EMBOSS::GUI(3pm) User Contributed Perl Documentation EMBOSS::GUI(3pm)
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.
perl v5.14.2 2006-11-13 EMBOSS::GUI(3pm)