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

NAME

       Bio::SeqFeature::Generic - Generic SeqFeature

SYNOPSIS

          $feat = Bio::SeqFeature::Generic->new(
                   -start        => 10,
                   -end          => 100,
                   -strand       => -1,
                   -primary      => 'repeat', # -primary_tag is a synonym
                   -source_tag   => 'repeatmasker',
                   -display_name => 'alu family',
                   -score        => 1000,
                   -tag          => { new => 1,
                                      author => 'someone',
                                      sillytag => 'this is silly!' } );

          $feat = Bio::SeqFeature::Generic->new( -gff_string => $string );
          # if you want explicitly GFF1
          $feat = Bio::SeqFeature::Generic->new( -gff1_string => $string );

          # add it to an annotated sequence

          $annseq->add_SeqFeature($feat);

DESCRIPTION

       Bio::SeqFeature::Generic is a generic implementation for the Bio::SeqFeatureI interface,
       providing a simple object to provide all the information for a feature on a sequence.

       For many Features, this is all you will need to use (for example, this is fine for Repeats
       in DNA sequence or Domains in protein sequence). For other features, which have more
       structure, this is a good base class to extend using inheritence to have new things: this
       is what is done in the Bio::SeqFeature::Gene, Bio::SeqFeature::Transcript and
       Bio::SeqFeature::Exon, which provide well coordinated classes to represent genes on DNA
       sequence (for example, you can get the protein sequence out from a transcript class).

       For many Features, you want to add some piece of information, for example a common one is
       that this feature is 'new' whereas other features are 'old'.  The tag system, which here
       is implemented using a hash can be used here.  You can use the tag system to extend the
       Bio::SeqFeature::Generic programmatically: that is, you know that you have read in more
       information into the tag 'mytag' which you can then retrieve. This means you do not need
       to know how to write inherited Perl to provide more complex information on a feature,
       and/or, if you do know but you do not want to write a new class every time you need some
       extra piece of information, you can use the tag system to easily store and then retrieve
       information.

       The tag system can be written in/out of GFF format, and also into EMBL format via the
       Bio::SeqIO system

Implemented Interfaces

       This class implementes the following interfaces.

       Bio::SeqFeatureI
           Note that this includes implementing Bio::RangeI.

       Bio::AnnotatableI
       Bio::FeatureHolderI
           Features held by a feature are essentially sub-features.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney

       Ewan Birney <birney@sanger.ac.uk>

DEVELOPERS

       This class has been written with an eye out for inheritance. The fields the actual object
       hash are:

          _gsf_tag_hash  = reference to a hash for the tags
          _gsf_sub_array = reference to an array for subfeatures

APPENDIX

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

   set_attributes
        Title   : set_attributes
        Usage   :
        Function: Sets a whole array of parameters at once.
        Example :
        Returns : none
        Args    : Named parameters, in the form as they would otherwise be passed
                  to new(). Currently recognized are:

                           -start          start position
                           -end            end position
                           -strand         strand
                           -phase          the phase of the feature (0..2)
                           -primary_tag    primary tag
                           -primary        (synonym for -primary_tag)
                           -source         source tag
                           -frame          frame
                           -score          score value
                           -tag            a reference to a tag/value hash
                           -gff_string     GFF v.2 string to initialize from
                           -gff1_string    GFF v.1 string to initialize from
                           -seq_id         the display name of the sequence
                           -annotation     the AnnotationCollectionI object
                           -location       the LocationI object

   direct_new
        Title   : direct_new
        Usage   : my $obj = Bio::SeqFeature::Generic->direct_new
        Function: create a blessed hash - for performance improvement in
                  object creation
        Returns : Bio::SeqFeature::Generic object
        Args    : none

   location
        Title   : location
        Usage   : my $location = $seqfeature->location()
        Function: returns a location object suitable for identifying location
                  of feature on sequence or parent feature
        Returns : Bio::LocationI object
        Args    : [optional] Bio::LocationI object to set the value to.

