diff variant_effect_predictor/Bio/LiveSeq/Range.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/LiveSeq/Range.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,138 @@
+# $Id: Range.pm,v 1.7 2001/06/18 08:27:53 heikki Exp $
+#
+# bioperl module for Bio::LiveSeq::Range
+#
+# Cared for by Joseph Insana <[e-mail]> <[e-mail]>
+#
+# Copyright Joseph Insana
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::LiveSeq::Range - Range abstract class for LiveSeq
+
+=head1 SYNOPSIS
+
+  # documentation needed
+
+=head1 DESCRIPTION
+
+This is used as parent for exon and intron classes.
+
+=head1 AUTHOR - Joseph A.L. Insana
+
+Email:  [e-mail], [e-mail]
+
+Address: 
+
+     EMBL Outstation, European Bioinformatics Institute
+     Wellcome Trust Genome Campus, Hinxton
+     Cambs. CB10 1SD, United Kingdom 
+
+=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::LiveSeq::Range;
+$VERSION=1.6;
+
+# Version history:
+# Mon Mar 20 22:21:44 GMT 2000 v 1.0 begun
+# Tue Mar 21 00:50:05 GMT 2000 v 1.1 new() added
+# Tue Mar 21 02:44:45 GMT 2000 v 1.2 private start(), more checks in new()
+# Thu Mar 23 19:06:03 GMT 2000 v 1.3 follows() replaces is_downstream
+# Wed Apr 12 16:35:12 BST 2000 v 1.4 added valid()
+# Mon Jun 26 15:25:14 BST 2000 v 1.44 ranges with start=end are now accepted / valid() removed because inherited now from SeqI
+# Tue Jun 27 14:06:06 BST 2000 v 1.5 croak changed to carp and return(-1) in new() function
+# Wed Mar 28 16:47:36 BST 2001 v 1.6 carp -> warn,throw (coded methods in SeqI)
+
+use strict;
+use vars qw($VERSION @ISA);
+use Bio::LiveSeq::SeqI 3.2; # uses SeqI, inherits from it
+@ISA=qw(Bio::LiveSeq::SeqI);
+
+=head2 new
+
+  Title   : new
+  Usage   : $range1 = Bio::LiveSeq::Range->new(-seq => $obj_ref,
+                                               -start => $beginlabel,
+                                               -end => $endlabel, -strand => 1);
+
+  Function: generates a new Bio::LiveSeq::Range
+  Returns : reference to a new object of class Range
+  Errorcode -1
+  Args    : two labels, an obj_ref and an integer
+            strand 1=forward strand, strand -1=reverse strand
+            if strand not specified, it defaults to 1
+            the -seq argument must point to the underlying DNA LiveSeq object
+
+=cut
+
+sub new {
+  my ($thing, %args) = @_;
+  my $class = ref($thing) || $thing;
+  my ($obj,%range);
+
+  my ($seq,$start,$end,$strand)=($args{-seq},$args{-start},$args{-end},$args{-strand});
+
+  $obj = \%range;
+  $obj = bless $obj, $class;
+
+  unless ($seq->valid($start)) {
+    $obj->warn("$class not initialised because start label not valid");
+    return (-1);
+  }
+  unless ($seq->valid($end)) {
+    $obj->warn("$class not initialised because end label not valid");
+    return (-1);
+  }
+  unless (defined $strand) {
+    $strand = 1;
+  }
+  if (($strand != 1)&&($strand != -1)) {
+    $obj->warn("$class not initialised because strand identifier not valid. Use 1 (forward strand) or -1 (reverse strand).");
+    return (-1);
+  }
+  if ($start eq $end) {
+    $obj->warn("$class reports: start and end label are the same....");
+  } else {
+    unless ($seq->follows($start,$end,$strand)==1) {
+      $obj->warn("Fatal: end label $end doesn't follow start label $start for strand $strand!");
+      return (-1);
+    }
+  }
+  #if ($strand == 1) {
+  #  unless ($seq->is_downstream($start,$end)==1) {
+  #    croak "Fatal: end label not downstream of start label for forward strand!";
+  #  }
+  #} else {
+  #  unless ($seq->is_upstream($start,$end)==1) {
+  #    croak "Fatal: end label not upstream of start label for reverse strand!";
+  #  }
+  #}
+  $obj->{'seq'}=$seq;
+  $obj->{'start'}=$start;
+  $obj->{'end'}=$end;
+  $obj->{'strand'}=$strand;
+  return $obj;
+}
+
+=head2 valid
+
+  Title   : valid
+  Usage   : $boolean = $obj->valid($label)
+  Function: tests if a label exists AND is part of the object
+  Returns : boolean
+  Args    : label
+
+=cut
+
+1;