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    :