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.

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