---
name: "EMBOSS::GUI"
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"
---

# EMBOSS::GUI(3pm)

provide web-based access to EMBOSS

## NAME

EMBOSS::GUI - provide web-based access to EMBOSS

## AUTHOR

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

## SYNOPSIS

```
  use EMBOSS::GUI;
  $emboss = EMBOSS::GUI->new();

  $emboss->intro_page;
  $emboss->about_page;
  $emboss->menu_page;
  $emboss->app_page;
  $emboss->help_page;
  $emboss->default_page;
```

## DESCRIPTION

EMBOSS::GUI provides a simple web-based interface to the EMBOSS suite of bioinformatics tools.  The distribution should have included a sample CGI script that wraps the module appropriately.

Alternatively, EMBOSS::GUI can be used to gather information about the local EMBOSS installation.  Public methods for that purpose are described below:

- new(%args)

  Returns a new EMBOSS::GUI object.

  `%args` is a hash of optional named arguments.  The following arguments are `%recognized:`

  - html =\> $object

    Specifies an alternative HTML renderer object to use when generating the web interface.  See EMBOSS::GUI::XHTML for the methods the replacement object must implement.

- **go()**

  Process CGI arguments and display the corresponding page.

- **intro\_page()**

  Generates an introductory page describing EMBOSS and the GUI.

- **about\_page()**

  Generates a page describing the local EMBOSS configuration, including the version and filesystem location of each perl module required by the GUI.

- **menu\_page()**

  Generates the main menu page.

- **app\_page()**

  Generates the application-specific input page or runs an EMBOSS application and generates the output page.

- **help\_page()**

  Generates the application-specific manual page.

- **output\_page()**

  Generates the application output page, or a placeholder page if the application is still running.

- **default\_page()**

  Generates a default page according to the current configuration.

- **frameset\_page()**

  Generates a page that sets up the menu and main content frames.

- **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.

## 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.