diff variant_effect_predictor/Bio/EnsEMBL/ProjectionSegment.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/ProjectionSegment.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,120 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::ProjectionSegment - part of the list that is returned from
+project function calls
+
+=head1 SYNOPSIS
+
+  $slice =
+    $sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
+
+  my $projection = $slice->project("clone");
+
+  foreach my $projection_segment (@$projection) {
+    print( "  from_start ", $projection_segment->from_start(), "\n" );
+    print( "  from_end   ", $projection_segment->from_end(),   "\n" );
+    print( "  to_Slice   ",
+      $projection_segment->to_Slice()->name(), "\n" );
+  }
+
+=head1 DESCRIPTION
+
+The ProjectionSegment is a helper object to make the arrays returned by
+project more accessible. Instead of writing $segment->[0], $segment->[1]
+or $segment->[2] its possible to use the more descriptive notation of
+$segment->from_start(), $segement->from_end(), $segment->to_Slice().
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::ProjectionSegment;
+
+#
+# WARNING: THIS CLASS IS REPRESENTED BY A BLESSED ARRAY REFERENCE
+#  NOT A HASH REFERENCE
+#
+
+
+
+
+
+=head2 from_start
+
+  Args       : none
+  Example    : $coord_in_fetaure_start = $segment->from_start()
+  Description: First element in projects returned segment lists
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub from_start {
+  my $self = shift;
+  return $self->[0];
+}
+
+
+
+=head2 from_end
+
+  Args       : none
+  Example    : $coord_in_feature_end = $segment->from_end()
+  Description: Second element in projects returned segment lists
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub from_end {
+  my $self = shift;
+  return $self->[1];
+}
+
+
+
+
+=head2 to_Slice
+
+  Args       : none
+  Example    : $target_slice = $segment->to_Slice()
+  Description: Third element in projects returned segment lists
+  Returntype : Bio::EnsEMBL::Slice
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub to_Slice {
+  my $self = shift;
+  return $self->[2];
+}
+
+
+
+1;