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.\"
.IX Title "Ace::Sequence::Homol 3pm"
.TH Ace::Sequence::Homol 3pm "2021-02-20" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Ace::Sequence::Homol \- Temporary Sequence Homology Class
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    # Get all similarity features from an Ace::Sequence
\&    @homol = $seq\->features(\*(AqSimilarity\*(Aq);
\&
\&    # sort by score
\&    @sorted = sort { $a\->score <=> $b\->score } @homol;
\&
\&    # the last one has the highest score
\&    $best = $sorted[$#sorted];
\&
\&    # fetch its associated Ace::Sequence::Homol
\&    $homol = $best\->target;
\&
\&    # print out the sequence name, DNA, start and end
\&    print $homol\->name,\*(Aq \*(Aq,$homol\->start,\*(Aq\-\*(Aq,$homol\->end,"\en";
\&    print $homol\->asDNA;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fIAce::Sequence::Homol\fR is a subclass of Ace::Object (\fBnot\fR
Ace::Sequence) which is specialized for returning information about
a \s-1DNA\s0 or protein homology.  This is a temporary placeholder for a more
sophisticated homology class which will include support for
alignments.
.SH "OBJECT CREATION"
.IX Header "OBJECT CREATION"
You will not ordinarily create an \fIAce::Sequence::Homol\fR object
directly.  Instead, objects will be created in response to an \fBinfo()\fR
or \fBgroup()\fR method call on a similarity feature in an
\&\fIAce::Sequence::Feature\fR object.  If you wish to create an
\&\fIAce::Sequence::Homol\fR object directly, please consult the source
code for the \fI\f(BInew()\fI\fR method.
.SH "OBJECT METHODS"
.IX Header "OBJECT METHODS"
Most methods are inherited from \fIAce::Object\fR.  The following
methods are also supported:
.IP "\fBstart()\fR" 4
.IX Item "start()"
.Vb 1
\&  $start = $homol\->start;
.Ve
.Sp
Returns the start of the area that is similar to the
\&\fIAce::Sequence::Feature\fR from which his homology was derived.
Coordinates are relative to the target homology.
.IP "\fBend()\fR" 4
.IX Item "end()"
.Vb 1
\&  $end = $homol\->end;
.Ve
.Sp
Returns the end of the area that is similar to the
\&\fIAce::Sequence::Feature\fR from which his homology was derived.
Coordinates are relative to the target homology.
.IP "\fBasString()\fR" 4
.IX Item "asString()"
.Vb 1
\&  $label = $homol\->asString;
.Ve
.Sp
Returns a human-readable identifier describing the nature of the
feature.  The format is:
.Sp
.Vb 1
\& $name/$start\-$end
.Ve
.Sp
for example:
.Sp
.Vb 1
\& HUMGEN13/1\-67
.Ve
.Sp
This method is also called automatically when the object is treated in
a string context.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Ace, Ace::Object,
Ace::Sequence,Ace::Sequence::FeatureList,
Ace::Sequence::Feature, \s-1GFF\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@w3.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs\-mop.fr>
.PP
Copyright (c) 1999, Lincoln D. Stein
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.