emboss::gui::conf(3pm) [debian man page]

EMBOSS::GUI::Conf(3pm)					User Contributed Perl Documentation				    EMBOSS::GUI::Conf(3pm)

NAME

       EMBOSS::GUI::Conf - repository for EMBOSS::GUI site-specific configuration

AUTHOR

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

SYNOPSIS

	 use EMBOSS::GUI::Conf;

	 $conf = EMBOSS::GUI::Conf->new();

	 foreach $app ($conf->apps) {
	       ($name, $doc) = @$app;
	       if (!$conf->is_excluded($name)) {
		       ...
	       }
	 }

	 foreach $group ($conf->groups) {
	       $group_name = shift @$group;
	       if (!conf->is_excluded($group_name) {
		       foreach $app (@$group) {
			       ($name, $doc) = @$app;
			       ...
		       }
	       }
	 }

DESCRIPTION

       EMBOSS::GUI::Conf contains site-specific configuration information for EMBOSS::GUI.  Consult the source for a description of the variables
       that can be set.

       Public methods are described below:

       new()
	   Returns a new EMBOSS::GUI::Conf object.  This method stores the EMBOSS::GUI::Conf package variables in the object hash, ensures that
	   the specified output path is writeable and adds the EMBOSS binaries to the path.

       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.

       matrices()
	   Returns a list of available alignment scoring matrices.  Each element of the list is a reference to an array containing the filename of
	   the scoring matrix, suitable for use as the value of a matrix or matrixf argument, and a description of the matrix.

       codon_usage_tables()
	   Returns a list of available codon usage tables.  Each element of the list is a reference to an array containing the filename of the
	   codon usage table, suitable for use as the value of a codon argument, and the name of the species from which it is derived.

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							    2013-09-16						    EMBOSS::GUI::Conf(3pm)

EMBOSS::ACD(3pm)					User Contributed Perl Documentation					  EMBOSS::ACD(3pm)

NAME

       EMBOSS::ACD - parse EMBOSS ACD (AJAX Command Definition) files

AUTHOR

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

SYNOPSIS

	 use EMBOSS::ACD;

	 $acd = EMBOSS::ACD->new($acdfile);

	 $application = $acd->name;

	 $description = $acd->documentation;

	 @groups = $acd->groups;

	 foreach $parameter ($acd->param) {
	       while (($attribute, $value) = each %$parameter) {
		       ...
	       }
	 }

DESCRIPTION

       EMBOSS::ACD parses EMBOSS Ajax Command Definition files and provides object-oriented access to the data contained therein.

       For a complete specification of the ACD format, see http://emboss.sourceforge.net/developers/acd

       Note that no checks are performed to ensure that the ACD file is semantically valid.  Specifically, datatypes and attributes that aren't
       defined in the specification can occur in the file and will be parsed as normal.  This is a good thing, as the module remains useful even
       if new datatypes are added by local developers or the EMBOSS crew.

       Public methods are described below:

       new($acdfile)
	   Parses the specified ACD file.  Returns a new EMBOSS::ACD object on success, and dies on failure.

	   $acdfile is the full path to a valid ACD file.

       name()
	   Returns the name of the application whose ACD file was parsed.

       documentation()
	   Returns a short description of the application whose ACD file was parsed.

       groups()
	   Returns a list of functional groups to which the application belongs.  For a list of possible groups, see
	   http://emboss.sourceforge.net/developers/acd/syntax.html#sect2214

       param($param)
	   Returns a reference to a hash describing the specified parameter.  The hash contains key-value pairs corresponding to the attributes
	   specified in the ACD file, plus the keys 'name' and 'datatype'.  The value of the 'datatype' key is the canonical name of the data
	   type, regardless of any abbreviation in the ACD file.  For a list of possible data types, see
	   http://emboss.sourceforge.net/developers/acd/syntax.html#sect23

	   If no parameter is specified, a list of all parameters is returned.	The members of the list are hash references as described above.

	   Note that, in accordance with the ACD specification, attribute names are not expanded if they are abbreviated in the ACD file.

	   $param is either undefined (see above) or the name of the desired parameter.

       canonical_datatype($datatype)
	   Returns the canonical name of the specified abbreviated datatype, or undefined if the abbreviation is ambiguous or not recognized.

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							    2005-10-27							  EMBOSS::ACD(3pm)