Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::DB::SeqFeature::Store -- Storage and retrieval of sequence annotation data

SYNOPSIS

         use Bio::DB::SeqFeature::Store;

         # Open the feature database
         my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
                                                   -dsn     => 'dbi:mysql:test',
                                                   -create  => 1 );

         # Get a feature from somewhere
         my $feature = Bio::SeqFeature::Generic->new(...);

         # Store it
         $db->store($feature) or die "Couldn't store!";

         # If absent, a primary ID is added to the feature when it is stored in the
         # database. Retrieve the primary ID
         my $id = $feature->primary_id;

         # Get the feature back out
         my $feature = $db->fetch($id);

         # .... which is identical to
         my $feature = $db->get_feature_by_primary_id($id);

         # Change the feature and update it
         $f->start(100);
         $db->store($f) or die "Couldn't update!";

         # Get all features at once
         my @features = $db->features( );

         # Retrieve multiple features by primary id
         my @features = $db->fetch_many(@list_of_ids);

         # ...by name
         @features = $db->get_features_by_name('ZK909');

         # ...by alias
         @features = $db->get_features_by_alias('sma-3');

         # ...by type
         @features = $db->get_features_by_type('gene');

         # ...by location
         @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);

         # ...by attribute
         @features = $db->get_features_by_attribute({description => 'protein kinase'})

         # ...by the GFF "Note" field
         @result_list = $db->search_notes('kinase');

         # ...by arbitrary combinations of selectors
         @features = $db->features(-name => $name,
                                   -type => $types,
                                   -seq_id => $seqid,
                                   -start  => $start,
                                   -end    => $end,
                                   -attributes => $attributes);

         # Loop through the features using an iterator
         my $iterator = $db->get_seq_stream(-name => $name,
                                            -type => $types,
                                            -seq_id => $seqid,
                                            -start  => $start,
                                            -end    => $end,
                                            -attributes => $attributes);

         while (my $feature = $iterator->next_seq) {
           # do something with the feature
         }

         # ...limiting the search to a particular region
         my $segment  = $db->segment('Chr1',5000=>6000);
         my @features = $segment->features(-type=>['mRNA','match']);

         # Getting coverage statistics across a region
         my $summary = $db->feature_summary('Chr1',10_000=>1_110_000);
         my ($bins)  = $summary->get_tag_values('coverage');
         my $first_bin = $bins->[0];

         # Getting & storing sequence information
         # Warning: this returns a string, and not a PrimarySeq object
         $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...');
         my $sequence = $db->fetch_sequence('Chr1',5000=>6000);

         # What feature types are defined in the database?
         my @types    = $db->types;

         # Create a new feature in the database
         my $feature = $db->new_feature(-primary_tag => 'mRNA',
                                        -seq_id      => 'chr3',
                                        -start      => 10000,
                                        -end        => 11000);

         # Load an entire GFF3 file, using the GFF3 loader...
         my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store    => $db,
                                                                  -verbose  => 1,
                                                                  -fast     => 1);

         $loader->load('./my_genome.gff3');

DESCRIPTION

       Bio::DB::SeqFeature::Store implements the Bio::SeqFeature::CollectionI interface to allow
       you to persistently store Bio::SeqFeatureI objects in a database and to later to retrieve
       them by a variety of searches. This module is similar to the older Bio::DB::GFF module,
       with the following differences:

       1.  No limitation on Bio::SeqFeatureI implementations

           Unlike Bio::DB::GFF, Bio::DB::SeqFeature::Store works with any Bio::SeqFeatureI
           object.

       2.  No limitation on nesting of features & subfeatures

           Bio::DB::GFF is limited to features that have at most one level of subfeature.
           Bio::DB::SeqFeature::Store can work with features that have unlimited levels of
           nesting.

       3.  No aggregators

           The aggregator architecture, which was necessary to impose order on the GFF2 files
           that Bio::DB::GFF works with, does not apply to Bio::DB::SeqFeature::Store. It is
           intended to store features that obey well-defined ontologies, such as the Sequence
           Ontology (http://song.sourceforge.net).

       4.  No relative locations

           All locations defined by this module are relative to an absolute sequence ID, unlike
           Bio::DB::GFF which allows you to define the location of one feature relative to
           another.

       We'll discuss major concepts in Bio::DB::SeqFeature::Store and then describe how to use
       the module.

   Adaptors
       Bio::DB::SeqFeature::Store is designed to work with a variety of storage back ends called
       "adaptors." Adaptors are subclasses of Bio::DB::SeqFeature::Store and provide the
       interface between the store() and fetch() methods and the physical database. Currently the
       number of adaptors is quite limited, but the number will grow soon.

       memory
           An implementation that stores all data in memory. This is useful for small data sets
           of no more than 10,000 features (more or less, depending on system memory).

       DBI::mysql
           A full-featured implementation on top of the MySQL relational database system.

       berkeleydb
           A full-feature implementation that runs on top of the BerkeleyDB database. See
           Bio::DB::SeqFeature::Store::berkeleydb.

       If you do not explicitly specify the adaptor, then DBI::mysql will be used by default.

   Serializers
       When Bio::DB::SeqFeature::Store stores a Bio::SeqFeatureI object into the database, it
       serializes it into binary or text form. When it later fetches the feature from the
       database, it unserializes it. Two serializers are available: Recent versions of

       Storable
           This is a fast binary serializer. It is available in Perl versions 5.8.7 and higher
           and is used when available.

       Data::Dumper
           This is a slow text serializer that is available in Perl 5.8.0 and higher. It is used
           when Storable is unavailable.

       If you do not specify the serializer, then Storable will be used if available; otherwise
       Data::Dumper.

   Loaders and Normalized Features
       The Bio::DB::SeqFeature::Store::GFF3Loader parses a GFF3-format file and loads the
       annotations and sequence data into the database of your choice. The script
       bp_seqfeature_load.pl (found in the scripts/Bio-SeqFeature-Store/ subdirectory) is a thin
       front end to the GFF3Loader. Other loaders may be written later.

       Although Bio::DB::SeqFeature::Store should work with any Bio::SeqFeatureI object, there
       are some disadvantages to using Bio::SeqFeature::Generic and other vanilla
       implementations. The major issue is that if two vanilla features share the same subfeature
       (e.g. two transcripts sharing an exon), the shared subfeature will be cloned when stored
       into the database.

