t/SeqFeature/Clone.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2
   3 use strict;
   4
   5 BEGIN {
   6     use Bio::Root::Test;
   7     use Bio::SeqFeature::Generic;
   8     use Bio::Location::Split;
   9
  10     test_begin(-tests => 17);
  11 }
  12
  13 my $DEBUG = test_debug();
  14
  15 my $orig = Bio::SeqFeature::Generic->new(
  16                                        -start => 40,
  17                                        -end => 80,
  18                                        -strand => 1,
  19                                        -primary => 'exon',
  20                                        -source  => 'internal',
  21                                        -tag => {
  22                                            silly => 20,
  23                                            new => 1
  24                                            }
  25                                        );
  26
  27 # ----------
  28 # Verify simple attributes work and are independent of each other
  29 ok(my $clone = $orig->clone(),                'clone()');
  30 ok($clone->start(140),                        'start() clone set');
  31 is($clone->start(),     140,                  'start() clone get');
  32 is($orig->start(),      40,                   'start() original unchanged');
  33
  34 # ----------
  35 # Verify that arguments passed into clone() are applied to the cloned object
  36 # and that the attributes are still independent.
  37 ok($clone = $orig->clone(-start => 150, -end => 157),   'clone() with arguments');
  38 is($orig->start(),       40,                  'start() orig get');
  39 is($orig->end(),         80,                  'end() orig get');
  40 is($clone->start(),     150,                  'start() clone get');
  41 is($clone->end(),       157,                  'end() clone get');
  42 ok($clone->start(140),                        'start() clone set');
  43 is($clone->start(),     140,                  'start() clone get');
  44 is($orig->start(),       40,                  'start() original unchanged');
  45
  46 # ----------
  47 # Verify that object attributes can be cloned, and are independent after cloning
  48 my $splitlocation = Bio::Location::Split->new();
  49 $splitlocation->add_sub_Location(Bio::Location::Simple->new(
  50    -start=>1, -end=>30, -strand=>1
  51 ));
  52 $splitlocation->add_sub_Location(Bio::Location::Simple->new(
  53    -start=>50, -end=>61, -strand=>1
  54 ));
  55 ok($orig->location($splitlocation),                      'location() Bio::Location::Split');
  56 ok($clone = $orig->clone(),                           'clone()');
  57 ok(($clone->location->sub_Location())[1]->start(51),     'start() clone set');
  58 is(($clone->location->sub_Location())[1]->start,     51, 'start() clone get');
  59 is(($orig->location->sub_Location())[1]->start,      50, 'start() original unchanged');
  60
  61