NAME

       Ace::Sequence::FeatureList - Lightweight Access to Features

SYNOPSIS

           # get a megabase from the middle of chromosome I
           $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                                     -db     => $db,
                                     -offset => 3_000_000,
                                     -length => 1_000_000);

           # find out what's there
           $list = $seq->feature_list;

           # Scalar context: count all the features
           $feature_count = $list->types;

           # Array context: list all the feature types
           @feature_types = $list->types;

           # Scalar context, 1 argument.  Count this type
           $gene_cnt = $list->types('Predicted_gene');
           print "There are $gene_cnt genes here.\n";

           # Array context, 1 argument.  Get list of subtypes
           @subtypes = $list->types('Predicted_gene');

           # Two arguments. Count type & subtype
           $genefinder_cnt = $list->types('Predicted_gene','genefinder');

DESCRIPTION

       Ace::Sequence::FeatureList is a small class that provides statistical information about
       sequence features.  From it you can obtain summary counts of the features and their types
       within a selected region.

OBJECT CREATION

       You will not ordinarily create an Ace::Sequence::FeatureList object directly.  Instead,
       objects will be created by calling a Ace::Sequence object's feature_list() method.  If you
       wish to create an Ace::Sequence::FeatureList object directly, please consult the source
       code for the new() method.

OBJECT METHODS

       There are only two methods in Ace::Sequence::FeatureList.

       type()
           This method has five distinct behaviors, depending on its context and the number of
           parameters.  Usage should be intuitive

            Context       Arguments       Behavior
            -------       ---------       --------

            scalar         -none-         total count of features in list
            array          -none-         list feature types (e.g. "exon")
            scalar          type          count features of this type
            array           type          list subtypes of this type
            -any-       type,subtype      count features of this type & subtype

           For example, this code fragment will count the number of exons present on the list:

             $exon_count = $list->type('exon');

           This code fragment will count the number of exons found by "genefinder":

             $predicted_exon_count = $list->type('exon','genefinder');

           This code fragment will print out all subtypes of "exon" and their counts:

             for my $subtype ($list->type('exon')) {
                 print $subtype,"\t",$list->type('exon',$subtype),"\n";
             }

       asString()
             print $list->asString;

           This dumps the list out in tab-delimited format.  The order of columns is type,
           subtype, count.

SEE ALSO

       Ace, Ace::Object, Ace::Sequence, 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.