       The special-purpose Bio::DB::SeqFeature class is able to normalize its subfeatures in the
       database, so that shared subfeatures are stored only once. This minimizes wasted storage
       space. In addition, when in-memory caching is turned on, each shared subfeature will
       usually occupy only a single memory location upon restoration.

Methods for Connecting and Initializating a Database

       ## TODO: http://iowg.brcdevel.org/gff3.html#a_fasta is a dead link

   new
        Title   : new
        Usage   : $db = Bio::DB::SeqFeature::Store->new(@options)
        Function: connect to a database
        Returns : A descendent of Bio::DB::Seqfeature::Store
        Args    : several - see below
        Status  : public

       This class method creates a new database connection. The following -name=>$value arguments
       are accepted:

        Name               Value
        ----               -----

        -adaptor           The name of the Adaptor class (default DBI::mysql)

        -serializer        The name of the serializer class (default Storable)

        -index_subfeatures Whether or not to make subfeatures searchable
                           (default false)

        -cache             Activate LRU caching feature -- size of cache

        -compress          Compresses features before storing them in database
                           using Compress::Zlib

        -create            (Re)initialize the database.

       The -index_subfeatures argument, if true, tells the module to create indexes for a feature
       and all its subfeatures (and its subfeatures' subfeatures). Indexing subfeatures means
       that you will be able to search for the gene, its mRNA subfeatures and the exons inside
       each mRNA. It also means when you search the database for all features contained within a
       particular location, you will get the gene, the mRNAs and all the exons as individual
       objects as well as subfeatures of each other. NOTE: this option is only honored when
       working with a normalized feature class such as Bio::DB::SeqFeature.

       The -cache argument, if true, tells the module to try to create a LRU (least-recently-
       used) object cache using the Tie::Cacher module. Caching will cause two objects that share
       the same primary_id to (often, but not always) share the same memory location, and may
       improve performance modestly. The argument is taken as the desired size for the cache. If
       you pass "1" as the cache value, a reasonable default cache size will be chosen. Caching
       requires the Tie::Cacher module to be installed. If the module is not installed, then
       caching will silently be disabled.

       The -compress argument, if true, will cause the feature data to be compressed before
       storing it. This will make the database somewhat smaller at the cost of decreasing
       performance.

       The -create argument, if true, will either initialize or reinitialize the database. It is
       needed the first time a database is used.

       The new() method of individual adaptors recognize additional arguments. The default
       DBI::mysql adaptor recognizes the following ones:

        Name               Value
        ----               -----

        -dsn               DBI data source (default dbi:mysql:test)

        -autoindex         A flag that controls whether or not to update
                           all search indexes whenever a feature is stored
                           or updated (default true).

        -namespace         A string that will be used to qualify each table,
                           thereby allowing you to store several independent
                           sequence feature databases in a single Mysql
                           database.

        -dumpdir           The path to a temporary directory that will be
                           used during "fast" loading. See
                           L<Bio::DB::SeqFeature::Store::GFF3Loader> for a
                           description of this. Default is the current
                           directory.

        -write             Make the database writable (implied by -create)

        -fasta             Provide an alternative DNA accessor object or path.

       By default the database will store DNA sequences internally. However, you may override
       this behavior by passing either a path to a FASTA file, or any Perl object that recognizes
       the seq($seqid,$start,$end) method. In the former case, the FASTA path will be passed to
       Bio::DB::Fasta, possibly causing an index to be constructed. Suitable examples of the
       latter type of object include the Bio::DB::Sam and Bio::DB::Sam::Fai classes.

   init_database
        Title   : init_database
        Usage   : $db->init_database([$erase_flag])
        Function: initialize a database
        Returns : true
        Args    : (optional) flag to erase current data
        Status  : public

       Call this after Bio::DB::SeqFeature::Store->new() to initialize a new database. In the
       case of a DBI database, this method installs the schema but does not create the database.
       You have to do this offline using the appropriate command-line tool. In the case of the
       "berkeleydb" adaptor, this creates an empty BTREE database.

       If there is any data already in the database, init_database() called with no arguments
       will have no effect. To permanently erase the data already there and prepare to receive a
       fresh set of data, pass a true argument.

   post_init
       This method is invoked after init_database for use by certain adaptors (currently only the
       memory adaptor) to do automatic data loading after initialization. It is passed a copy of
       the init_database() args.

   add_features
        Title   : add_features
        Usage   : $success = $db->add_features(\@features)
        Function: store one or more features into the database
        Returns : true if successful
        Args    : array reference of Bio::SeqFeatureI objects
        Status  : public

   store
        Title   : store
        Usage   : $success = $db->store(@features)
        Function: store one or more features into the database
        Returns : true if successful
        Args    : list of Bio::SeqFeatureI objects
        Status  : public

       This method stores a list of features into the database. Each feature is updated so that
       its primary_id becomes the primary ID of the serialized feature stored in the database. If
       all features were successfully stored, the method returns true. In the DBI implementation,
       the store is performed as a single transaction and the transaction is rolled back if one
       or more store operations failed.

       In most cases, you should let the database assign the primary id. If the object you store
       already has a primary_id, then the ID must adhere to the datatype expected by the adaptor:
       an integer in the case of the various DB adaptors, and a string in the case of the memory
       and berkeley adaptors.

       You can find out what the primary ID of the feature has become by calling the feature's
       primary_id() method:

         $db->store($my_feature) or die "Oh darn";
         my $id = $my_feature->primary_id;

       If the feature contains subfeatures, they will all be stored recursively. In the case of
       Bio::DB::SeqFeature and Bio::DB::SeqFeature::Store::NormalizedFeature, the subfeatures
       will be stored in a normalized way so that each subfeature appears just once in the
       database.

       Subfeatures will be indexed for separate retrieval based on the current value of
       index_subfeatures().

