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 a lot in Pfam
Example :
Returns : A string
Args    : Optional separator 1 and separator 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    :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq