Bio::Location SplitLocationI
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Summary
Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence
which has multiple locations (start/end points)
Package variables
No package variables defined.
Included modules
Carp
Inherit
Bio::LocationI
Synopsis
  # get a SplitLocationI somehow
print $splitlocation->start, "..", $splitlocation->end, "\n";
my @sublocs = $splitlocation->sub_Location();
my $count = 1; # print the start/end points of the sub locations foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) { printf "sub feature %d [%d..%d]\n", $location->start,$location->end; $count++; }
Description
This interface encapsulates the necessary methods for representing the
location of a sequence feature that has more that just a single
start/end pair. Some examples of this are the annotated exons in a
gene or the annotated CDS in a sequence file.
Methods
sub_LocationDescriptionCode
splittypeDescriptionCode
is_single_sequenceDescriptionCode
Methods description
sub_Locationcode    nextTop
 Title   : sub_Location
Usage : @locations = $feat->sub_Location();
Function: Returns an array of LocationI objects
Returns : An array
Args : none
splittypecodeprevnextTop
  Title   : splittype
Usage : $splittype = $fuzzy->splittype();
Function: get/set the split splittype
Returns : the splittype of split feature (join, order)
Args : splittype to set
is_single_sequencecodeprevnextTop
  Title   : is_single_sequence
Usage : if($splitloc->is_single_sequence()) {
print "Location object $splitloc is split ".
"but only across a single sequence\n";
}
Function: Determine whether this location is split across a single or
multiple sequences.
Returns : TRUE if all sublocations lie on the same sequence as the root
location (feature), and FALSE otherwise.
Args : none
Methods code
sub_LocationdescriptionprevnextTop
sub sub_Location {
    my ($self,@args) = @_;
    $self->throw_not_implemented();
}
splittypedescriptionprevnextTop
sub splittype {
    my($self) = @_;
    $self->throw_not_implemented();
}
is_single_sequencedescriptionprevnextTop
sub is_single_sequence {
    my ($self) = @_;
    $self->throw_not_implemented();
}
General documentation
FEEDBACKTop
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 - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Bio::LocationI methodsTop
Bio::LocationI inherited methods follow
min_startTop
  Title   : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : none
max_startTop
  Title   : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : none
start_pos_typeTop
  Title   : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
min_endTop
  Title   : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args : none
max_endTop
  Title   : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending location of feature endpoint
Returns : integer or undef if no maximum ending point.
Args : none
end_pos_typeTop
  Title   : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
seq_idTop
  Title   : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args : [optional] seq_id value to set
coordinate_policyTop
  Title   : coordinate_policy
Usage : $policy = $location->coordinate_policy();
$location->coordinate_policy($mypolicy); # set may not be possible
Function: Get the coordinate computing policy employed by this object.
See Bio::Location::CoordinatePolicyI for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A Bio::Location::CoordinatePolicyI implementing object. Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
to_FTstringTop
  Title   : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none