Ace::Sequence::Homol(3User Contributed Perl DocumentatiAce::Sequence::Homol(3)NAMEAce::Sequence::Homol - Temporary Sequence Homology Class
SYNOPSIS
# Get all similarity features from an Ace::Sequence
@homol = $seq->features('Similarity');
# 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 $homol->name,' ',$homol->start,'-',$homol->end,"\n";
print $homol->asDNA;
DESCRIPTIONAce::Sequence::Homol is a subclass of Ace::Object (not Ace::Sequence)
which is specialized for returning information about a DNA or protein
homology. This is a temporary placeholder for a more sophisticated
homology class which will include support for alignments.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Homol object directly.
Instead, objects will be created in response to an info() or group()
method call on a similarity feature in an Ace::Sequence::Feature
object. If you wish to create an Ace::Sequence::Homol object directly,
please consult the source code for the new() method.
OBJECT METHODS
Most methods are inherited from Ace::Object. The following methods are
also supported:
start()
$start = $homol->start;
Returns the start of the area that is similar to the
Ace::Sequence::Feature from which his homology was derived.
Coordinates are relative to the target homology.
end()
$end = $homol->end;
Returns the end of the area that is similar to the
Ace::Sequence::Feature from which his homology was derived.
Coordinates are relative to the target homology.
asString()
$label = $homol->asString;
Returns a human-readable identifier describing the nature of the
feature. The format is:
$name/$start-$end
for example:
HUMGEN13/1-67
This method is also called automatically when the object is treated
in a string context.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::FeatureList,
Ace::Sequence::Feature, GFF
AUTHOR
Lincoln Stein <lstein@w3.org> with extensive help from Jean Thierry-
Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.1 2001-09-17 Ace::Sequence::Homol(3)