Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

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

SYNOPSIS

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

          $seq->add_SeqFeature($feat);

DESCRIPTION

       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.

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

       Ewan Birney <birney@sanger.ac.uk>

DEVELOPERS

       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

APPENDIX

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

   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    : none

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

   start
        Title   : start
        Usage   : $start = $feat->start
                  $feat->start(20)
        Function: Get
        Returns : integer
        Args    : none

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

   length
        Title   : length
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   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

   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    :

   seq
        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

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

   seqname
        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)

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

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

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

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

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

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