       If you call store() with one or more features that already have valid primary_ids, then
       any existing objects will be replaced. Note that when using normalized features such as
       Bio::DB::SeqFeature, the subfeatures are not recursively updated when you update the
       parent feature. You must manually update each subfeatures that has changed.

   store_noindex
        Title   : store_noindex
        Usage   : $success = $db->store_noindex(@features)
        Function: store one or more features into the database without indexing
        Returns : true if successful
        Args    : list of Bio::SeqFeatureI objects
        Status  : public

       This method stores a list of features into the database but does not make them searchable.
       The only way to access the features is via their primary IDs. This method is ordinarily
       only used internally to store subfeatures that are not indexed.

   no_blobs
        Title   : no_blobs
        Usage   : $db->no_blobs(1);
        Function: decide if objects should be stored in the database as blobs.
        Returns : boolean (default false)
        Args    : boolean (true to no longer store objects; when the corresponding
                  feature is retrieved it will instead be a minimal representation of
                  the object that was stored, as some simple Bio::SeqFeatureI object)
        Status  : dubious (new)

       This method saves lots of space in the database, which may in turn lead to large
       performance increases in extreme cases (over 7 million features in the db).

   new_feature
        Title   : new_feature
        Usage   : $feature = $db->new_feature(@args)
        Function: create a new Bio::DB::SeqFeature object in the database
        Returns : the new seqfeature
        Args    : see below
        Status  : public

       This method creates and stores a new Bio::SeqFeatureI object using the specialized
       Bio::DB::SeqFeature class. This class is able to store its subfeatures in a normalized
       fashion, allowing subfeatures to be shared among multiple parents (e.g. multiple exons
       shared among several mRNAs).

       The arguments are the same as for Bio::DB::SeqFeature->new(), which in turn are similar to
       Bio::SeqFeature::Generic->new() and Bio::Graphics::Feature->new(). The most important
       difference is the -index option, which controls whether the feature will be indexed for
       retrieval (default is true). Ordinarily, you would only want to turn indexing off when
       creating subfeatures, because features stored without indexes will only be reachable via
       their primary IDs or their parents.

       Arguments are as follows:

         -seq_id       the reference sequence
         -start        the start position of the feature
         -end          the stop position of the feature
         -display_name the feature name (returned by seqname)
         -primary_tag  the feature type (returned by primary_tag)
         -source       the source tag
         -score        the feature score (for GFF compatibility)
         -desc         a description of the feature
         -segments     a list of subfeatures (see Bio::Graphics::Feature)
         -subtype      the type to use when creating subfeatures
         -strand       the strand of the feature (one of -1, 0 or +1)
         -phase        the phase of the feature (0..2)
         -url          a URL to link to when rendered with Bio::Graphics
         -attributes   a hashref of tag value attributes, in which the key is the tag
                         and the value is an array reference of values
         -index        index this feature if true

       Aliases:

         -id           an alias for -display_name
         -seqname      an alias for -display_name
         -display_id   an alias for -display_name
         -name         an alias for -display_name
         -stop         an alias for end
         -type         an alias for primary_tag

       You can change the seqfeature implementation generated by new() by passing the name of the
       desired seqfeature class to $db->seqfeature_class().

   delete
        Title   : delete
        Usage   : $success = $db->delete(@features)
        Function: delete a list of feature from the database
        Returns : true if successful
        Args    : list of features
        Status  : public

       This method looks up the primary IDs from a list of features and deletes them from the
       database, returning true if all deletions are successful.

       WARNING: The current DBI::mysql implementation has some issues that need to be resolved,
       namely (1) normalized subfeatures are NOT recursively deleted; and (2) the deletions are
       not performed in a transaction.

   fetch / get_feature_by_id / get_feature_by_primary_id
        Title   : fetch
                  get_feature_by_id
                  get_feature_by_primary_id
        Usage   : $feature = $db->fetch($primary_id)
        Function: fetch a feature from the database using its primary ID
        Returns : a feature
        Args    : primary ID of desired feature
        Status  : public

       This method returns a previously-stored feature from the database using its primary ID. If
       the primary ID is invalid, it returns undef.  Use fetch_many() to rapidly retrieve
       multiple features.

   fetch_many
        Title   : fetch_many
        Usage   : @features = $db->fetch_many($primary_id,$primary_id,$primary_id...)
        Function: fetch many features from the database using their primary ID
        Returns : list of features
        Args    : a list of primary IDs or an array ref of primary IDs
        Status  : public

       Same as fetch() except that you can pass a list of primary IDs or a ref to an array of
       IDs.

   get_seq_stream
        Title   : get_seq_stream
        Usage   : $iterator = $db->get_seq_stream(@args)
        Function: return an iterator across all features in the database
        Returns : a Bio::DB::SeqFeature::Store::Iterator object
        Args    : feature filters (optional)
        Status  : public

       When called without any arguments this method will return an iterator object that will
       traverse all indexed features in the database. Call the iterator's next_seq() method to
       step through them (in no particular order):

         my $iterator = $db->get_seq_stream;
         while (my $feature = $iterator->next_seq) {
           print $feature->primary_tag,' ',$feature->display_name,"\n";
         }

       You can select a subset of features by passing a series of filter arguments. The arguments
       are identical to those accepted by $db->features().

   get_features_by_name
        Title   : get_features_by_name
        Usage   : @features = $db->get_features_by_name($name)
        Function: looks up features by their display_name
        Returns : a list of matching features
        Args    : the desired name
        Status  : public

       This method searches the display_name of all features for matches against the provided
       name. GLOB style wildcares ("*", "?") are accepted, but may be slow.

       The method returns the list of matches, which may be zero, 1 or more than one features. Be
       prepared to receive more than one result, as display names are not guaranteed to be
       unique.

       For backward compatibility with gbrowse, this method is also known as
       get_feature_by_name().

   get_feature_by_name
        Title   : get_feature_by_name
        Usage   : @features = $db->get_feature_by_name($name)
        Function: looks up features by their display_name
        Returns : a list of matching features
        Args    : the desired name
        Status  : Use get_features_by_name instead.

       This method is provided for backward compatibility with gbrowse.

   get_features_by_alias
        Title   : get_features_by_alias
        Usage   : @features = $db->get_features_by_alias($name)
        Function: looks up features by their display_name or alias
        Returns : a list of matching features
        Args    : the desired name
        Status  : public

       This method is similar to get_features_by_name() except that it will also search through
       the feature aliases.  Aliases can be created by storing features that contain one or more
       Alias tags. Wildards are accepted.

   get_features_by_type
        Title   : get_features_by_type
        Usage   : @features = $db->get_features_by_type(@types)
        Function: looks up features by their primary_tag
        Returns : a list of matching features
        Args    : list of primary tags
        Status  : public

       This method will return a list of features that have any of the primary tags given in the
       argument list. For compatibility with gbrowse and Bio::DB::GFF, types can be qualified
       using a colon:

         primary_tag:source_tag

       in which case only features that match both the primary_tag and the indicated source_tag
       will be returned. If the database was loaded from a GFF3 file, this corresponds to the
       third and second columns of the row, in that order.

