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.\" ========================================================================
.\"
.IX Title "Bio::Tools::HMMER::Domain 3pm"
.TH Bio::Tools::HMMER::Domain 3pm "2019-10-29" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Tools::HMMER::Domain \- One particular domain hit from HMMER
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Read the Bio::Tools::HMMER::Results docs
.SH "DESCRIPTION"
.IX Header "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.
.PP
Don't forget this inherits off Bio::SeqFeature, so all your usual
nice start/end/score stuff is ready for use.
.SH "CONTACT"
.IX Header "CONTACT"
Ewan Birney, birney@ebi.ac.uk
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Jason Stajich, jason@bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "add_alignment_line"
.IX Subsection "add_alignment_line"
.Vb 5
\& 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\*(Aqre right. This is *not
\&nice* and not the right way to do it.  C\*(Aqest la vie.
.Ve
.SS "each_alignment_line"
.IX Subsection "each_alignment_line"
.Vb 7
\& 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
.Ve
.SS "get_nse"
.IX Subsection "get_nse"
.Vb 8
\& 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 \-)
.Ve
.SS "hmmacc"
.IX Subsection "hmmacc"
.Vb 7
\& 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    :
.Ve
.SS "hmmname"
.IX Subsection "hmmname"
.Vb 7
\& 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    :
.Ve
.SS "bits"
.IX Subsection "bits"
.Vb 6
\& Title   : bits
\& Usage   :
\& Function: backward compatibility. Same as score
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "evalue"
.IX Subsection "evalue"
.Vb 6
\& Title   : evalue
\& Usage   :
\& Function: $domain\->evalue($value);
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "seqbits"
.IX Subsection "seqbits"
.Vb 6
\& Title   : seqbits
\& Usage   :
\& Function: $domain\->seqbits($value);
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "seq_range"
.IX Subsection "seq_range"
.Vb 6
\& Title   : seq_range
\& Usage   :
\& Function: Throws an exception to catch scripts which need to upgrade
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "hmm_range"
.IX Subsection "hmm_range"
.Vb 6
\& Title   : hmm_range
\& Usage   :
\& Function: Throws an exception to catch scripts which need to upgrade
\& Example :
\& Returns :
\& Args    :
.Ve