debian man page for emboss::gui::conf

EMBOSS::GUI::Conf(3pm)					User Contributed Perl Documentation				    EMBOSS::GUI::Conf(3pm)

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 v5.14.2							    2013-09-16						    EMBOSS::GUI::Conf(3pm)