.\" Automatically generated by Pod::Man 4.10 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Algorithm::HMM::Hit::Domain 3pm"
.TH Algorithm::HMM::Hit::Domain 3pm "2018-11-01" "perl v5.28.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Algorithm::HMM::Hit::Domain \- Object encapsulating information about a Hidden Markov Model domain hit.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The Algorithm::HMM::Hit::Domain object encapsulates information about a domain hit in the Hidden Markov Model.  Unlike global hits which attempt to match the provided sequence against the entire model, a domain hit indicates a match against a smaller subsequence in the model.
.SH "METHODS"
.IX Header "METHODS"
.Vb 3
\&  $dhit\->pvalue()
\&  $dhit\->evalue()
\&  $dhit\->score()
.Ve
.PP
Returns the pvalue, evalue and score values respectively for the hit.
.PP
.Vb 3
\&  $dhit\->seq_from()
\&  $dhit\->seq_to()
\&  $dhit\->seq_length()
.Ve
.PP
Returns the starting and ends points in the sequence that matched the model.  seq_length returns the length of the hit.
.PP
.Vb 2
\&  $dhit\->hmm_from()
\&  $dhit\->hmm_to()
.Ve
.PP
Returns the starting and end points in the model.
.PP
.Vb 3
\&  $dhit\->parent_pvalue()
\&  $dhit\->parent_evalue()
\&  $dhit\->parent_score()
.Ve
.PP
Returns the parent pvalue, evalue and score values respectively.
.SH "AUTHOR"
.IX Header "AUTHOR"
The Algorithm::HMM package was originally written by Cory Spencer <cspencer@sfu.ca> of the Simon Fraser University Brinkman Laboratory.  It is currently maintained by Matthew Laird <matt@brinkman.mbb.sfu.ca>.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Algorithm::HMM, Algorithm::HMM::Hit::Global, Algorithm::HMM::Report