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)