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Ace/Sequence/FeatureList.pm  view on Meta::CPAN

    # 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');

=head1 DESCRIPTION

I<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.

=head1 OBJECT CREATION

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

=head1 OBJECT METHODS

There are only two methods in I<Ace::Sequence::FeatureList>.

=over 4

=item 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";
  }

=item asString()

  print $list->asString;

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

=back

=head1 SEE ALSO

L<Ace>, L<Ace::Object>, L<Ace::Sequence>,
L<Ace::Sequence::Feature>, L<GFF>

=head1 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.

=cut