Bio::Search::Hit hmmer3Hit
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Summary
Bio::Search::Hit::hmmer3Hit - DESCRIPTION of Object
Package variables
No package variables defined.
Inherit
Bio::Search::Hit::GenericHit
Synopsis
Give standard usage here
Description
Describe the object here
Methods
next_domainDescriptionCode
domainsDescriptionCode
bitsDescriptionCode
iterationDescriptionCode
Methods description
next_domaincode    nextTop
 Title   : next_domain 
 Usage   : my $domain = $hit->next_domain();
 Function: An alias for next_hsp(), this will return the next HSP
 Returns : Bio::Search::HSP::HSPI object
 Args    : none
domainscodeprevnextTop
 Title   : domains
 Usage   : my @domains = $hit->domains();
 Function: An alias for hsps(), this will return the full list of hsps
 Returns : array of Bio::Search::HSP::HSPI objects
 Args    : none
bitscodeprevnextTop
 Usage     : $hit_object->bits();
 Purpose   : Gets the bit score of the best HSP for the current hit.
 Example   : $bits = $hit_object->bits();
 Returns   : Integer or undef if bit score is not set
 Argument  : n/a
See Also : score()
iterationcodeprevnextTop
 Title   : iteration
 Usage   : $obj->iteration($newval)
 Function: PSI-BLAST iteration
 Returns : value of iteration
 Args    : newvalue (optional)
Methods code
next_domaindescriptionprevnextTop
sub next_domain {
shift->next_hsp
}
domainsdescriptionprevnextTop
sub domains {
shift->hsps()
}
bitsdescriptionprevnextTop
sub bits {
 return 0
}
iterationdescriptionprevnextTop
sub iteration {
 return 0
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
SupportTop
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Thomas SharptonTop
Email thomas.sharpton@gmail.com
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
 Usage   : my $obj = Bio::Search::Hit::HMMERHit->new();
 Function: Builds a new Bio::Search::Hit::HMMERHit object 
 Returns : Bio::Search::Hit::HMMERHit
 Args    : 

 Plus the Bio::Search::Hit::GenericHit inherited params
           -name         => Name of Hit (required)
           -description  => Description (optional)
           -accession    => Accession number (optional)
           -length       => Length of the Hit (optional)
           -score        => Raw Score for the Hit (optional)
           -significance => Significance value for the Hit (optional)
           -algorithm    => Algorithm used (BLASTP, FASTX, etc...)
           -hsps         => Array ref of HSPs for this Hit.