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emboss::acd(3pm) [debian man page]

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)

Check Out this Related Man Page

Bio::AlignIO::emboss(3pm)				User Contributed Perl Documentation				 Bio::AlignIO::emboss(3pm)

NAME

       Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)

SYNOPSIS

	   # do not use the object directly
	   use Bio::AlignIO;
	   # read in an alignment from the EMBOSS program water
	   my $in = Bio::AlignIO->new(-format => 'emboss',
				     -file   => 'seq.water');
	   while( my $aln = $in->next_aln ) {
	   # do something with the alignment
	   }

DESCRIPTION

       This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln()
	Function: returns the next alignment in the stream.
	Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
		   or on error
	Args	: NONE

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: writes the $aln object into the stream in emboss format
	Returns : 1 for success and 0 for error
	Args	: L<Bio::Align::AlignI> object

perl v5.14.2							    2012-03-02						 Bio::AlignIO::emboss(3pm)
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