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line endings
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Chris Fields committed Mar 21, 2012
1 parent feece49 commit c64217b
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Showing 5 changed files with 41 additions and 41 deletions.
2 changes: 1 addition & 1 deletion lib/Bio/Coordinate/Result/Gap.pm
Expand Up @@ -37,7 +37,7 @@ of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
=head2 Support
Please direct usage questions or support issues to the mailing list:
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4 changes: 2 additions & 2 deletions t/Coordinate/CoordinateBoundaryTest.t
Expand Up @@ -7,9 +7,9 @@ use Data::Dumper;
BEGIN {
use lib '.';
use Bio::Root::Test;

test_begin( -tests => 174 );

use_ok('Bio::Location::Simple');
use_ok('Bio::Coordinate::Pair');
}
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6 changes: 3 additions & 3 deletions t/Coordinate/CoordinateGraph.t
Expand Up @@ -3,12 +3,12 @@

use strict;

BEGIN {
BEGIN {
use lib '.';
use Bio::Root::Test;

test_begin(-tests => 7);

use_ok('Bio::Coordinate::Graph');
}

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28 changes: 14 additions & 14 deletions t/Coordinate/CoordinateMapper.t
Expand Up @@ -3,12 +3,12 @@

use strict;

BEGIN {
BEGIN {
use lib '.';
use Bio::Root::Test;

test_begin(-tests => 175);

use_ok('Bio::Location::Simple');
use_ok('Bio::Coordinate::Pair');
use_ok('Bio::Coordinate::Result::Match');
Expand All @@ -23,7 +23,7 @@ ok $c = Bio::Coordinate::Result::Match-> new;
ok $c = Bio::Coordinate::Result::Gap-> new;

# propepide
my $match1 = Bio::Location::Simple->new
my $match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
Expand All @@ -45,7 +45,7 @@ my ($count, $pos, $pos2, $res, $match, $res2);
#
# match within
#
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 25, -end => 25, -strand=> -1 );

# results are in Bio::Coordinate::Result
Expand Down Expand Up @@ -232,7 +232,7 @@ is $res->match->end, 11;
is $res->match->strand, 1;

#
# partial match2 = match & gap
# partial match2 = match & gap
#

$pos = Bio::Location::Simple->new
Expand Down Expand Up @@ -271,7 +271,7 @@ is $gap2->strand, -1;
#

# propepide
$match1 = Bio::Location::Simple->new
$match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 5, -end => 40, -strand=>1 );
# peptide
$match2 = Bio::Location::Simple->new
Expand Down Expand Up @@ -310,7 +310,7 @@ is $match->strand, 1;
# pair1 pair2

# gene
$match1 = Bio::Location::Simple->new
$match1 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 5, -end => 9, -strand=>1 );
# exon2
$match2 = Bio::Location::Simple->new
Expand All @@ -320,7 +320,7 @@ ok my $pair1 = Bio::Coordinate::Pair->new(-in => $match1,
-out => $match2,
);
# gene
my $match3 = Bio::Location::Simple->new
my $match3 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 15, -end => 19, -strand=>1 );
# exon
my $match4 = Bio::Location::Simple->new
Expand Down Expand Up @@ -377,7 +377,7 @@ is $res->each_match, 2;
#
# create the third pair
# gene
my $match5 = Bio::Location::Simple->new
my $match5 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 25, -end => 29, -strand=>1 );
# exon
my $match6 = Bio::Location::Simple->new
Expand Down Expand Up @@ -444,7 +444,7 @@ compare (shift @res, shift @testres);
compare (shift @res, shift @testres);

ok $mapper->swap;
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 2, -end => 5, -strand => -1, -seq_id => '627012');
$res = $mapper->map($pos);
is $res->match->start, 2;
Expand All @@ -457,7 +457,7 @@ is $res->match->seq_id, 'chr1';
#

# testing a simple pair
$match1 = Bio::Location::Simple->new
$match1 = Bio::Location::Simple->new
(-seq_id => 'a', -start => 5, -end => 17, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'b', -start => 1, -end => 13, -strand=>-1 );
Expand Down Expand Up @@ -526,7 +526,7 @@ is $mapper->return_match, 1;
is $mapper->return_match(1), 1;


$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 4, -end => 8, -strand => 1);
$res = $mapper->map($pos);
#print Dumper $res;
Expand Down Expand Up @@ -664,7 +664,7 @@ chr1 625357 1189804 1213915 1 24112 1
chr1 625359 1214016 1216330 1 2315 1
} );
# test the auto-sorting feature
# @sgp_dump = reverse (@sgp_dump) if defined $reverse;
# @sgp_dump = reverse (@sgp_dump) if defined $reverse;

my $first = 1;
for my $line ( @sgp_dump ) {
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42 changes: 21 additions & 21 deletions t/Coordinate/GeneCoordinateMapper.t
Expand Up @@ -3,12 +3,12 @@

use strict;