       For example, given the GFF3 lines:

         ctg123 geneFinder exon 1300 1500 . + . ID=exon001
         ctg123 fgenesH    exon 1300 1520 . + . ID=exon002

       exon001 and exon002 will be returned by searching for type "exon", but only exon001 will
       be returned by searching for type "exon:fgenesH".

   get_features_by_location
        Title   : get_features_by_location
        Usage   : @features = $db->get_features_by_location(@args)
        Function: looks up features by their location
        Returns : a list of matching features
        Args    : see below
        Status  : public

       This method fetches features based on a location range lookup. You call it using a
       positional list of arguments, or a list of (-argument=>$value) pairs.

       The positional form is as follows:

        $db->get_features_by_location($seqid [[,$start,]$end])

       The $seqid is the name of the sequence on which the feature resides, and start and end are
       optional endpoints for the match. If the endpoints are missing then any feature on the
       indicated seqid is returned.

       Examples:

        get_features_by_location('chr1');      # all features on chromosome 1
        get_features_by_location('chr1',5000); # features between 5000 and the end
        get_features_by_location('chr1',5000,8000); # features between 5000 and 8000

       Location lookups are overlapping. A feature will be returned if it partially or completely
       overlaps the indicated range.

       The named argument form gives you more control:

         Argument       Value
         --------       -----

         -seq_id        The name of the sequence on which the feature resides
         -start         Start of the range
         -end           End of the range
         -strand        Strand of the feature
         -range_type    Type of range to search over

       The -strand argument, if present, can be one of "0" to find features that are on both
       strands, "+1" to find only plus strand features, and "-1" to find only minus strand
       features. Specifying a strand of undef is the same as not specifying this argument at all,
       and retrieves all features regardless of their strandedness.

       The -range_type argument, if present, can be one of "overlaps" (the default), to find
       features whose positions overlap the indicated range, "contains," to find features whose
       endpoints are completely contained within the indicated range, and "contained_in" to find
       features whose endpoints are both outside the indicated range.

   get_features_by_attribute
        Title   : get_features_by_attribute
        Usage   : @features = $db->get_features_by_attribute(@args)
        Function: looks up features by their attributes/tags
        Returns : a list of matching features
        Args    : see below
        Status  : public

       This implements a simple tag filter. Pass a list of tag names and their values. The module
       will return a list of features whose tag names and values match. Tag names are case
       insensitive. If multiple tag name/value pairs are present, they will be ANDed together. To
       match any of a list of values, use an array reference for the value.

       Examples:

        # return all features whose "function" tag is "GO:0000123"
        @features = $db->get_features_by_attribute(function => 'GO:0000123');

        # return all features whose "function" tag is "GO:0000123" or "GO:0000555"
        @features = $db->get_features_by_attribute(function => ['GO:0000123','GO:0000555']);

        # return all features whose "function" tag is "GO:0000123" or "GO:0000555"
        # and whose "confirmed" tag is 1
        @features = $db->get_features_by_attribute(function  => ['GO:0000123','GO:0000555'],
                                                   confirmed => 1);

   features
        Title   : features
        Usage   : @features = $db->features(@args)
        Function: generalized query & retrieval interface
        Returns : list of features
        Args    : see below
        Status  : Public

       This is the workhorse for feature query and retrieval. It takes a series of -name=>$value
       arguments filter arguments. Features that match all the filters are returned.

         Argument       Value
         --------       -----

        Location filters:
         -seq_id        Chromosome, contig or other DNA segment
         -seqid         Synonym for -seq_id
         -ref           Synonym for -seqid
         -start         Start of range
         -end           End of range
         -stop          Synonym for -end
         -strand        Strand
         -range_type    Type of range match ('overlaps','contains','contained_in')

        Name filters:
         -name          Name of feature (may be a glob expression)
         -aliases       If true, match aliases as well as display names
         -class         Archaic argument for backward compatibility.
                         (-class=>'Clone',-name=>'ABC123') is equivalent
                         to (-name=>'Clone:ABC123')

        Type filters:
         -types         List of feature types (array reference) or one type (scalar)
         -type          Synonym for the above
         -primary_tag   Synonym for the above

         -attributes    Hashref of attribute=>value pairs as per
                           get_features_by_attribute(). Multiple alternative values
                           can be matched by providing an array reference.
         -attribute     synonym for -attributes

       You may also provide features() with a list of scalar values (the first element of which
       must not begin with a dash), in which case it will treat the list as a feature type
       filter.

       Examples:

       All features:
        @features = $db->features( );

       All features on chromosome 1:

        @features = $db->features(-seqid=>'Chr1');

       All features on chromosome 1 between 5000 and 6000:

        @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000);

       All mRNAs on chromosome 1 between 5000 and 6000:

        @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');

       All confirmed mRNAs and repeats on chromosome 1 that overlap the range 5000..6000:

        @features = $db->features(-seqid     => 'Chr1',-start=>5000,-end=>6000,
                                  -types     => ['mRNA','repeat'],
                                  -attributes=> {confirmed=>1}
                                 );

       All confirmed mRNAs and repeats on chromosome 1 strictly contained within the range
       5000..6000:

        @features = $db->features(-seqid     => 'Chr1',-start=>5000,-end=>6000,
                                  -types     => ['mRNA','repeat'],
                                  -attributes=> {confirmed=>1}
                                  -range_type => 'contained_in',
                                 );

       All genes and repeats:

        @features = $db->features('gene','repeat_region');

   get_all_features
        Title   : get_all_features
        Usage   : @features = $db->get_all_features()
        Function: get all feature in the database
        Returns : list of features
        Args    : none
        Status  : Public

   seq_ids
        Title   : seq_ids
        Usage   : @ids = $db->seq_ids()
        Function: Return all sequence IDs contained in database
        Returns : list of sequence Ids
        Args    : none
        Status  : public

   search_attributes
        Title   : search_attributes
        Usage   : @result_list = $db->search_attributes("text search string",[$tag1,$tag2...],$limit)
        Function: Search attributes for keywords occurring in a text string
        Returns : array of results
        Args    : full text search string, array ref of attribute names, and an optional feature limit
        Status  : public

       Given a search string, this method performs a full-text search of the specified attributes
       and returns an array of results.  You may pass a scalar attribute name to search the
       values of one attribute (e.g. "Note") or you may pass an array reference to search inside
       multiple attributes (['Note','Alias','Parent']).Each row of the returned array is a
       arrayref containing the following fields:

         column 1     The display name of the feature
         column 2     The text of the note
         column 3     A relevance score.
         column 4     The feature type
         column 5     The unique ID of the feature

       NOTE: This search will fail to find features that do not have a display name!

