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


       Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a


          $proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc,
                                                        -parent => $basefeature);



       PositionProxy is a Proxy Sequence Feature to handle truncation and revcomp without
       duplicating all the data within the sequence features.  It holds a new location for a
       sequence feature and the original feature it came from to provide the additional
       annotation information.


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AUTHOR - Ewan Birney

       Ewan Birney <>


       This class has been written with an eye out of 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 sub arrays
          _gsf_start     = scalar of the start point
          _gsf_end       = scalar of the end point
          _gsf_strand    = scalar of the strand


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

        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    : none

        Title   : parent
        Usage   : my $sf = $proxy->parent()
        Function: returns the seqfeature parent of this proxy
        Returns : Bio::SeqFeatureI object
        Args    : none

        Title   : start
        Usage   : $start = $feat->start
        Function: Get
        Returns : integer
        Args    : none

        Title   : end
        Usage   : $end = $feat->end
        Function: get
        Returns : integer
        Args    : none

        Title   : length
        Usage   :
        Example :
        Returns :
        Args    :

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

        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    :

        Title   : seq
        Usage   : $tseq = $sf->seq()
        Function: returns the truncated sequence (if there) for this
        Example :
        Returns : sub seq on attached sequence bounded by start & end
        Args    : none

        Title   : entire_seq
        Usage   : $whole_seq = $sf->entire_seq()
        Function: gives the entire sequence that this seqfeature is attached to
        Example :
        Returns :
        Args    :

        Title   : seqname
        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 seqname.

                  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 seqname
        Args    : newvalue (optional)

       These functions chain back to the parent for all non sequence related stuff.

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

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

        Title   : has_tag
        Usage   : $tag_exists = $self->has_tag('some_tag')
        Returns : TRUE if the specified tag exists, and FALSE otherwise
        Args    :

        Title   : get_tag_values
        Usage   : @values = $self->get_tag_values('some_tag')
        Returns : An array comprising the values of the specified tag.
        Args    :

        Title   : get_all_tags
        Usage   : @tags = $feat->get_all_tags()
        Function: gives all tags for this feature
        Returns : an array of strings
        Args    : none