t/SeqFeature/RangeI.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 45);
  10
  11     use_ok('Bio::SeqFeature::Generic');
  12 }
  13
  14 my @funcs = qw(start end length strand overlaps contains
  15     equals intersection union overlap_extent disconnected_ranges
  16     offsetStranded subtract);
  17
  18 my $i = 1;
  19 while (my $func = shift @funcs ) {
  20     $i++;
  21
  22     # test for presence of method
  23     ok exists $Bio::RangeI::{$func};
  24
  25     # union get caught in an infinite loop w/o parameters; skip invoke test.
  26     next if $func eq 'union';
  27
  28     # call to strand complains without a value; skip invoke test.
  29     next if $func eq 'disconnected_ranges';
  30
  31     # test invocation of method
  32     eval { $Bio::RangeI::{$func}->(); };
  33     ok($@);
  34 }
  35
  36 ### unit tests for subtract method ###
  37 # contributed by Stephen Montgomery (sm8 at sanger.ac.uk), who also
  38 # wrote the subtract method
  39 my $feature1 =  Bio::SeqFeature::Generic->new( -start => 1, -end =>
  40 1000, -strand => 1);
  41 my $feature2 =  Bio::SeqFeature::Generic->new( -start => 100, -end =>
  42 900, -strand => -1);
  43
  44 my $subtracted = $feature1->subtract($feature2);
  45 ok(defined($subtracted));
  46 is(scalar(@$subtracted), 2);
  47 foreach my $range (@$subtracted) {
  48     ok($range->start == 1 || $range->start == 901);
  49     ok($range->end == 99 || $range->end == 1000);
  50 }
  51
  52 $subtracted = $feature2->subtract($feature1);
  53 ok(!defined($subtracted));
  54 $subtracted = $feature1->subtract($feature2, 'weak');
  55 ok(!defined($subtracted));
  56 $subtracted = $feature1->subtract($feature2, 'strong');
  57 ok(!defined($subtracted));
  58
  59 my $feature3 =  Bio::SeqFeature::Generic->new( -start => 500, -end =>
  60 1500, -strand => 1);
  61 $subtracted = $feature1->subtract($feature3);
  62 ok(defined($subtracted));
  63 is scalar(@$subtracted), 1;
  64 my $subtracted_i = @$subtracted[0];
  65 is($subtracted_i->start, 1);
  66 is($subtracted_i->end, 499);
  67
  68
  69 # ---------------
  70 # Added Bio::Location::SplitLocationI support to subtract().  --jhannah 20091018
  71 $feature1 =  Bio::SeqFeature::Generic->new();
  72 $feature2 =  Bio::SeqFeature::Generic->new();
  73 my $loc = Bio::Location::Split->new();
  74 $loc->add_sub_Location(Bio::Location::Simple->new(-start=>100, -end=>200, -strand=>1));
  75 $loc->add_sub_Location(Bio::Location::Simple->new(-start=>300, -end=>400, -strand=>1));
  76 $loc->add_sub_Location(Bio::Location::Simple->new(-start=>500, -end=>600, -strand=>1));
  77 $feature1->location($loc);
  78 $loc = Bio::Location::Split->new();
  79 $loc->add_sub_Location(Bio::Location::Simple->new(-start=>350, -end=>400, -strand=>1));
  80 $loc->add_sub_Location(Bio::Location::Simple->new(-start=>500, -end=>510, -strand=>1));
  81 $feature2->location($loc);
  82 $subtracted = $feature1->subtract($feature2);
  83 is(@$subtracted, 3,                              "subtract() of split features");
  84 is($subtracted->[0]->start, 100,                 "   0 start");
  85 is($subtracted->[0]->end,   200,                 "   0 end");
  86 is($subtracted->[1]->start, 300,                 "   1 start");
  87 is($subtracted->[1]->end,   349,                 "   1 end");
  88 is($subtracted->[2]->start, 511,                 "   2 start");
  89 is($subtracted->[2]->end,   600,                 "   2 end");
  90 # ---------------
  91
  92