Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::SeqFeature::Collection - A container class for SeqFeatures suitable for performing
       operations such as finding features within a range, that match a certain feature type,


         use Bio::SeqFeature::Collection;
         use Bio::Location::Simple;
         use Bio::Tools::GFF;
         use Bio::Root::IO;
         use File::Spec;
         # let's first input some features
         my $gffio = Bio::Tools::GFF->new(-file => File::Spec->catfile
                                        -gff_version => 2);
         my @features = ();
         # loop over the input stream
         while(my $feature = $gffio->next_feature()) {
             # do something with feature
             push @features, $feature;
         # build the Collection object
         my $col = Bio::SeqFeature::Collection->new();
         # add these features to the object
         my $totaladded = $col->add_features(\@features);

         my @subset = $col->features_in_range(-start => 1,
                                            -end => 25000,
                                            -strand => 1,
                                            -contain => 0);
         # subset should have 18 entries for this dataset
         print "size is ", scalar @subset, "\n";
         @subset = $col->features_in_range(-range => Bio::Location::Simple->new
                                         (-start => 70000,
                                          -end => 150000,
                                          -strand => -1),
                                         -contain => 1,
                                         -strandmatch => 'strong');

         # subset should have 22 entries for this dataset
         print "size is ", scalar @subset, "\n";
         print "total number of features in collection is ",


       This object will efficiently allow one for query subsets of ranges within a large
       collection of sequence features (in fact the objects just have to be Bio::RangeI
       compliant).  This is done by the creation of bins which are stored in order in a B-Tree
       data structure as provided by the DB_File interface to the Berkeley DB.

       This is based on work done by Lincoln for storage in a mysql instance - this is intended
       to be an embedded in-memory implementation for easily querying for subsets of a large
       range set.

       Collections can be made persistent by keeping the indexfile and passing in the -keep flag
       like this:

         my $collection = Bio::SeqFeature::Collection->new(-keep => 1,
                                                          -file => 'col.idx');
         undef $collection;

         # To reuse this collection, next time you initialize a Collection object
         # specify the filename and the index will be reused.
         $collection = Bio::SeqFeature::Collection->new(-keep => 1,
                                                       -file => 'col.idx');


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AUTHOR - Jason Stajich



       Using code and strategy developed by Lincoln Stein ( in Bio::DB::GFF
       implementation.  Credit also to Lincoln for suggesting using Storable to serialize
       features rather than my previous implementation which kept the features in memory.


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = Bio::SeqFeature::Collection->new();
        Function: Builds a new Bio::SeqFeature::Collection object
        Returns : Bio::SeqFeature::Collection
        Args    :

                  -minbin        minimum value to use for binning
                                 (default is 100,000,000)
                  -maxbin        maximum value to use for binning
                                 (default is 1,000)
                  -file          filename to store/read the
                                 BTREE from rather than an in-memory structure
                                 (default is false and in-memory).
                  -keep          boolean, will not remove index file on
                                 object destruction.
                  -features      Array ref of features to add initially

        Title   : add_features
        Usage   : $collection->add_features(\@features);
        Returns : number of features added
        Args    : arrayref of Bio::SeqFeatureI objects to index

        Title   : features_in_range
        Usage   : my @features = $collection->features_in_range($range)
        Function: Retrieves a list of features which were contained or overlap the
                  the requested range (see Args for way to specify overlap or
                                       only those containe)d
        Returns : List of Bio::SeqFeatureI objects
        Args    : -range => Bio::RangeI object defining range to search,
                  -start  => start,
                  -end    => end,
                  -strand  => strand

                  -contain => boolean - true if feature must be completely
                              contained with range
                              OR false if should include features that simply overlap
                              the range. Default: true.
                  -strandmatch =>  'strong',  ranges must have the same strand
                                   'weak',    ranges must have the same
                                                  strand or no strand
                                   'ignore', ignore strand information
                                  Default. 'ignore'.

        Title   : remove_features
        Usage   : $collection->remove_features(\@array)
        Function: Removes the requested sequence features (based on features
                  which have the same location)
        Returns : Number of features removed
        Args    : Arrayref of Bio::RangeI objects

        Title   : get_all_features
        Usage   : my @f = $col->get_all_features()
        Function: Return all the features stored in this collection (Could be large)
        Returns : Array of Bio::RangeI objects
        Args    : None

        Title   : min_bin
        Usage   : my $minbin= $self->min_bin;
        Function: Get/Set the minimum value to use for binning
        Returns : integer
        Args    : [optional] minimum bin value

        Title   : max_bin
        Usage   : my $maxbin= $self->max_bin;
        Function: Get/Set the maximum value to use for binning
        Returns : integer
        Args    : [optional] maximum bin value

        Title   : feature_count
        Usage   : my $c = $col->feature_count()
        Function: Retrieve the total number of features in the collection
        Returns : integer
        Args    : none

        Title   : indexfile
        Usage   : $obj->indexfile($newval)
        Function: Get/set the filename where index is kept
        Returns : value of indexfile (a filename string)
        Args    : on set, new value (a filename string )

        Title   : keep
        Usage   : $obj->keep($newval)
        Function: Get/set boolean flag to keep the indexfile after
                  exiting program
        Example :
        Returns : value of keep (boolean)
        Args    : on set, new value (boolean)