Bio::Tools::HMMER::Domain - One particular domain hit from HMMER Read the Bio::Tools::HMMER::Results docs 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. Ewan Birney, birney@ebi.ac.uk Jason Stajich, jason@bioperl.org 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 :