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Bio::Tools::HMMER::SetUser Contributed Perl DocumentaBio::Tools::HMMER::Set(3)

NAME
       Bio::Tools::HMMER::Set -	Set of identical domains from HMMER matches

SYNOPSIS
	   # get a Set object probably from the	results	object
	   print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";

	   foreach $domain ( $set->each_Domain ) {
	       print "Domain start ",$domain->start," end ",$domain->end,"\n";
	   }

DESCRIPTION
       Represents a set	of HMMER domains hitting one sequence. HMMER reports
       two different scores, a per sequence total score	(and evalue) and a per
       domain score and	evalue.	This object represents a collection of the
       same domain with	the sequence bits score	and evalue. (these attributes
       are also	on the per domain scores, which	you can	get there).

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 one
       of the Bioperl mailing lists.  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
       the bugs	and their resolution.Bug reports can be	submitted via the web:

	https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney
       Email birney-at-ebi.ac.uk

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

   add_Domain
	Title	: add_Domain
	Usage	: $set->add_Domain($domain)
	Function: adds the domain to the list
	Returns	: nothing
	Args	: A Bio::Tools::HMMER::Domain object

   each_Domain
	Title	: each_Domain
	Usage	: foreach $domain ( $set->each_Domain()	)
	Function: returns an array of domain objects in	this set
	Returns	: array
	Args	: none

   name
	Title	: name
	Usage	: $obj->name($newval)
	Function:
	Example	:
	Returns	: value	of name
	Args	: newvalue (optional)

   desc
	Title	: desc
	Usage	: $obj->desc($newval)
	Function:
	Example	:
	Returns	: value	of desc
	Args	: newvalue (optional)

   accession
	Title	: accession
	Usage	: $obj->accession($newval)
	Function:
	Example	:
	Returns	: value	of accession
	Args	: newvalue (optional)

   bits
	Title	: bits
	Usage	: $obj->bits($newval)
	Function:
	Example	:
	Returns	: value	of bits
	Args	: newvalue (optional)

   evalue
	Title	: evalue
	Usage	: $obj->evalue($newval)
	Function:
	Example	:
	Returns	: value	of evalue
	Args	: newvalue (optional)

perl v5.24.1			  2017-07-08	     Bio::Tools::HMMER::Set(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney | APPENDIX

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