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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Location.t,v 1.21 2002/02/03 21:00:19 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 45;
}
use Bio::Location::Simple;
use Bio::Location::Split;
use Bio::Location::Fuzzy;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::SimilarityPair;
use Bio::SeqFeature::FeaturePair;
ok(1);
my $simple = new Bio::Location::Simple('-start' => 10, '-end' => 20,
'-strand' => 1);
ok $simple->isa('Bio::LocationI') && $simple->isa('Bio::RangeI');
ok $simple->start, 10;
ok $simple->end, 20;
my $generic = new Bio::SeqFeature::Generic('-start' => 5, '-end' => 30,
'-strand' => 1);
ok $generic->isa('Bio::SeqFeatureI') && $generic->isa('Bio::RangeI');
ok $generic->start, 5;
ok $generic->end, 30;
my $similarity = new Bio::SeqFeature::SimilarityPair();
my $feat1 = new Bio::SeqFeature::Generic('-start' => 30, '-end' => 43,
'-strand' => -1);
my $feat2 = new Bio::SeqFeature::Generic('-start' => 80, '-end' => 90,
'-strand' => -1);
my $featpair = new Bio::SeqFeature::FeaturePair('-feature1' => $feat1,
'-feature2' => $feat2 );
my $feat3 = new Bio::SeqFeature::Generic('-start' => 35, '-end' => 50,
'-strand' => -1);
ok($featpair->start, 30);
ok($featpair->end, 43);
ok($featpair->length, 14);
ok($featpair->overlaps($feat3));
ok($generic->overlaps($simple));
ok($generic->contains($simple));
# fuzzy location tests
my $fuzzy = new Bio::Location::Fuzzy('-start' =>'<10', '-end' => 20,
-strand=>1);
ok($fuzzy->strand, 1);
ok($fuzzy->start, 10);
ok($fuzzy->end,20);
ok(! defined $fuzzy->min_start);
ok($fuzzy->max_start, 10);
ok($fuzzy->min_end, 20);
ok($fuzzy->max_end, 20);
ok($fuzzy->location_type, 'EXACT');
ok($fuzzy->start_pos_type, 'BEFORE');
ok($fuzzy->end_pos_type, 'EXACT');
# split location tests
my $splitlocation = new Bio::Location::Split;
my $f = new Bio::Location::Simple('-start'=>13,
'-end'=>30,
'-strand'=>1);
$splitlocation->add_sub_Location($f);
ok($f->start, 13);
ok($f->min_start, 13);
ok($f->max_start,13);
$f = new Bio::Location::Simple('-start'=>30,
'-end'=>90,
'-strand'=>1);
$splitlocation->add_sub_Location($f);
$f = new Bio::Location::Simple('-start'=>18,
'-end'=>22,
'-strand'=>1);
$splitlocation->add_sub_Location($f);
$f = new Bio::Location::Simple('-start'=>19,
'-end'=>20,
'-strand'=>1);
$splitlocation->add_sub_Location($f);
$f = new Bio::Location::Fuzzy('-start'=>"<50",
'-end'=>61,
'-strand'=>1);
ok($f->start, 50);
ok(! defined $f->min_start);
ok($f->max_start, 50);
$splitlocation->add_sub_Location($f);
ok($splitlocation->max_end, 90);
ok($splitlocation->min_start, 13);
ok($splitlocation->end, 90);
ok($splitlocation->start, 13);
ok($splitlocation->sub_Location(),5);
ok($fuzzy->to_FTstring(), '<10..20');
$fuzzy->strand(-1);
ok($fuzzy->to_FTstring(), 'complement(<10..20)');
ok($simple->to_FTstring(), '10..20');
$simple->strand(-1);
ok($simple->to_FTstring(), 'complement(10..20)');
ok( $splitlocation->to_FTstring(), 'join(13..30,30..90,18..22,19..20,<50..61)');
# test for bug #1074
$f = new Bio::Location::Simple(-start => 5,
-end => 12,
-strand => -1);
$splitlocation->add_sub_Location($f);
ok( $splitlocation->to_FTstring(), 'join(13..30,30..90,18..22,19..20,<50..61,complement(5..12))');
$splitlocation->strand(-1);
ok( $splitlocation->to_FTstring(), 'join(13..30,30..90,18..22,19..20,<50..61,complement(5..12))');
$f = new Bio::Location::Fuzzy(-start => '45.60',
-end => '75^80');
ok($f->to_FTstring(), '45.60..75^80');
$f->start('20>');
ok($f->to_FTstring(), '>20..75^80');
# test that even when end < start that length is always positive
$f = new Bio::Location::Simple(-verbose => -1,
-start => 100, -end => 20, -strand => 1);
ok($f->length, 81);
ok($f->strand,-1);
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