Bio::Tools::HMMER::SetUser Contributed Perl DocumentaBio::Tools::HMMER::Set(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Tools::HMMER::Set(3)