   start
        Title   : start
        Usage   : $start = $feat->start
                  $feat->start(20)
        Function: Get/set on the start coordinate of the feature
        Returns : integer
        Args    : none

   end
        Title   : end
        Usage   : $end = $feat->end
                  $feat->end($end)
        Function: get/set on the end coordinate of the feature
        Returns : integer
        Args    : none

   length
        Title   : length
        Usage   : my $len = $feature->length
        Function: Get the feature length computed as
                  $feat->end - $feat->start + 1
        Returns : integer
        Args    : none

   strand
        Title   : strand
        Usage   : $strand = $feat->strand()
                  $feat->strand($strand)
        Function: get/set on strand information, being 1,-1 or 0
        Returns : -1,1 or 0
        Args    : none

   score
        Title   : score
        Usage   : $score = $feat->score()
                  $feat->score($score)
        Function: get/set on score information
        Returns : float
        Args    : none if get, the new value if set

   frame
        Title   : frame
        Usage   : $frame = $feat->frame()
                  $feat->frame($frame)
        Function: get/set on frame information
        Returns : 0,1,2, '.'
        Args    : none if get, the new value if set

   primary_tag
        Title   : primary_tag
        Usage   : $tag = $feat->primary_tag()
                  $feat->primary_tag('exon')
        Function: get/set on the primary tag for a feature,
                  eg 'exon'
        Returns : a string
        Args    : none

   source_tag
        Title   : source_tag
        Usage   : $tag = $feat->source_tag()
                  $feat->source_tag('genscan');
        Function: Returns the source tag for a feature,
                  eg, 'genscan'
        Returns : a string
        Args    : none

   has_tag
        Title   : has_tag
        Usage   : $value = $self->has_tag('some_tag')
        Function: Tests wether a feature contaings a tag
        Returns : TRUE if the SeqFeature has the tag,
                  and FALSE otherwise.
        Args    : The name of a tag

   add_tag_value
        Title   : add_tag_value
        Usage   : $self->add_tag_value('note',"this is a note");
        Returns : TRUE on success
        Args    : tag (string) and one or more values (any scalar(s))

   get_tag_values
        Title   : get_tag_values
        Usage   : @values = $gsf->get_tag_values('note');
        Function: Returns a list of all the values stored
                  under a particular tag.
        Returns : A list of scalars
        Args    : The name of the tag

   get_all_tags
        Title   : get_all_tags
        Usage   : @tags = $feat->get_all_tags()
        Function: Get a list of all the tags in a feature
        Returns : An array of tag names
        Args    : none

       # added a sort so that tags will be returned in a predictable order # I still think we
       should be able to specify a sort function # to the object at some point # -js

   remove_tag
        Title   : remove_tag
        Usage   : $feat->remove_tag('some_tag')
        Function: removes a tag from this feature
        Returns : the array of values for this tag before removing it
        Args    : tag (string)

   attach_seq
        Title   : attach_seq
        Usage   : $sf->attach_seq($seq)
        Function: Attaches a Bio::Seq object to this feature. This
                  Bio::Seq object is for the *entire* sequence: ie
                  from 1 to 10000
        Example :
        Returns : TRUE on success
        Args    : a Bio::PrimarySeqI compliant object

   seq
        Title   : seq
        Usage   : $tseq = $sf->seq()
        Function: returns the truncated sequence (if there) for this
        Example :
        Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
                  bounded by start & end, or undef if there is no sequence attached
        Args    : none

   entire_seq
        Title   : entire_seq
        Usage   : $whole_seq = $sf->entire_seq()
        Function: gives the entire sequence that this seqfeature is attached to
        Example :
        Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
                  sequence attached
        Args    :

   seq_id
        Title   : seq_id
        Usage   : $obj->seq_id($newval)
        Function: There are many cases when you make a feature that you
                  do know the sequence name, but do not know its actual
                  sequence. This is an attribute such that you can store
                  the ID (e.g., display_id) of the sequence.

                  This attribute should *not* be used in GFF dumping, as
                  that should come from the collection in which the seq
                  feature was found.
        Returns : value of seq_id
        Args    : newvalue (optional)

   display_name
        Title   : display_name
        Usage   : $featname = $obj->display_name
        Function: Implements the display_name() method, which is a human-readable
                  name for the feature.
        Returns : value of display_name (a string)
        Args    : Optionally, on set the new value or undef

Methods for implementing Bio::AnnotatableI

   annotation
        Title   : annotation
        Usage   : $obj->annotation($annot_obj)
        Function: Get/set the annotation collection object for annotating this
                  feature.

