Commit 76b7ff0a authored by Arne Stabenau's avatar Arne Stabenau
Browse files

minor changes, formatting

parent d154c61e
......@@ -129,7 +129,7 @@ sub register_region{
$self->throw("$assmapper is not a Bio::EnsEMBL::AssemblyMapper")
unless $assmapper->isa("Bio::EnsEMBL::AssemblyMapper");
my $chr = $self->db->get_ChromosomeAdaptor()->fetch_by_name( $chr_name );
my $chr = $self->db->get_ChromosomeAdaptor()->fetch_by_chr_name( $chr_name );
my $chr_id = $chr->dbID();
my $max_assembly_contig = $self->db()->get_MetaContainer->get_max_assembly_contig();
......@@ -142,7 +142,7 @@ sub register_region{
ass.chr_start,
ass.chr_end
from
assembly ass,
assembly ass
where
ass.chromosome_id = $chr_id and
? <= ass.chr_end and
......
......@@ -1124,7 +1124,8 @@ sub set_adaptor() {
Arg [1] : List of names of feature adaptors to get. If no adaptor names are given, all the defined adaptors are returned.
Example : $db->get_GenericFeature("SomeFeature", "SomeOtherFeature")
Description: Returns a hash containing the named feature adaptors (or all feature adaptors).
Returntype : Hash containing the named feature adaptors (or all feature adaptors).
Returntype : reference to a Hash containing the named
feature adaptors (or all feature adaptors).
Exceptions : If any of the the named generic feature adaptors do not exist.
Caller : external
......@@ -1132,22 +1133,22 @@ sub set_adaptor() {
sub get_GenericFeatureAdaptors() {
my ($self, @names) = @_;
my ($self, @names) = @_;
my %adaptors = {};
my %adaptors = ();
if (!@names) {
%adaptors = %{$self->{'generic_feature_adaptors'}};
} else {
foreach my $name (@names) {
if (!exists($self->{'generic_feature_adaptors'}->{$name})) {
$self->throw("No generic feature adaptor has been defined for $name" );
}
%adaptors->{$name} = $self->{'generic_feature_adaptors'}->{$name};
}
}
if (!@names) {
%adaptors = %{$self->{'generic_feature_adaptors'}};
} else {
foreach my $name (@names) {
if (!exists($self->{'generic_feature_adaptors'}->{$name})) {
$self->throw("No generic feature adaptor has been defined for $name" );
}
$adaptors{$name} = $self->{'generic_feature_adaptors'}->{$name};
}
}
return %adaptors;
return \%adaptors;
}
......
......@@ -70,6 +70,8 @@ sub fetch_by_RawContig_start_end_strand {
my ( $self, $contig, $start, $end, $strand, $compressed ) = @_;
my $sth;
$compressed ||= 0;
if( $start < 1 ) {
$self->throw( "Wrong parameters" );
}
......
......@@ -1496,25 +1496,25 @@ sub get_generic_features() {
my ($self, @names) = @_;
my $db = $self->adaptor()->db();
my $db = $self->adaptor()->db();
my %features = {}; # this will hold the results
my %features = (); # this will hold the results
# get the adaptors for each feature
my %adaptors = $db->get_GenericFeatureAdaptors(@names);
# get the adaptors for each feature
my %adaptors = %{$db->get_GenericFeatureAdaptors(@names)};
foreach my $adaptor_name (keys(%adaptors)) {
foreach my $adaptor_name (keys(%adaptors)) {
my $adaptor_obj = %adaptors->{$adaptor_name};
# get the features and add them to the hash
my $features_ref = $adaptor_obj->fetch_all_by_Slice($self);
# add each feature to the hash to be returned
foreach my $feature (@$features_ref) {
%features->{$adaptor_name} = $feature;
}
}
return %features;
my $adaptor_obj = %adaptors->{$adaptor_name};
# get the features and add them to the hash
my $features_ref = $adaptor_obj->fetch_all_by_Slice($self);
# add each feature to the hash to be returned
foreach my $feature (@$features_ref) {
$features{$adaptor_name} = $feature;
}
}
return \%features;
}
......
......@@ -119,11 +119,11 @@ ok($db->add_GenericFeatureAdaptor("Simple", $sfa));
# Check get-ing the above
# by name ...
my %generic_adaptors = $db->get_GenericFeatureAdaptors("Simple", "Repeat");
my %generic_adaptors = %{$db->get_GenericFeatureAdaptors("Simple", "Repeat")};
ok(%generic_adaptors);
# no arg should return all
%generic_adaptors = $db->get_GenericFeatureAdaptors();
%generic_adaptors = %{$db->get_GenericFeatureAdaptors()};
my $size = keys(%generic_adaptors);
ok($size == 2);
......@@ -135,5 +135,5 @@ ok($@);
my $slice = $db->get_SliceAdaptor()->fetch_by_chr_start_end('X', 1, 10000);
ok($slice);
my %features = $slice->get_generic_features();
ok(%features);
my %features = %{$slice->get_generic_features()};
ok(!%features);
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