       You can use fetch() or fetch_many() with the returned IDs to get to the features
       themselves.

   search_notes
        Title   : search_notes
        Usage   : @result_list = $db->search_notes("full text search string",$limit)
        Function: Search the notes for a text string
        Returns : array of results
        Args    : full text search string, and an optional feature limit
        Status  : public

       Given a search string, this method performs a full-text search of the "Notes" attribute
       and returns an array of results.  Each row of the returned array is a arrayref containing
       the following fields:

         column 1     The display_name of the feature, suitable for passing to get_feature_by_name()
         column 2     The text of the note
         column 3     A relevance score.
         column 4     The type

       NOTE: This is equivalent to $db->search_attributes('full text search
       string','Note',$limit). This search will fail to find features that do not have a display
       name!

   types
        Title   : types
        Usage   : @type_list = $db->types
        Function: Get all the types in the database
        Returns : array of Bio::DB::GFF::Typename objects
        Args    : none
        Status  : public

   insert_sequence
        Title   : insert_sequence
        Usage   : $success = $db->insert_sequence($seqid,$sequence_string,$offset)
        Function: Inserts sequence data into the database at the indicated offset
        Returns : true if successful
        Args    : see below
        Status  : public

       This method inserts the DNA or protein sequence fragment $sequence_string, identified by
       the ID $seq_id, into the database at the indicated offset $offset. It is used internally
       by the GFF3Loader to load sequence data from the files.

   fetch_sequence
        Title   : fetch_sequence
        Usage   : $sequence = $db->fetch_sequence(-seq_id=>$seqid,-start=>$start,-end=>$end)
        Function: Fetch the indicated subsequene from the database
        Returns : The sequence string (not a Bio::PrimarySeq object!)
        Args    : see below
        Status  : public

       This method retrieves a portion of the indicated sequence. The arguments are:

         Argument       Value
         --------       -----
         -seq_id        Chromosome, contig or other DNA segment
         -seqid         Synonym for -seq_id
         -name          Synonym for -seq_id
         -start         Start of range
         -end           End of range
         -class         Obsolete argument used for Bio::DB::GFF compatibility. If
                         specified will qualify the seq_id as "$class:$seq_id".
         -bioseq        Boolean flag; if true, returns a Bio::PrimarySeq object instead
                         of a sequence string.

       You can call fetch_sequence using the following shortcuts:

        $seq = $db->fetch_sequence('chr3');  # entire chromosome
        $seq = $db->fetch_sequence('chr3',1000);        # position 1000 to end of chromosome
        $seq = $db->fetch_sequence('chr3',undef,5000);  # position 1 to 5000
        $seq = $db->fetch_sequence('chr3',1000,5000);   # positions 1000 to 5000

   segment
        Title   : segment
        Usage   : $segment = $db->segment($seq_id [,$start] [,$end] [,$absolute])
        Function: restrict the database to a sequence range
        Returns : a Bio::DB::SeqFeature::Segment object
        Args    : sequence id, start and end ranges (optional)
        Status  : public

       This is a convenience method that can be used when you are interested in the contents of a
       particular sequence landmark, such as a contig. Specify the ID of a sequence or other
       landmark in the database and optionally a start and endpoint relative to that landmark.
       The method will look up the region and return a Bio::DB::SeqFeature::Segment object that
       spans it. You can then use this segment object to make location-restricted queries on the
       database.

       Example:

        $segment  = $db->segment('contig23',1,1000);  # first 1000 bp of contig23
        my @mRNAs = $segment->features('mRNA');       # all mRNAs that overlap segment

       Although you will usually want to fetch segments that correspond to physical sequences in
       the database, you can actually use any feature in the database as the sequence ID. The
       segment() method will perform a get_features_by_name() internally and then transform the
       feature into the appropriate coordinates.

       The named feature should exist once and only once in the database. If it exists multiple
       times in the database and you attempt to call segment() in a scalar context, you will get
       an exception. A workaround is to call the method in a list context, as in:

         my ($segment) = $db->segment('contig23',1,1000);

       or

         my @segments  = $db->segment('contig23',1,1000);

       However, having multiple same-named features in the database is often an indication of
       underlying data problems.

       If the optional $absolute argument is a true value, then the specified coordinates are
       relative to the reference (absolute) coordinates.

   seqfeature_class
        Title   : seqfeature_class
        Usage   : $classname = $db->seqfeature_class([$new_classname])
        Function: get or set the name of the Bio::SeqFeatureI class generated by new_feature()
        Returns : name of class
        Args    : new classname (optional)
        Status  : public

   reindex
        Title   : reindex
        Usage   : $db->reindex
        Function: reindex the database
        Returns : nothing
        Args    : nothing
        Status  : public

       This method will force the secondary indexes (name, location, attributes, feature types)
       to be recalculated. It may be useful to rebuild a corrupted database.

   attributes
        Title   : attributes
        Usage   : @a = $db->attributes
        Function: Returns list of all known attributes
        Returns : Returns list of all known attributes
        Args    : nothing
        Status  : public

   start_bulk_update,finish_bulk_update
        Title   : start_bulk_update,finish_bulk_update
        Usage   : $db->start_bulk_update
                  $db->finish_bulk_update
        Function: Activate optimizations for large number of insertions/updates
        Returns : nothing
        Args    : nothing
        Status  : public

       With some adaptors (currently only the DBI::mysql adaptor), these methods signal the
       adaptor that a large number of insertions or updates are to be performed, and activate
       certain optimizations. These methods are called automatically by the
       Bio::DB::SeqFeature::Store::GFF3Loader module.

