Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::GFF::Aggregator -- Aggregate GFF groups into composite features

SYNOPSIS

        use Bio::DB::GFF;

        my $agg1 = Bio::DB::GFF::Aggregator->new(-method       => 'cistron',
                                                 -main_method  => 'locus',
                                                 -sub_parts    => ['allele','variant']
                                                );

        my $agg2 = Bio::DB::GFF::Aggregator->new(-method       => 'splice_group',
                                                 -sub_parts    => 'transcript');

        my $db      = Bio::DB::GFF->new( -adaptor    => 'dbi:mysql',
                                         -aggregator => [$agg1,$agg2],
                                         -dsn        => 'dbi:mysql:elegans42',
                                        );

DESCRIPTION

       Bio::DB::GFF::Aggregator is used to aggregate GFF groups into composite features.  Each
       composite feature has a "main part", the top-level feature, and a series of zero or more
       subparts, retrieved with the sub_SeqFeature() method.  The aggregator class is designed to
       be subclassable, allowing a variety of GFF feature types to be supported.

       The base Bio::DB::GFF::Aggregator class is generic, and can be used to create specific
       instances to be passed to the -aggregator argument of Bio::DB::GFF->new() call.  The
       various subclasses of Bio::DB::GFF::Aggregator are tuned for specific common feature types
       such as clones, gapped alignments and transcripts.

       Instances of Bio::DB::GFF::Aggregator have three attributes:

       ·  method

          This is the GFF method field of the composite feature as a whole.  For example,
          "transcript" may be used for a composite feature created by aggregating individual
          intron, exon and UTR features.

       ·  main method

          Sometimes GFF groups are organized hierarchically, with one feature logically
          containing another.  For example, in the C. elegans schema, methods of type
          "Sequence:curated" correspond to regions covered by curated genes.  There can be zero
          or one main methods.

       ·  subparts

          This is a list of one or more methods that correspond to the component features of the
          aggregates.  For example, in the C. elegans database, the subparts of transcript are
          "intron", "exon" and "CDS".

       Aggregators have two main methods that can be overridden in subclasses:

       ·   disaggregate()

           This method is called by the Adaptor object prior to fetching a list of features.  The
           method is passed an associative array containing the [method,source] pairs that the
           user has requested, and it returns a list of raw features that it would like the
           adaptor to fetch.

       ·   aggregate()

           This method is called by the Adaptor object after it has fetched features.  The method
           is passed a list of raw features and is expected to add its composite features to the
           list.

       The disaggregate() and aggregate() methods provided by the base Aggregator class should be
       sufficient for many applications.  In this case, it suffices for subclasses to override
       the following methods:

       ·   method()

           Return the default method for the composite feature as a whole.

       ·   main_name()

           Return the default main method name.

       ·   part_names()

           Return a list of subpart method names.

       Provided that method() and part_names() are overridden (and optionally main_name() as
       well), then the bare name of the aggregator subclass can be passed to the -aggregator of
       Bio::DB::GFF->new().  For example, this is a small subclass that will aggregate features
       of type "allele" and "polymorphism" into an aggregate named "mutant":

         package Bio::DB::GFF::Aggregator::mutant;

         use strict;
         use Bio::DB::GFF::Aggregator;

         use base qw(Bio::DB::GFF::Aggregator);

         sub method { 'mutant' }

         sub part_names {
           return qw(allele polymorphism);
         }

         1;

       Once installed, this aggregator can be passed to Bio::DB::GFF->new() by name like so:

        my $db      = Bio::DB::GFF->new( -adaptor    => 'dbi:mysql',
                                         -aggregator => 'mutant',
                                         -dsn        => 'dbi:mysql:elegans42',
                                        );

API

       The remainder of this document describes the public and private methods implemented by
       this module.

   new
        Title   : new
        Usage   : $a = Bio::DB::GFF::Aggregator->new(@args)
        Function: create a new aggregator
        Returns : a Bio::DB::GFF::Aggregator object
        Args    : see below
        Status  : Public

       This is the constructor for Bio::DB::GFF::Aggregator.  Named arguments are as follows:

         -method           the method for the composite feature

         -main_method      the top-level raw feature, if any

         -sub_parts        the list of raw features that will form the subparts
                           of the composite feature (array reference or scalar)

   disaggregate
        Title   : disaggregate
        Usage   : $a->disaggregate($types,$factory)
        Function: disaggregate type list into components
        Returns : a true value if this aggregator should be called to reaggregate
        Args    : see below
        Status  : Public

       This method is called to disaggregate a list of types into the set of low-level features
       to be retrieved from the GFF database.  The list of types is passed as an array reference
       containing a series of [method,source] pairs.  This method synthesizes a new set of
       [method,source] pairs, and appends them to the list of requested types, changing the list
       in situ.