BEGIN {
BEGIN {
use lib '.';
use Bio::Root::Test;

test_begin(-tests => 116);

use_ok('Bio::Location::Simple');
use_ok('Bio::Coordinate::Pair');
use_ok('Bio::Coordinate::ExtrapolatingPair');
Expand All @@ -32,7 +32,7 @@ ok my $pairr = Bio::Coordinate::ExtrapolatingPair->
-out => $outr
);

my $posr = Bio::Location::Simple->new
my $posr = Bio::Location::Simple->new
(-start => 3, -end => 4, -strand=> 1 );
my $resr = $pairr->map($posr);
is $resr->start, 11;
Expand All @@ -42,7 +42,7 @@ is $resr->strand, -1;


# propepide
my $match1 = Bio::Location::Simple->new
my $match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
Expand All @@ -62,7 +62,7 @@ is $pair->strict(), 1;
my ($count, $pos, $pos2, $res, $match, $res2);

# match within
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 25, -end => 25, -strand=> -1 );
$res = $pair->map($pos);

Expand Down Expand Up @@ -114,7 +114,7 @@ is $res->end, 20;
#

# chr
$match1 = Bio::Location::Simple->new
$match1 = Bio::Location::Simple->new
(-seq_id => 'chr', -start => 21, -end => 40, -strand=>1 );
# gene
$match2 = Bio::Location::Simple->new
Expand All @@ -127,14 +127,14 @@ $match2 = Bio::Location::Simple->new
-strict => 0
);

$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 38, -end => 40, -strand=> 1 );
$res = $pair->map($pos);
is $res->start, 1;
is $res->end, 3;
is $res->strand, -1;

$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 1, -end => 3, -strand=> 1 );
$res = $pair->map($pos);
is $res->start, 38;
Expand All @@ -156,7 +156,7 @@ is $m->peptide_offset(5), 5;


# match within
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 25, -end => 25, -strand=> 1 );
$res = $m->map($pos);

Expand All @@ -171,7 +171,7 @@ is $res->seq_id, 'peptide';
#

# match within
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 4, -end => 5, -strand=> 1 );
$res = $m->map($pos);
is $res->start, -1;
Expand All @@ -186,7 +186,7 @@ is $m->nozero(0), 0;


ok $m->swap;
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 5, -end => 5, -strand=> 1 );
$res = $m->map($pos);
is $res->start, 10;
Expand All @@ -203,7 +203,7 @@ ok $res = $m->_reverse_translate($pos);
is $res->start, 13;
is $res->end, 15;

$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 26, -end => 26, -strand=> 1 );
$m->out('peptide');
$res = $m->map($pos);
Expand All @@ -214,7 +214,7 @@ is $res->start, 4;
# frame
#

$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 1, -end => 3, -strand=> 1 );
$res = $m->_frame($pos);
is $res->start, 1;
Expand All @@ -232,11 +232,11 @@ is $res->end, 3;
# pair1 pair2 pair3

# gene
my $e1 = Bio::Location::Simple->new
my $e1 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 5, -end => 9, -strand=>1 );
my $e2 = Bio::Location::Simple->new
my $e2 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 15, -end => 19, -strand=>1 );
my $e3 = Bio::Location::Simple->new
my $e3 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 25, -end => 29, -strand=>1 );
my @cexons = ($e1, $e2, $e3);

Expand All @@ -257,7 +257,7 @@ is $res->start, 2;
is $res->end, 3;

$m->out('negative_intron');
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 12, -end => 14, -strand=> 1 );
$res = $m->map($pos);
is $res->start, -3;
Expand Down Expand Up @@ -427,7 +427,7 @@ $g2->exons(@exons);
#map_snps($g2, @snp_dump);


$match1 = Bio::Location::Simple->new
$match1 = Bio::Location::Simple->new
(-seq_id => 'a', -start => 5, -end => 17, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'b', -start => 1, -end => 13, -strand=>-1 );
Expand Down Expand Up @@ -472,7 +472,7 @@ is $sublocs[1]->end, 12;
# gene
$e1 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 5, -end => 9, -strand=>-1 );
$e2 = Bio::Location::Simple->new
$e2 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 15, -end => 19, -strand=>-1 );
@cexons = ($e1, $e2);
my $cds= Bio::Location::Simple->new
Expand Down Expand Up @@ -502,7 +502,7 @@ is $sublocs[1]->end, 16;
$m->in('gene');
$m->out('inex');

$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 2, -end => 10, -strand=> 1 );

$res = $m->map($pos);
Expand Down

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