       Example:

         $db->start_bulk_update;
         for my $f (@features) {
           $db->store($f);
         }
         $db->finish_bulk_update;

   add_SeqFeature
        Title   : add_SeqFeature
        Usage   : $count = $db->add_SeqFeature($parent,@children)
        Function: store a parent/child relationship between a $parent and @children
                  features that are already stored in the database
        Returns : number of children successfully stored
        Args    : parent feature or primary ID and children features or primary IDs
        Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

       If can_store_parentage() returns true, then some store-aware features (e.g.
       Bio::DB::SeqFeature) will invoke this method to store feature/subfeature relationships in
       a normalized table.

   fetch_SeqFeatures
        Title   : fetch_SeqFeatures
        Usage   : @children = $db->fetch_SeqFeatures($parent_feature)
        Function: return the immediate subfeatures of the indicated feature
        Returns : list of subfeatures
        Args    : the parent feature and an optional list of children types
        Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

       If can_store_parentage() returns true, then some store-aware features (e.g.
       Bio::DB::SeqFeature) will invoke this method to retrieve feature/subfeature relationships
       from the database.

Changing the Behavior of the Database

       These methods allow you to modify the behavior of the database.

   debug
        Title   : debug
        Usage   : $debug_flag = $db->debug([$new_flag])
        Function: set the debug flag
        Returns : current debug flag
        Args    : new debug flag
        Status  : public

       This method gets/sets a flag that turns on verbose progress messages. Currently this will
       not do very much.

   serializer
        Title   : serializer
        Usage   : $serializer = $db->serializer([$new_serializer])
        Function: get/set the name of the serializer
        Returns : the name of the current serializer class
        Args    : (optional) the name of a new serializer
        Status  : public

       You can use this method to set the serializer, but do not attempt to change the serializer
       once the database is initialized and populated.

   dna_accessor
        Title   : dna_accessor
        Usage   : $dna_accessor = $db->dna_accessor([$new_dna_accessor])
        Function: get/set the name of the dna_accessor
        Returns : the current dna_accessor object, if any
        Args    : (optional) the dna_accessor object
        Status  : public

       You can use this method to request or set the DNA accessor.

   index_subfeatures
        Title   : index_subfeatures
        Usage   : $flag = $db->index_subfeatures([$new_value])
        Function: flag whether to index subfeatures
        Returns : current value of the flag
        Args    : (optional) new value of the flag
        Status  : public

       If true, the store() method will add a searchable index to both the top-level feature and
       all its subfeatures, allowing the search functions to return features at any level of the
       containment hierarchy. If false, only the top level feature will be indexed, meaning that
       you will only be able to get at subfeatures by fetching the top-level feature and then
       traversing downward using get_SeqFeatures().

       You are free to change this setting at any point during the creation and population of a
       database. One database can contain both indexed and unindexed subfeatures.

   clone
       The clone() method should be used when you want to pass the Bio::DB::SeqFeature::Store
       object to a child process across a fork(). The child must call clone() before making any
       queries.

       The default behavior is to do nothing, but adaptors that use the DBI interface may need to
       implement this in order to avoid database handle errors. See the dbi adaptor for an
       example.

TIE Interface

       This module implements a full TIEHASH interface. The keys are the primary IDs of the
       features in the database. Example:

        tie %h,'Bio::DB::SeqFeature::Store',-adaptor=>'DBI::mysql',-dsn=>'dbi:mysql:elegans';
        $h{123} = $feature1;
        $h{124} = $feature2;
        print $h{123}->display_name;

   _init_database
        Title   : _init_database
        Usage   : $success = $db->_init_database([$erase])
        Function: initialize an empty database
        Returns : true on success
        Args    : optional boolean flag to erase contents of an existing database
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

       This method is the back end for init_database(). It must be implemented by an adaptor that
       inherits from Bio::DB::SeqFeature::Store. It returns true on success. @features =
       $db->features(-seqid=>'Chr1');

   _store
        Title   : _store
        Usage   : $success = $db->_store($indexed,@objects)
        Function: store seqfeature objects into database
        Returns : true on success
        Args    : a boolean flag indicating whether objects are to be indexed,
                  and one or more objects
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

       This method is the back end for store() and store_noindex(). It should write the
       seqfeature objects into the database. If indexing is requested, the features should be
       indexed for query and retrieval. Otherwise the features should be stored without indexing
       (it is not required that adaptors respect this).

       If the object has no primary_id (undef), then the object is written into the database and
       assigned a new primary_id. If the object already has a primary_id, then the system will
       perform an update, replacing whatever was there before.

       In practice, the implementation will serialize each object using the freeze() method and
       then store it in the database under the corresponding primary_id. The object is then
       updated with the primary_id.

   _fetch
        Title   : _fetch
        Usage   : $feature = $db->_fetch($primary_id)
        Function: fetch feature from database
        Returns : feature
        Args    : primary id
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

       This method is the back end for fetch(). It accepts a primary_id and returns a feature
       object. It must be implemented by the adaptor.

       In practice, the implementation will retrieve the serialized Bio::SeqfeatureI object from
       the database and pass it to the thaw() method to unserialize it and synchronize the
       primary_id.

   _fetch_many
        Title   : _fetch_many
        Usage   : $feature = $db->_fetch_many(@primary_ids)
        Function: fetch many features from database
        Returns : feature
        Args    : primary id
        Status  : private -- does not need to be implemented

       This method fetches many features specified by a list of IDs. The default implementation
       simply calls _fetch() once for each primary_id. Implementors can override it if needed for
       efficiency.

   _update_indexes
        Title   : _update_indexes
        Usage   : $success = $db->_update_indexes($feature)
        Function: update the indexes for a feature
        Returns : true on success
        Args    : A seqfeature object
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

       This method is called by reindex() to update the searchable indexes for a feature object
       that has changed.

   _start_reindexing, _end_reindexing
        Title   : _start_reindexing, _end_reindexing
        Usage   : $db->_start_reindexing()
                  $db->_end_reindexing
        Function: flag that a series of reindexing operations is beginning/ending
        Returns : true on success
        Args    : none
        Status  : MAY BE IMPLEMENTED BY AN ADAPTOR (optional)

       These methods are called by reindex() before and immediately after a series of reindexing
       operations. The default behavior is to do nothing, but these methods can be overridden by
       an adaptor in order to perform optimizations, turn off autocommits, etc.

   _features
        Title   : _features
        Usage   : @features = $db->_features(@args)
        Function: back end for all get_feature_by_*() queries
        Returns : list of features
        Args    : see below
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

       This is the backend for features(), get_features_by_name(), get_features_by_location(),
       etc. Arguments are as described for the features() method, except that only the named-
       argument form is recognized.

