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untabify, remove extra spacing

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1 parent 39585f9 commit feece49067eda9185a055b012e0938cd05edbb2a Chris Fields committed Mar 21, 2012
@@ -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>
#
@@ -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
@@ -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;
@@ -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
@@ -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
@@ -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
@@ -190,7 +190,7 @@ sub map {
Function: Swap the direction of mapping;input <-> output
Example :
Returns : 1
- Args :
+ Args :
=cut
@@ -214,4 +214,3 @@ sub sort{
}
1;
-
@@ -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);
@@ -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;
$self->_is_sorted(0);
@@ -175,18 +175,18 @@ sub add_mapper {
=cut
sub mappers{
- my ($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'}};
}
@@ -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;
@@ -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;
@@ -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>
#
@@ -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;
@@ -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
@@ -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;
@@ -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';
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