---
name: "EMBOSS::GUI::Conf"
section: "3pm"
platform: "linux"
package: "emboss-explorer"
version: "2.2.0-12"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/EMBOSS::GUI::Conf"
---

# EMBOSS::GUI::Conf(3pm)

repository for EMBOSS::GUI site-specific configuration

## 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.