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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Location/FuzzyLocationI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,204 @@
+# $Id: FuzzyLocationI.pm,v 1.17 2002/12/01 00:05:20 jason Exp $
+#
+# BioPerl module for Bio::Location::FuzzyLocationI
+# 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::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence
+which has unclear start/end location
+
+=head1 SYNOPSIS
+
+    # Get a FuzzyLocationI object somehow
+    print "Fuzzy FT location string is ", $location->to_FTstring();
+    print "location is of the type ", $location->loc_type, "\n";
+
+=head1 DESCRIPTION
+
+This interface encapsulates the necessary methods for representing a
+Fuzzy Location, one that does not have clear start and/or end points.
+This will initially serve to handle features from Genbank/EMBL feature
+tables that are written as 1^100 meaning between bases 1 and 100 or
+E<lt>100..300 meaning it starts somewhere before 100.  Advanced
+implementations of this interface may be able to handle the necessary
+logic of overlaps/intersection/contains/union.  It was constructed to
+handle fuzzy locations that can be represented in Genbank/EMBL.
+
+=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::FuzzyLocationI;
+use vars qw(@ISA);
+use strict;
+
+use Bio::LocationI;
+use Carp;
+
+@ISA = qw(Bio::LocationI);
+
+=head1 LocationI methods
+
+=head2 location_type
+
+  Title   : loc_type
+  Usage   : my $location_type = $location->location_type();
+  Function: Get location type encoded as text
+  Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
+  Args    : none
+
+=cut
+
+sub location_type {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head1 Bio::LocationI methods
+
+Bio::LocationI 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;