acdcheck(1p) [debian man page]

ACDCHECK(1p)						User Contributed Perl Documentation					      ACDCHECK(1p)

NAME

       acdcheck

AUTHOR

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

SYNOPSIS

       acdcheck [ --output FORMAT ] FILE [ FILE ... ]

DESCRIPTION

       Reads one or more named input FILEs and attempts to parse them as if they were EMBOSS ACD (AJAX Command Definition) files.

OPTIONS

       --output FORMAT
	   Upon successful parsing of each ACD file, print a representation of the parse tree to standard output in the specified format.  FORMAT
	   must be one of either 'XML' or 'Perl' (case-insensitive and without the quotes.)

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.

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 52:
	   Unknown directive: =over4

       Around line 54:
	   '=item' outside of any '=over'

       Around line 60:
	   You forgot a '=back' before '=head1'

perl v5.14.2							    2005-10-27							      ACDCHECK(1p)

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)