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# -*-Perl-*- Test Harness script for Bioperl
# $Id: Range.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 49);
use_ok('Bio::Range');
}
my $range = Bio::Range->new(-start=>10,
-end=>20,
-strand=>1);
isa_ok($range,'Bio::Range', 'BioRange object');
is($range->strand, 1);
my $range2 = Bio::Range->new(-start=>15,
-end=>25,
-strand=>1);
isa_ok($range2,'Bio::Range', 'BioRange object');
is($range2->strand, 1);
my $r = Bio::Range->new();
is ( $r->strand(0), 0 ) ;
is ( $r->start(27), 27 );
is ( $r->end(28), 28 ) ;
ok(! defined $r->intersection($range2));
$r = $range->union($range2);
is($r->start, 10);
is($r->end, 25);
$r = $range->intersection($range2);
is ( $r->start, 15 ) ;
is ( $r->end, 20 );
is ( $r->strand, 1 );
# intersection and union can also take lists
my $range3 = Bio::Range->new(-start=>18,-end=>30);
isa_ok($range3,'Bio::Range', 'BioRange object');
$r = $range->intersection([$range2, $range3]);
ok( ( $r->start == 18 ) && ( $r->end == 20 ));
$r = Bio::Range->intersection([$range, $range2, $range3]);
ok($r->start == 18 && $r->end == 20);
$r = $range->union($range2, $range3);
ok( ( $r->start == 10 ) && ( $r->end == 30 ) );
$r = Bio::Range->union($range, $range2, $range3);
ok( ( $r->start == 10 ) && ( $r->end == 30 ) );
$range3->start(21);
ok (! $range->intersection([$range2, $range3]));
ok (! $range->contains($range2));
ok (! $range2->contains($range));
ok ($range->overlaps($range2));
ok ($range2->overlaps($range));
# testing strand
$range3 = Bio::Range->new(-start => 15,
-end => 25,
-strand => 1);
my $range4 = Bio::Range->new(-start => 15,
-end => 25,
-strand => -1);
isa_ok($range4,'Bio::Range', 'BioRange object');
my $range5 = Bio::Range->new(-start => 15,
-end => 25,
-strand => 0);
isa_ok($range5,'Bio::Range', 'BioRange object');
my $range6 = Bio::Range->new(-start => 20,
-end => 30,
-strand => -1);
isa_ok($range6,'Bio::Range', 'BioRange object');
ok $range3->_ignore($range4), ' 1 & -1' ;
ok $range3->_weak($range3),' 1 & 1 true' ;
ok $range3->_weak($range5), ' 1 & 0 true' ;
ok (! $range3->_weak($range4), ' 1 & -1 false' );
ok $range3->_strong($range3), ' 1 & 1 true' ;
ok (! $range3->_strong($range5), ' 1 & 0 false' );
ok (! $range3->_strong($range4), ' 1 & -1 false' );
ok ! ( $range3->overlaps($range4,'weak'));
ok ! ( $range4->overlaps($range3,'weak'));
ok ! ( $range3->overlaps($range4,'strong'));
ok ! ( $range4->overlaps($range3,'strong'));
$range3->strand(0);
ok ( $range3->overlaps($range4,'weak'));
ok ( $range4->overlaps($range3,'weak'));
ok ! ( $range3->overlaps($range4,'strong'));
ok ! ( $range4->overlaps($range3,'strong'));
# if strands are different then intersection() should return 0...
$r = $range3->intersection($range4);
is ( $r->strand, 0 );
# or if both strands are -1 then -1 should be returned
$r = $range6->intersection($range4);
is ( $r->strand, -1 );
# test implemention of offsetStranded:
$r = Bio::Range->new(-start => 30, -end => 40, -strand => -1);
isa_ok($r, 'Bio::Range', 'Bio::Range object') ;
is ($r->offsetStranded(-5,10)->toString, '(20, 45) strand=-1');
is ($r->offsetStranded(+5,-10)->toString, '(30, 40) strand=-1');
$r->strand(1);
is ($r->offsetStranded(-5,10)->toString, '(25, 50) strand=1');
is ($r->offsetStranded(+5,-10)->toString, '(30, 40) strand=1');
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