   _search_attributes
        Title   : _search_attributes
        Usage   : @result_list = $db->_search_attributes("text search string",[$tag1,$tag2...],$limit)
        Function: back end for the search_attributes() method
        Returns : results list
        Args    : as per search_attributes()
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

       See search_attributes() for the format of the results list. The only difference between
       this and the public method is that the tag list is guaranteed to be an array reference.

   can_store_parentage
        Title   : can_store_parentage
        Usage   : $flag = $db->can_store_parentage
        Function: return true if this adaptor can store parent/child relationships
        Returns : boolean
        Args    : none
        Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

       Override this method and return true if this adaptor supports the _add_SeqFeature() and
       _get_SeqFeatures() methods, which are used for storing feature parent/child relationships
       in a normalized fashion. Default is false (parent/child relationships are stored in
       denormalized form in each feature).

   _add_SeqFeature
        Title   : _add_SeqFeature
        Usage   : $count = $db->_add_SeqFeature($parent,@children)
        Function: store a parent/child relationship between $parent and @children
        Returns : number of children successfully stored
        Args    : parent feature and one or more children
        Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

       If can_store_parentage() returns true, then some store-aware features (e.g.
       Bio::DB::SeqFeature) will invoke this method to store feature/subfeature relationships in
       a normalized table.

   _fetch_SeqFeatures
        Title   : _fetch_SeqFeatures
        Usage   : @children = $db->_fetch_SeqFeatures($parent_feature)
        Function: return the immediate subfeatures of the indicated feature
        Returns : list of subfeatures
        Args    : the parent feature
        Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

       If can_store_parentage() returns true, then some store-aware features (e.g.
       Bio::DB::SeqFeature) will invoke this method to retrieve feature/subfeature relationships
       from the database.

   _insert_sequence
        Title   : _insert_sequence
        Usage   : $success = $db->_insert_sequence($seqid,$sequence_string,$offset)
        Function: Inserts sequence data into the database at the indicated offset
        Returns : true if successful
        Args    : see below
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

       This is the back end for insert_sequence(). Adaptors must implement this method in order
       to store and retrieve nucleotide or protein sequence.

   _fetch_sequence
        Title   : _fetch_sequence
        Usage   : $sequence = $db->_fetch_sequence(-seq_id=>$seqid,-start=>$start,-end=>$end)
        Function: Fetch the indicated subsequence from the database
        Returns : The sequence string (not a Bio::PrimarySeq object!)
        Args    : see below
        Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

       This is the back end for fetch_sequence(). Adaptors must implement this method in order to
       store and retrieve nucleotide or protein sequence.

   _seq_ids
        Title   : _seq_ids
        Usage   : @ids = $db->_seq_ids()
        Function: Return all sequence IDs contained in database
        Returns : list of sequence Ids
        Args    : none
        Status  : TO BE IMPLEMENTED BY ADAPTOR

       This method is invoked by seq_ids() to return all sequence IDs (coordinate systems) known
       to the database.

   _start_bulk_update,_finish_bulk_update
        Title   : _start_bulk_update, _finish_bulk_update
        Usage   : $db->_start_bulk_update
                  $db->_finish_bulk_update
        Function: Activate optimizations for large number of insertions/updates
        Returns : nothing
        Args    : nothing
        Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTOR

       These are the backends for start_bulk_update() and finish_bulk_update(). The default
       behavior of both methods is to do nothing.

   Optional methods needed to implement full TIEHASH interface
       The core TIEHASH interface will work if just the _store() and _fetch() methods are
       implemented. To support the full TIEHASH interface, including support for keys(), each(),
       and exists(), the following methods should be implemented:

       $id = $db->_firstid()
           Return the first primary ID in the database. Needed for the each() function.

       $next_id = $db->_nextid($id)
           Given a primary ID, return the next primary ID in the series. Needed for the each()
           function.

       $boolean = $db->_existsid($id)
           Returns true if the indicated primary ID is in the database. Needed for the exists()
           function.

       $db->_deleteid($id)
           Delete the feature corresponding to the given primary ID. Needed for delete().

       $db->_clearall()
           Empty the database. Needed for %tied_hash = ().

       $count = $db->_featurecount()
           Return the number of features in the database. Needed for scalar %tied_hash.

Internal Methods

       These methods are internal to Bio::DB::SeqFeature::Store and adaptors.

   new_instance
        Title   : new_instance
        Usage   : $db = $db->new_instance()
        Function: class constructor
        Returns : A descendent of Bio::DB::SeqFeature::Store
        Args    : none
        Status  : internal

       This method is called internally by new() to create a new uninitialized instance of
       Bio::DB::SeqFeature::Store. It is used internally and should not be called by application
       software.

   init
        Title   : init
        Usage   : $db->init(@args)
        Function: initialize object
        Returns : none
        Args    : Arguments passed to new()
        Status  : private

       This method is called internally by new() to initialize a newly-created object using the
       arguments passed to new(). It is to be overridden by Bio::DB::SeqFeature::Store adaptors.

   default_settings
        Title   : default_settings
        Usage   : $db->default_settings()
        Function: set up default settings for the adaptor
        Returns : none
        Args    : none
        Status  : private

       This method is may be overridden by adaptors. It is responsible for setting up object
       default settings.

   default_serializer
        Title   : default_serializer
        Usage   : $serializer = $db->default_serializer
        Function: finds an available serializer
        Returns : the name of an available serializer
        Args    : none
        Status  : private

       This method returns the name of an available serializer module.

   setting
        Title   : setting
        Usage   : $value = $db->setting('setting_name' [=> $new_value])
        Function: get/set the value of a setting
        Returns : the value of the current setting
        Args    : the name of the setting and optionally a new value for the setting
        Status  : private

       This is a low-level procedure for persistently storing database settings. It can be
       overridden by adaptors.

   subfeatures_are_indexed
        Title   : subfeatures_are_indexed
        Usage   : $flag = $db->subfeatures_are_indexed([$new_value])
        Function: flag whether subfeatures are indexed
        Returns : a flag indicating that all subfeatures are indexed
        Args    : (optional) new value of the flag
        Status  : private

       This method is used internally by the Bio::DB::SeqFeature class to optimize some of its
       operations. It returns true if all of the subfeatures in the database are indexed; it
       returns false if at least one of the subfeatures is not indexed. Do not attempt to change
       the value of this setting unless you are writing an adaptor.

   subfeature_types_are_indexed
        Title   : subfeature_types_are_indexed
        Usage   : $flag = $db->subfeature_types_are_indexed
        Function: whether subfeatures are indexed by type
        Returns : a flag indicating that all subfeatures are indexed
        Args    : none
        Status  : private

