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Bio::Tools::HMMER::DomUser3Contributed Perl DocumeBio::Tools::HMMER::Domain(3)

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 v5.24.1			  2017-07-08	  Bio::Tools::HMMER::Domain(3)

NAME | SYNOPSIS | DESCRIPTION | CONTACT | CONTRIBUTORS | APPENDIX

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