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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)

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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