ace::sequence::homol(3pm) [debian man page]

Ace::Sequence::Homol(3pm)				User Contributed Perl Documentation				 Ace::Sequence::Homol(3pm)

NAME

       Ace::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,"
";
	   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, 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 v5.14.2							    2001-09-17						 Ace::Sequence::Homol(3pm)