUI site-specific configuration

AUTHOR

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

SYNOPSIS

         use EMBOSS::GUI::Conf;

         $conf = EMBOSS::GUI::Conf->new();

         foreach $app ($conf->apps) {
               ($name, $doc) = @$app;
               if (!$conf->is_excluded($name)) {
                       ...
               }
         }

         foreach $group ($conf->groups) {
               $group_name = shift @$group;
               if (!conf->is_excluded($group_name) {
                       foreach $app (@$group) {
                               ($name, $doc) = @$app;
                               ...
                       }
               }
         }

DESCRIPTION

       EMBOSS::GUI::Conf contains site-specific configuration information for EMBOSS::GUI.
       Consult the source for a description of the variables that can be set.

       Public methods are described below:

       new()
           Returns a new EMBOSS::GUI::Conf object.  This method stores the EMBOSS::GUI::Conf
           package variables in the object hash, ensures that the specified output path is
           writeable and adds the EMBOSS binaries to the path.

       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.

       matrices()
           Returns a list of available alignment scoring matrices.  Each element of the list is a
           reference to an array containing the filename of the scoring matrix, suitable for use
           as the value of a matrix or matrixf argument, and a description of the matrix.

       codon_usage_tables()
           Returns a list of available codon usage tables.  Each element of the list is a
           reference to an array containing the filename of the codon usage table, suitable for
           use as the value of a codon argument, and the name of the species from which it is
           derived.

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.