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Ace::Sequence::Homol.3pm
Langue: en
Version: 2001-09-17 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Ace::Sequence::Homol - Temporary Sequence Homology ClassSYNOPSIS
# 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;
DESCRIPTION
Ace::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, GFFAUTHOR
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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre