Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches # 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"; } 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).

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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://www.bioperl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://www.bugzilla.bioperl.org/ Email birney@sanger.ac.uk 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)