diff variant_effect_predictor/Bio/Location/SplitLocationI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Location/SplitLocationI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,244 @@
+# $Id: SplitLocationI.pm,v 1.14 2002/12/01 00:05:20 jason Exp $
+#
+# BioPerl module for Bio::Location::SplitLocationI
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SplitLocationI - Abstract interface of a Location on a Sequence
+which has multiple locations (start/end points)
+
+=head1 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++;
+    }
+
+=head1 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.
+
+=head1 FEEDBACK
+
+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.
+
+  [e-mail]             - General discussion
+  http://bio.perl.org/MailList.html - About the mailing lists
+
+=head2 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 email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+
+package Bio::Location::SplitLocationI;
+use vars qw(@ISA);
+use strict;
+
+use Bio::LocationI;
+use Carp;
+
+@ISA = qw(Bio::LocationI);
+
+
+=head2 sub_Location
+
+ Title   : sub_Location
+ Usage   : @locations = $feat->sub_Location();
+ Function: Returns an array of LocationI objects
+ Returns : An array
+ Args    : none
+
+=cut
+
+sub sub_Location {
+    my ($self,@args) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 splittype
+
+  Title   : splittype
+  Usage   : $splittype = $fuzzy->splittype();
+  Function: get/set the split splittype
+  Returns : the splittype of split feature (join, order)
+  Args    : splittype to set
+
+=cut
+
+sub splittype {
+    my($self) = @_;
+    $self->throw_not_implemented();
+}
+
+
+=head2 is_single_sequence
+
+  Title   : is_single_sequence
+  Usage   : if($splitloc->is_single_sequence()) {
+                print "Location object $splitloc is split ".
+                      "but only across a single sequence\n";
+	    }
+  Function: Determine whether this location is split across a single or
+            multiple sequences.
+  Returns : TRUE if all sublocations lie on the same sequence as the root
+            location (feature), and FALSE otherwise.
+  Args    : none
+
+=cut
+
+sub is_single_sequence {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head1 Bio::LocationI methods
+
+Bio::LocationI inherited methods follow
+
+=head2 min_start
+
+  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
+
+=cut
+
+=head2 max_start
+
+  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
+
+=cut
+
+=head2 start_pos_type
+
+  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
+
+=cut
+
+=head2 min_end
+
+  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
+
+=cut
+
+=head2 max_end
+
+  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
+
+=cut
+
+=head2 end_pos_type
+
+  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
+
+=cut
+
+=head2 seq_id
+
+  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
+
+=cut
+
+=head2 coordinate_policy
+
+  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.
+
+=cut
+
+=head2 to_FTstring
+
+  Title   : to_FTstring
+  Usage   : my $locstr = $location->to_FTstring()
+  Function: returns the FeatureTable string of this location
+  Returns : string
+  Args    : none
+
+=cut
+
+1;
+