Bio::SeqFeature PositionProxy
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Summary
Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature
Package variables
No package variables defined.
Included modules
Bio::Tools::GFF
Inherit
Bio::Root::Root Bio::SeqFeatureI
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.
Methods
new
No description
Code
locationDescriptionCode
parentDescriptionCode
startDescriptionCode
endDescriptionCode
lengthDescriptionCode
strandDescriptionCode
attach_seqDescriptionCode
seqDescriptionCode
entire_seqDescriptionCode
seqnameDescriptionCode
primary_tagDescriptionCode
source_tagDescriptionCode
has_tagDescriptionCode
get_tag_valuesDescriptionCode
get_all_tagsDescriptionCode
Methods description
locationcode    nextTop
 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
parentcodeprevnextTop
 Title   : parent
Usage : my $sf = $proxy->parent()
Function: returns the seqfeature parent of this proxy
Returns : Bio::SeqFeatureI object
Args : none
startcodeprevnextTop
 Title   : start
Usage : $start = $feat->start
$feat->start(20)
Function: Get
Returns : integer
Args : none
endcodeprevnextTop
 Title   : end
Usage : $end = $feat->end
$feat->end($end)
Function: get
Returns : integer
Args : none
lengthcodeprevnextTop
 Title   : length
Usage :
Function:
Example :
Returns :
Args :
strandcodeprevnextTop
 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_seqcodeprevnextTop
 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 :
seqcodeprevnextTop
 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_seqcodeprevnextTop
 Title   : entire_seq
Usage : $whole_seq = $sf->entire_seq()
Function: gives the entire sequence that this seqfeature is attached to
Example :
Returns :
Args :
seqnamecodeprevnextTop
 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)
primary_tagcodeprevnextTop
 Title   : primary_tag
Usage : $tag = $feat->primary_tag()
Function: Returns the primary tag for a feature,
eg 'exon'
Returns : a string
Args : none
source_tagcodeprevnextTop
 Title   : source_tag
Usage : $tag = $feat->source_tag()
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
has_tagcodeprevnextTop
 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_valuescodeprevnextTop
 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_tagscodeprevnextTop
 Title   : get_all_tags
Usage : @tags = $feat->get_all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller, @args) = @_;
    my $self = $caller->SUPER::new(@args);

    my ($feature,$location) = $self->_rearrange([qw(PARENT LOC)],@args);

    if( !defined $feature || !ref $feature || !$feature->isa('Bio::SeqFeatureI') ) {
      $self->throw("Must have a parent feature, not a [$feature]");
    }

    if( $feature->isa("Bio::SeqFeature::PositionProxy") ) {
      $feature = $feature->parent();
    }

    if( !defined $location || !ref $location || !$location->isa('Bio::LocationI') ) {
      $self->throw("Must have a location, not a [$location]");
    }


    return $self;
}
locationdescriptionprevnextTop
sub location {
    my($self, $value ) = @_;  

    if (defined($value)) {
        unless (ref($value) and $value->isa('Bio::LocationI')) {
            $self->throw("object $value pretends to be a location but ".
                "does not implement Bio::LocationI");
        }
        $self->{'_location'} = $value;
    }
    elsif (! $self->{'_location'}) {
        # guarantees a real location object is returned every time
$self->{'_location'} = Bio::Location::Simple->new(); } return $self->{'_location'};
}
parentdescriptionprevnextTop
sub parent {
    my($self, $value ) = @_;  

    if (defined($value)) {
        unless (ref($value) and $value->isa('Bio::SeqFeatureI')) {
            $self->throw("object $value pretends to be a location but ".
                "does not implement Bio::SeqFeatureI");
        }
        $self->{'_parent'} = $value;
    }

    return $self->{'_parent'};
}
startdescriptionprevnextTop
sub start {
   my ($self,$value) = @_;
   return $self->location->start($value);
}
enddescriptionprevnextTop
sub end {
   my ($self,$value) = @_;
   return $self->location->end($value);
}
lengthdescriptionprevnextTop
sub length {
   my ($self) = @_;
   return $self->end - $self->start() + 1;
}
stranddescriptionprevnextTop
sub strand {
   my ($self,$value) = @_;
   return $self->location->strand($value);
}
attach_seqdescriptionprevnextTop
sub attach_seq {
   my ($self, $seq) = @_;

   if ( !defined $seq || !ref $seq || ! $seq->isa("Bio::PrimarySeqI") ) {
       $self->throw("Must attach Bio::PrimarySeqI objects to SeqFeatures");
   }

   $self->{'_gsf_seq'} = $seq;

   # attach to sub features if they want it
foreach my $sf ( $self->sub_SeqFeature() ) { if ( $sf->can("attach_seq") ) { $sf->attach_seq($seq); } } return 1;
}
seqdescriptionprevnextTop
sub seq {
   my ($self, $arg) = @_;

   if ( defined $arg ) {
       $self->throw("Calling SeqFeature::PositionProxy->seq with an argument. You probably want attach_seq");
   }

   if ( ! exists $self->{'_gsf_seq'} ) {
       return;
   }

   # assumming our seq object is sensible, it should not have to yank
# the entire sequence out here.
my $seq = $self->{'_gsf_seq'}->trunc($self->start(), $self->end()); if ( $self->strand == -1 ) { $seq = $seq->revcom; } return $seq;
}
entire_seqdescriptionprevnextTop
sub entire_seq {
   my ($self) = @_;

   return unless exists($self->{'_gsf_seq'});
   return $self->{'_gsf_seq'};
}
seqnamedescriptionprevnextTop
sub seqname {
    my ($obj,$value) = @_;
    if ( defined $value ) {
        $obj->{'_gsf_seqname'} = $value;
    }
    return $obj->{'_gsf_seqname'};
}
primary_tagdescriptionprevnextTop
sub primary_tag {
   my ($self,@args) = @_;

   return $self->parent->primary_tag();
}
source_tagdescriptionprevnextTop
sub source_tag {
   my ($self) = @_;

   return $self->parent->source_tag();
}
has_tagdescriptionprevnextTop
sub has_tag {
   my ($self,$tag) = @_;

   return $self->parent->has_tag($tag);
}
get_tag_valuesdescriptionprevnextTop
sub get_tag_values {
   my ($self,$tag) = @_;

   return $self->parent->get_tag_values($tag);
}
get_all_tagsdescriptionprevnextTop
sub get_all_tags {
   my ($self) = @_;

   return $self->parent->all_tags();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 BirneyTop
Ewan Birney <birney@sanger.ac.uk>
DEVELOPERSTop
This class has been written with an eye out of inheritence. 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
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
ProxiesTop
These functions chain back to the parent for all non sequence related stuff.