Bio::Tools::HMMER::Domain(3pm) User Contributed Perl Documentation Bio::Tools::HMMER::Domain(3pm)
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 :
perl v5.14.2 2012-03-02 Bio::Tools::HMMER::Domain(3pm)