EMBOSS::GUI3pm

Usage

  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;

Overview

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.