bionic (3) Ace::Sequence::Homol.3pm.gz

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,"\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, 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.