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.\" ========================================================================
.\"
.IX Title "EMBOSS::GUI::Conf 3pm"
.TH EMBOSS::GUI::Conf 3pm "2020-11-25" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
EMBOSS::GUI::Conf \- repository for EMBOSS::GUI site\-specific configuration
.SH "AUTHOR"
.IX Header "AUTHOR"
Luke McCarthy <lukem@gene.pbi.nrc.ca>
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  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;
\&                        ...
\&                }
\&        }
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
EMBOSS::GUI::Conf contains site-specific configuration information for
\&\s-1EMBOSS::GUI.\s0  Consult the source for a description of the variables that can
be set.
.PP
Public methods are described below:
.IP "\fBnew()\fR" 4
.IX Item "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 \s-1EMBOSS\s0 binaries to the path.
.IP "\fBapps()\fR" 4
.IX Item "apps()"
Returns a list of available \s-1EMBOSS\s0 applications.  Each element of the list is
a reference to an array containing the name and description of an application.
.IP "\fBgroups()\fR" 4
.IX Item "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 \fBapps()\fR above.)  Note that an individual application can appear
in multiple groups.
.IP "is_excluded($subject)" 4
.IX Item "is_excluded($subject)"
Returns true if the subject is being excluded from public display, false
otherwise.
.Sp
\&\f(CW$subject\fR is the name of an application or application group as it appears in
the output from wossname.
.IP "\fBdatabases()\fR" 4
.IX Item "databases()"
Returns a list of available databases.  Each element of the list is the name
of a database, suitable for use in a \s-1USA.\s0
.IP "\fBmatrices()\fR" 4
.IX Item "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.
.IP "\fBcodon_usage_tables()\fR" 4
.IX Item "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.
.SH "BUGS"
.IX Header "BUGS"
None that I know of.
.SH "COPYRIGHT"
.IX Header "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.