        Example :
        Returns : A Bio::AnnotationCollectionI object
        Args    : newvalue (optional)

Methods to implement Bio::FeatureHolderI

       This includes methods for retrieving, adding, and removing features. Since this is already
       a feature, features held by this feature holder are essentially sub-features.

   get_SeqFeatures
        Title   : get_SeqFeatures
        Usage   : @feats = $feat->get_SeqFeatures();
        Function: Returns an array of sub Sequence Features
        Returns : An array
        Args    : none

   add_SeqFeature
        Title   : add_SeqFeature
        Usage   : $feat->add_SeqFeature($subfeat);
                  $feat->add_SeqFeature($subfeat,'EXPAND')
        Function: Adds a SeqFeature into the subSeqFeature array.
                  With no 'EXPAND' qualifer, subfeat will be tested
                  as to whether it lies inside the parent, and throw
                  an exception if not.

                  If EXPAND is used, the parent's start/end/strand will
                  be adjusted so that it grows to accommodate the new
                  subFeature
        Returns : nothing
        Args    : An object which has the SeqFeatureI interface

   remove_SeqFeatures
        Title   : remove_SeqFeatures
        Usage   : $sf->remove_SeqFeatures
        Function: Removes all SeqFeatures

                  If you want to remove only a subset of features then remove that
                  subset from the returned array, and add back the rest.
        Example :
        Returns : The array of Bio::SeqFeatureI implementing features that was
                  deleted.
        Args    : none

GFF-related methods

   gff_format
        Title   : gff_format
        Usage   : # get:
                  $gffio = $feature->gff_format();
                  # set (change the default version of GFF2):
                  $feature->gff_format(Bio::Tools::GFF->new(-gff_version => 1));
        Function: Get/set the GFF format interpreter. This object is supposed to
                  format and parse GFF. See Bio::Tools::GFF for the interface.

                  If this method is called as class method, the default for all
                  newly created instances will be changed. Otherwise only this
                  instance will be affected.
        Example :
        Returns : a Bio::Tools::GFF compliant object
        Args    : On set, an instance of Bio::Tools::GFF or a derived object.

   gff_string
        Title   : gff_string
        Usage   : $str = $feat->gff_string;
                  $str = $feat->gff_string($gff_formatter);
        Function: Provides the feature information in GFF format.

                  We override this here from Bio::SeqFeatureI in order to use the
                  formatter returned by gff_format().

        Returns : A string
        Args    : Optionally, an object implementing gff_string().

   slurp_gff_file
        Title   : slurp_file
        Usage   : @features = Bio::SeqFeature::Generic::slurp_gff_file(\*FILE);
        Function: Sneaky function to load an entire file as in memory objects.
                  Beware of big files.

                  This method is deprecated. Use Bio::Tools::GFF instead, which can
                  also handle large files.

        Example :
        Returns :
        Args    :

   _from_gff_string
        Title   : _from_gff_string
        Usage   :
        Function: Set feature properties from GFF string.

                  This method uses the object returned by gff_format() for the
                  actual interpretation of the string. Set a different GFF format
                  interpreter first if you need a specific version, like GFF1. (The
                  default is GFF2.)
        Example :
        Returns :
        Args    : a GFF-formatted string

   _expand_region
        Title   : _expand_region
        Usage   : $self->_expand_region($feature);
        Function: Expand the total region covered by this feature to
                  accommodate for the given feature.

                  May be called whenever any kind of subfeature is added to this
                  feature. add_sub_SeqFeature() already does this.
        Returns :
        Args    : A Bio::SeqFeatureI implementing object.

   _parse
        Title   : _parse
        Usage   :
        Function: Parsing hints
        Example :
        Returns :
        Args    :

   _tag_value
        Title   : _tag_value
        Usage   :
        Function: For internal use only. Convenience method for those tags that
                  may only have a single value.
        Returns : The first value under the given tag as a scalar (string)
        Args    : The tag as a string. Optionally, the value on set.