EMBOSS::GUI - provide web-based access to EMBOSS
Luke McCarthy <lukem@gene.pbi.nrc.ca>
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;
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 => $object
- Specifies an alternative HTML renderer object to use when generating the
web interface. See EMBOSS::GUI::XHTML for the methods the replacement
object must implement.
- go()
- Process CGI arguments and display the corresponding page.
- intro_page()
- Generates an introductory page describing EMBOSS and the GUI.
- about_page()
- Generates a page describing the local EMBOSS configuration, including the
version and filesystem location of each perl module required by the
GUI.
- Generates the main menu page.
- app_page()
- Generates the application-specific input page or runs an EMBOSS
application and generates the output page.
- help_page()
- Generates the application-specific manual page.
- output_page()
- Generates the application output page, or a placeholder page if the
application is still running.
- default_page()
- Generates a default page according to the current configuration.
- frameset_page()
- Generates a page that sets up the menu and main content frames.
- apps()
- Returns a list of available EMBOSS applications. Each element of the list
is a reference to an array containing the name and description of an
application.
- groups()
- Returns a list of application groups. Each element of the list is a
reference to an array containing the name of the group and a list of
applications belonging to that group (each application is in turn a
reference to an array as described in apps() above.) Note that an
individual application can appear in multiple groups.
- is_excluded($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.
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.