       Arguments:

         $types           reference to an array of [method,source] pairs

         $factory         reference to the Adaptor object that is calling
                          this method

       Note that the API allows disaggregate() to remove types from the type list.  This feature
       is probably not desirable and may be deprecated in the future.

   aggregate
        Title   : aggregate
        Usage   : $features = $a->aggregate($features,$factory)
        Function: aggregate a feature list into composite features
        Returns : an array reference containing modified features
        Args    : see below
        Status  : Public

       This method is called to aggregate a list of raw GFF features into the set of composite
       features.  The method is called an array reference to a set of Bio::DB::GFF::Feature
       objects.  It runs through the list, creating new composite features when appropriate.  The
       method result is an array reference containing the composite features.

       Arguments:

         $features        reference to an array of Bio::DB::GFF::Feature objects

         $factory         reference to the Adaptor object that is calling
                          this method

       NOTE: The reason that the function result contains the raw features as well as the
       aggregated ones is to allow queries like this one:

         @features =  $segment->features('exon','transcript:curated');

       Assuming that "transcript" is the name of an aggregated feature and that "exon" is one of
       its components, we do not want the transcript aggregator to remove features of type "exon"
       because the user asked for them explicitly.

   method
        Title   : method
        Usage   : $string = $a->method
        Function: get the method type for the composite feature
        Returns : a string
        Args    : none
        Status  : Protected

       This method is called to get the method to be assigned to the composite feature once it is
       aggregated.  It is called if the user did not explicitly supply a -method argument when
       the aggregator was created.

       This is the method that should be overridden in aggregator subclasses.

   main_name
        Title   : main_name
        Usage   : $string = $a->main_name
        Function: get the method type for the "main" component of the feature
        Returns : a string
        Args    : none
        Status  : Protected

       This method is called to get the method of the "main component" of the composite feature.
       It is called if the user did not explicitly supply a -main-method argument when the
       aggregator was created.

       This is the method that should be overridden in aggregator subclasses.

   part_names
        Title   : part_names
        Usage   : @methods = $a->part_names
        Function: get the methods for the non-main various components of the feature
        Returns : a list of strings
        Args    : none
        Status  : Protected

       This method is called to get the list of methods of the "main component" of the composite
       feature.  It is called if the user did not explicitly supply a -main-method argument when
       the aggregator was created.

       This is the method that should be overridden in aggregator subclasses.

   require_whole_object
        Title   : require_whole_object
        Usage   : $bool = $a->require_whole_object
        Function: see below
        Returns : a boolean flag
        Args    : none
        Status  : Internal

       This method returns true if the aggregator should refuse to aggregate an object unless
       both its main part and its subparts are present.

   match_sub
        Title   : match_sub
        Usage   : $coderef = $a->match_sub($factory)
        Function: generate a code reference that will match desired features
        Returns : a code reference
        Args    : see below
        Status  : Internal

       This method is used internally to generate a code sub that will quickly filter out the raw
       features that we're interested in aggregating.  The returned sub accepts a Feature and
       returns true if we should aggregate it, false otherwise.

   strict_match
        Title   : strict_match
        Usage   : $strict = $a->strict_match
        Function: generate a hashref that indicates which subfeatures
                  need to be tested strictly for matching sources before
                  aggregating
        Returns : a hash ref
        Status  : Internal

   components
        Title   : components
        Usage   : @array= $a->components([$components])
        Function: get/set stored list of parsed raw feature types
        Returns : an array in list context, an array ref in scalar context
        Args    : new arrayref of feature types
        Status  : Internal

       This method is used internally to remember the parsed list of raw features that we will
       aggregate.  The need for this subroutine is seen when a user requests a composite feature
       of type "clone:cosmid".  This generates a list of components in which the source is
       appended to the method, like "clone_left_end:cosmid" and "clone_right_end:cosmid".
       components() stores this information for later use.

   get_part_names
        Title   : get_part_names
        Usage   : @array = $a->get_part_names
        Function: get list of sub-parts for this type of feature
        Returns : an array
        Args    : none
        Status  : Internal

       This method is used internally to fetch the list of feature types that form the components
       of the composite feature.  Type names in the format "method:source" are recognized, as are
       "method" and Bio::DB::GFF::Typename objects as well.  It checks instance variables first,
       and if not defined calls the part_names() method.

   get_main_name
        Title   : get_main_name
        Usage   : $string = $a->get_main_name
        Function: get the "main" method type for this feature
        Returns : a string
        Args    : none
        Status  : Internal

       This method is used internally to fetch the type of the "main part" of the feature.  It
       checks instance variables first, and if not defined calls the main_name() method.

   get_method
        Title   : get_method
        Usage   : $string = $a->get_method
        Function: get the method type for the composite feature
        Returns : a string
        Args    : none
        Status  : Internal

       This method is used internally to fetch the type of the method that will be assigned to
       the composite feature once it is synthesized.

BUGS

       None known yet.

SEE ALSO

       Bio::DB::GFF, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone,
       Bio::DB::GFF::Aggregator::coding, Bio::DB::GFF::Aggregator::match,
       Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::transcript,
       Bio::DB::GFF::Aggregator::none

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2001 Cold Spring Harbor Laboratory.

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.