Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Tools::HMMER::Set.3pm

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: 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)