       This method returns true if subfeature types are indexed. Default is to return the value
       of subfeatures_are_indexed().

   subfeature_locations_are_indexed
        Title   : subfeature_locations_are_indexed
        Usage   : $flag = $db->subfeature_locations_are_indexed
        Function: whether subfeatures are indexed by type
        Returns : a flag indicating that all subfeatures are indexed
        Args    : none
        Status  : private

       This method returns true if subfeature locations are indexed. Default is to return the
       value of subfeatures_are_indexed().

   setup_segment_args
        Title   : setup_segment_args
        Usage   : @args = $db->setup_segment_args(@args)
        Function: munge the arguments to the segment() call
        Returns : munged arguments
        Args    : see below
        Status  : private

       This method is used internally by segment() to translate positional arguments into named
       argument=>value pairs.

   store_and_cache
        Title   : store_and_cache
        Usage   : $success = $db->store_and_cache(@features)
        Function: store features into database and update cache
        Returns : number of features stored
        Args    : index the features? (0 or 1) and  list of features
        Status  : private

       This private method stores the list of Bio::SeqFeatureI objects into the database and
       caches them in memory for retrieval.

   init_cache
        Title   : init_cache
        Usage   : $db->init_cache($size)
        Function: initialize the in-memory feature cache
        Returns : the Tie::Cacher object
        Args    : desired size of the cache
        Status  : private

       This method is used internally by new() to create the Tie::Cacher instance used for the
       in-memory feature cache.

   cache
        Title   : cache
        Usage   : $cache = $db->cache
        Function: return the cache object
        Returns : the Tie::Cacher object
        Args    : none
        Status  : private

       This method returns the Tie::Cacher object used for the in-memory feature cache.

   load_class
        Title   : load_class
        Usage   : $db->load_class($blessed_object)
        Function: loads the module corresponding to a blessed object
        Returns : empty
        Args    : a blessed object
        Status  : private

       This method is used by thaw() to load the code for a blessed object. This ensures that all
       the object's methods are available.

   freeze
        Title   : freeze
        Usage   : $serialized_object = $db->freeze($feature)
        Function: serialize a feature object into a string
        Returns : serialized feature object
        Args    : a seqfeature object
        Status  : private

       This method converts a Bio::SeqFeatureI object into a serialized form suitable for storage
       into a database. The feature's primary ID is set to undef before it is serialized. This
       avoids any potential mismatch between the primary ID used as the database key and the
       primary ID stored in the serialized object.

   thaw
        Title   : thaw
        Usage   : $feature = $db->thaw($serialized_object,$primary_id)
        Function: unserialize a string into a feature object
        Returns : Bio::SeqFeatureI object
        Args    : serialized form of object from freeze() and primary_id of object
        Status  : private

       This method is the reverse of the freeze(). The supplied primary_id becomes the
       primary_id() of the returned Bio::SeqFeatureI object. This implementation checks for a
       deserialized object in the cache before it calls thaw_object() to do the actual
       deserialization.

   thaw_object
        Title   : thaw_object
        Usage   : $feature = $db->thaw_object($serialized_object,$primary_id)
        Function: unserialize a string into a feature object
        Returns : Bio::SeqFeatureI object
        Args    : serialized form of object from freeze() and primary_id of object
        Status  : private

       After thaw() checks the cache and comes up empty, this method is invoked to thaw the
       object.

   feature_names
        Title   : feature_names
        Usage   : ($names,$aliases) = $db->feature_names($feature)
        Function: get names and aliases for a feature
        Returns : an array of names and an array of aliases
        Args    : a Bio::SeqFeatureI object
        Status  : private

       This is an internal utility function which, given a Bio::SeqFeatureI object, returns two
       array refs. The first is a list of official names for the feature, and the second is a
       list of aliases. This is slightly skewed towards GFF3 usage, so the official names are the
       display_name(), plus all tag values named 'Name', plus all tag values named 'ID'. The
       aliases are all tag values named 'Alias'.

   feature_summary
        Title   : feature_summary
        Usage   : $summary = $db->feature_summary(@args)
        Function: returns a coverage summary across indicated region/type
        Returns : a Bio::SeqFeatureI object containing the "coverage" tag
        Args    : see below
        Status  : public

       This method is used to get coverage density information across a region of interest. You
       provide it with a region of interest, optional a list of feature types, and a count of the
       number of bins over which you want to calculate the coverage density. An object is
       returned corresponding to the requested region. It contains a tag called "coverage" that
       will return an array ref of "bins" length. Each element of the array describes the number
       of features that overlap the bin at this position.

       Arguments:

         Argument       Description
         --------       -----------

         -seq_id        Sequence ID for the region
         -start         Start of region
         -end           End of region
         -type/-types   Feature type of interest or array ref of types
         -bins          Number of bins across region. Defaults to 1000.
         -iterator      Return an iterator across the region

       Note that this method uses an approximate algorithm that is only accurate to 500 bp, so
       when dealing with bins that are smaller than 1000 bp, you may see some shifting of counts
       between adjacent bins.

       Although an -iterator option is provided, the method only ever returns a single feature,
       so this is fairly useless.

   coverage_array
        Title   : coverage_array
        Usage   : $arrayref = $db->coverage_array(@args)
        Function: returns a coverage summary across indicated region/type
        Returns : an array reference
        Args    : see below
        Status  : public

       This method is used to get coverage density information across a region of interest. The
       arguments are identical to feature_summary, except that instead of returning a
       Bio::SeqFeatureI object, it returns an array reference of the desired number of bins. The
       value of each element corresponds to the number of features in the bin.

       Arguments:

         Argument       Description
         --------       -----------

         -seq_id        Sequence ID for the region
         -start         Start of region
         -end           End of region
         -type/-types   Feature type of interest or array ref of types
         -bins          Number of bins across region. Defaults to 1000.

       Note that this method uses an approximate algorithm that is only accurate to 500 bp, so
       when dealing with bins that are smaller than 1000 bp, you may see some shifting of counts
       between adjacent bins.

BUGS

       This is an early version, so there are certainly some bugs. Please use the BioPerl bug
       tracking system to report bugs.

SEE ALSO

       Bio::DB::SeqFeature, Bio::DB::SeqFeature::Store::GFF3Loader, Bio::DB::SeqFeature::Segment,
       Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::berkeleydb
       Bio::DB::SeqFeature::Store::memory

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2006 Cold Spring Harbor Laboratory.

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