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Man Pages


Manual Reference Pages  -  BIO::TOOLS::HMMER::DOMAIN (3)

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NAME

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

CONTENTS

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. Youre right. This is *not
nice* and not the right way to do it.  Cest 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    :



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