Bio::Tools::HMMER::Domain.3pm

Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::HMMER::Domain - One particular domain hit from HMMER

SYNOPSIS

Read the Bio::Tools::HMMER::Results docs

DESCRIPTION

A particular domain score. We reuse the Homol SeqFeature system here, so this inherits off Homol SeqFeature. As this code originally came from a separate project, there are some backward compatibility stuff provided to keep this working with old code.

Don't forget this inherits off Bio::SeqFeature, so all your usual nice start/end/score stuff is ready for use.

CONTACT

Ewan Birney, birney@ebi.ac.uk

CONTRIBUTORS

Jason Stajich, jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

add_alignment_line

  Title   : add_alignment_line
  Usage   : $domain->add_alignment_line($line_from_hmmer_output);
  Function: add an alignment line to this Domain object
  Returns : Nothing
  Args    : scalar
 
  Adds an alignment line, mainly for storing the HMMER alignments
 as flat text which can be reguritated. You're right. This is *not
 nice* and not the right way to do it.  C'est la vie.
 
 

each_alignment_line

  Title   : each_alignment_line
  Usage   : foreach $line ( $domain->each_alignment_line )
  Function: reguritates the alignment lines as they were fed in.
            only useful realistically for printing.
  Example :
  Returns : 
  Args    : None
 
 

get_nse

  Title   : get_nse
  Usage   : $domain->get_nse()
  Function: Provides a seqname/start-end format, useful
            for unique keys. nse stands for name-start-end
            It is used alot in Pfam
  Example :
  Returns : A string
  Args    : Optional seperator 1 and seperator 2 (default / and -)
 
 

hmmacc

  Title   : hmmacc
  Usage   : $domain->hmmacc($newacc)
  Function: set get for HMM accession number. This is placed in the homol
            feature of the HMM
  Example :
  Returns : 
  Args    :
 
 

hmmname

  Title   : hmmname
  Usage   : $domain->hmmname($newname)
  Function: set get for HMM accession number. This is placed in the homol
            feature of the HMM
  Example :
  Returns : 
  Args    :
 
 

bits

  Title   : bits
  Usage   :
  Function: backward compatibility. Same as score
  Example :
  Returns : 
  Args    :
 
 

evalue

  Title   : evalue
  Usage   :
  Function: $domain->evalue($value);
  Example :
  Returns : 
  Args    :
 
 

seqbits

  Title   : seqbits
  Usage   :
  Function: $domain->seqbits($value);
  Example :
  Returns : 
  Args    :
 
 

seq_range

  Title   : seq_range
  Usage   : 
  Function: Throws an exception to catch scripts which need to upgrade
  Example :
  Returns : 
  Args    :
 
 

hmm_range

  Title   : hmm_range
  Usage   :
  Function: Throws an exception to catch scripts which need to upgrade
  Example :
  Returns : 
  Args    :