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untabify, remove extra spacing
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Chris Fields committed Mar 21, 2012
1 parent 39585f9 commit feece49
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Showing 12 changed files with 576 additions and 581 deletions.
31 changes: 15 additions & 16 deletions lib/Bio/Coordinate/Chain.pm
@@ -1,7 +1,7 @@
#
# bioperl module for Bio::Coordinate::Chain
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
Expand Down Expand Up @@ -64,15 +64,15 @@ 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:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Expand Down Expand Up @@ -126,19 +126,19 @@ sub map {
my ($self,$value) = @_;

$self->throw("Need to pass me a value.")
unless defined $value;
unless defined $value;
$self->throw("I need a Bio::Location, not [$value]")
unless $value->isa('Bio::LocationI');
unless $value->isa('Bio::LocationI');
$self->throw("No coordinate mappers!")
unless $self->each_mapper;
unless $self->each_mapper;

my $res = Bio::Coordinate::Result->new();

foreach my $mapper ($self->each_mapper) {

my $res = $mapper->map($value);
return unless $res->each_match;
$value = $res->match;
my $res = $mapper->map($value);
return unless $res->each_match;
$value = $res->match;
}

return $value;
Expand All @@ -155,7 +155,7 @@ sub map {
Usage : $obj->add_mapper($mapper)
Function: Pushes one Bio::Coodinate::MapperI into the list of mappers.
Sets _is_sorted() to false.
Example :
Example :
Returns : 1 when succeeds, 0 for failure.
Args : mapper object
Expand All @@ -166,7 +166,7 @@ sub map {
Title : mappers
Usage : $obj->mappers();
Function: Returns or sets a list of mappers.
Example :
Example :
Returns : array of mappers
Args : array of mappers
Expand All @@ -177,7 +177,7 @@ sub map {
Title : each_mapper
Usage : $obj->each_mapper();
Function: Returns a list of mappers.
Example :
Example :
Returns : array of mappers
Args : none
Expand All @@ -190,7 +190,7 @@ sub map {
Function: Swap the direction of mapping;input <-> output
Example :
Returns : 1
Args :
Args :
=cut

Expand All @@ -214,4 +214,3 @@ sub sort{
}

1;

68 changes: 34 additions & 34 deletions lib/Bio/Coordinate/Collection.pm
Expand Up @@ -119,13 +119,13 @@ sub new {
$self->{'_mappers'} = [];

my($in, $out, $strict, $mappers, $return_match) =
$self->_rearrange([qw(IN
$self->_rearrange([qw(IN
OUT
STRICT
MAPPERS
RETURN_MATCH
)],
@args);
)],
@args);

$in && $self->in($in);
$out && $self->out($out);
Expand Down Expand Up @@ -155,8 +155,8 @@ sub add_mapper {

# test pair range lengths
$self->warn("Coordinates in pair [". $value . ":" .
$value->in->seq_id . "/". $value->out->seq_id .
"] are not right.")
$value->in->seq_id . "/". $value->out->seq_id .
"] are not right.")
unless $value->test;

$self->_is_sorted(0);
Expand All @@ -175,18 +175,18 @@ sub add_mapper {
=cut

sub mappers{
my ($self,@args) = @_;

if (@args) {
if (@args == 1 && ref $args[0] eq 'ARRAY') {
@args = @{$args[0]};
}
$self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
unless defined $args[0] && $args[0]->isa('Bio::Coordinate::MapperI');
push(@{$self->{'_mappers'}}, @args);
}

return @{$self->{'_mappers'}};
my ($self,@args) = @_;

if (@args) {
if (@args == 1 && ref $args[0] eq 'ARRAY') {
@args = @{$args[0]};
}
$self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
unless defined $args[0] && $args[0]->isa('Bio::Coordinate::MapperI');
push(@{$self->{'_mappers'}}, @args);
}

return @{$self->{'_mappers'}};
}


Expand Down Expand Up @@ -266,10 +266,10 @@ sub test {

foreach my $mapper ($self->each_mapper) {
unless( $mapper->test ) {
$self->warn("Coordinates in pair [". $mapper . ":" .
$mapper->in->seq_id . "/". $mapper->out->seq_id .
"] are not right.");
$res = 0;
$self->warn("Coordinates in pair [". $mapper . ":" .
$mapper->in->seq_id . "/". $mapper->out->seq_id .
"] are not right.");
$res = 0;
}
}
$res;
Expand Down Expand Up @@ -343,31 +343,31 @@ IDMATCH: {
# bail out now we if are forcing the use of an ID
# and it is not in this collection
last IDMATCH if defined $value->seq_id &&
! $self->{'_in_ids'}->{$value->seq_id};
! $self->{'_in_ids'}->{$value->seq_id};

foreach my $pair ($self->each_mapper) {

# if we are limiting input to a certain ID
next if defined $value->seq_id && $value->seq_id ne $pair->in->seq_id;
# if we are limiting input to a certain ID
next if defined $value->seq_id && $value->seq_id ne $pair->in->seq_id;

# if we haven't even reached the start, move on
next if $pair->in->end < $value->start;
# if we have over run, break
last if $pair->in->start > $value->end;
# if we haven't even reached the start, move on
next if $pair->in->end < $value->start;
# if we have over run, break
last if $pair->in->start > $value->end;

my $subres = $pair->map($value);
$result->add_result($subres);
my $subres = $pair->map($value);
$result->add_result($subres);
}
}

$result->seq_id($result->match->seq_id) if $result->match;
unless ($result->each_Location) {
#build one gap;
my $gap = Bio::Location::Simple->new(-start => $value->start,
-end => $value->end,
-strand => $value->strand,
-location_type => $value->location_type
);
-end => $value->end,
-strand => $value->strand,
-location_type => $value->location_type
);
$gap->seq_id($value->seq_id) if defined $value->seq_id;
bless $gap, 'Bio::Coordinate::Result::Gap';
$result->seq_id($value->seq_id) if defined $value->seq_id;
Expand Down
34 changes: 17 additions & 17 deletions lib/Bio/Coordinate/ExtrapolatingPair.pm
@@ -1,7 +1,7 @@
#
# bioperl module for Bio::Coordinate::ExtrapolatingPair
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
Expand All @@ -22,18 +22,18 @@ Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate set
use Bio::Coordinate::ExtrapolatingPair;
$match1 = Bio::Location::Simple->new
$match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
$pair = Bio::Coordinate::ExtrapolatingPair->
new(-in => $match1,
-out => $match2,
-strict => 1
-out => $match2,
-strict => 1
);
$pos = Bio::Location::Simple->new
$pos = Bio::Location::Simple->new
(-start => 40, -end => 60, -strand=> 1 );
$res = $pair->map($pos);
$res->start eq 20;
Expand Down Expand Up @@ -67,15 +67,15 @@ 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:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Expand Down Expand Up @@ -115,9 +115,9 @@ sub new {
my $self = $class->SUPER::new(@args);

my($strict) =
$self->_rearrange([qw(STRICT
)],
@args);
$self->_rearrange([qw(STRICT
)],
@args);

$strict && $self->strict($strict);
return $self;
Expand Down Expand Up @@ -230,11 +230,11 @@ sub _map {

my $match = Bio::Location::Simple->
new(-start => $start,
-end => $end,
-strand => $self->strand,
-seq_id => $self->out->seq_id,
-location_type => $value->location_type
);
-end => $end,
-strand => $self->strand,
-seq_id => $self->out->seq_id,
-location_type => $value->location_type
);
$match->strand($match->strand * $value->strand) if $value->strand;
bless $match, 'Bio::Coordinate::Result::Match';

Expand Down

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