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