Commit 78aa1e3e authored by Magali Ruffier's avatar Magali Ruffier
Browse files

remove unused imports

parent fd2b45b5
......@@ -76,7 +76,7 @@ use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Mapper::RangeRegistry;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
=head2 new
......
......@@ -84,7 +84,7 @@ use strict;
use warnings;
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Scalar::Util qw(weaken);
use Bio::EnsEMBL::Utils::Scalar qw( check_ref);
......
......@@ -440,22 +440,12 @@ sub _ensembl_reverse_complement {
Exceptions : wrong parameters
Caller : general
Status : Medium Risk
: deprecation needs to be removed at some time
=cut
sub transform {
my $self = shift;
# catch for old style transform calls
if( ref $_[0] eq 'HASH') {
deprecate("Calling transform with a hashref is deprecate.\n" .
'Use $feat->transfer($slice) or ' .
'$feat->transform("coordsysname") instead.');
my (undef, $new_feat) = each(%{$_[0]});
return $self->transfer($new_feat->slice);
}
my $new_feature = $self->SUPER::transform(@_);
if ( !defined($new_feature)
|| $new_feature->length() != $self->length() )
......
......@@ -88,7 +88,7 @@ use integer; #use proper arithmetic bitshifts
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Mapper::RangeRegistry;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Scalar::Util qw(weaken);
use Bio::EnsEMBL::Utils::Scalar qw( check_ref);
......
......@@ -73,7 +73,7 @@ use Bio::PrimarySeqI;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception
qw(throw deprecate warning stack_trace_dump);
qw(throw warning);
use Bio::EnsEMBL::RepeatMaskedSlice;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
......@@ -151,15 +151,6 @@ sub new {
START END STRAND ADAPTOR EMPTY) ],
@_ );
#empty is only for backwards compatibility
if ($empty) {
deprecate( "Creation of empty slices is no longer needed "
. "and is deprecated" );
my $self = bless( { 'empty' => 1 }, $class );
$self->adaptor($adaptor);
return $self;
}
if ( !defined($seq_region_name) ) {
throw('SEQ_REGION_NAME argument is required');
}
......
......@@ -52,7 +52,6 @@ use Bio::EnsEMBL::Storable;
use Bio::Annotation::DBLink;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(deprecate);
our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink);
......
......@@ -88,7 +88,7 @@ use strict;
use warnings;
use Bio::EnsEMBL::DBFile::FileAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBFile::FileAdaptor);
......
......@@ -50,7 +50,7 @@ here and BaseFeatureAdaptor.
package Bio::EnsEMBL::DBFile::FileAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use strict;
use warnings;
......
......@@ -69,7 +69,7 @@ use warnings;
use base qw/Bio::EnsEMBL::DBSQL::BaseAdaptor/;
use Bio::EnsEMBL::AltAlleleGroup;
use Bio::EnsEMBL::Utils::Exception qw/throw deprecate warning/;
use Bio::EnsEMBL::Utils::Exception qw/throw warning/;
use Bio::EnsEMBL::Utils::Scalar qw/assert_ref/;
use DBI qw( :sql_types );
......
......@@ -120,7 +120,7 @@ our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
use Bio::EnsEMBL::ArchiveStableId;
use Bio::EnsEMBL::StableIdEvent;
use Bio::EnsEMBL::StableIdHistoryTree;
use Bio::EnsEMBL::Utils::Exception qw(deprecate warning throw);
use Bio::EnsEMBL::Utils::Exception qw(warning throw);
use constant MAX_ROWS => 30;
use constant NUM_HIGH_SCORERS => 20;
......@@ -1134,7 +1134,7 @@ sub add_all_current_to_history {
the stable_id_event tree of the given stable_id. Might well be
empty.
This method isn't deprecated, but in most cases you will rather
This method is valid, but in most cases you will rather
want to use fetch_history_tree_by_stable_id().
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Since every ArchiveStableId knows about it's successors, this is
......@@ -1195,7 +1195,7 @@ sub fetch_successor_history {
in the stable_id_event tree of the given stable_id. Might well
be empty.
This method isn't deprecated, but in most cases you will rather
This method is valid, but in most cases you will rather
want to use fetch_history_tree_by_stable_id().
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Since every ArchiveStableId knows about it's successors, this is
......
......@@ -89,8 +89,7 @@ use Bio::EnsEMBL::ChainedAssemblyMapper;
use Bio::EnsEMBL::TopLevelAssemblyMapper;
use Bio::EnsEMBL::Utils::Cache; #CPAN LRU cache
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
#use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Utils::SeqRegionCache;
use integer; #do proper arithmetic bitshifts
......@@ -233,14 +232,6 @@ sub fetch_by_CoordSystems {
if(!@mapping_path) {
# It is perfectly fine not to have a mapping. No warning needed really
# Just check the return code!!
# warning(
# "There is no mapping defined between these coord systems:\n" .
# $cs1->name() . " " . $cs1->version() . " and " . $cs2->name() . " " .
# $cs2->version()
# );
return undef;
}
......
......@@ -54,7 +54,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Cache;
use Bio::EnsEMBL::Utils::Exception qw(warning throw deprecate stack_trace_dump);
use Bio::EnsEMBL::Utils::Exception qw(warning throw);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Iterator;
use Bio::EnsEMBL::Utils::Scalar qw/assert_ref/;
......
......@@ -54,7 +54,7 @@ use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
......
......@@ -123,7 +123,7 @@ use strict;
use warnings;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::CoordSystem;
use vars qw(@ISA);
......
......@@ -69,7 +69,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::Utils::SeqRegionCache;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Scalar qw(check_ref scope_guard);
use Bio::EnsEMBL::Utils::ConfigRegistry;
......@@ -302,7 +302,6 @@ sub dbc{
Exceptions : none
Caller : EnsWeb
Status : At Risk
: may get deprecated, please use add_db from the registry instead
=cut
......@@ -329,7 +328,6 @@ sub add_db_adaptor {
Exceptions : none
Caller : ?
Status : At Risk
: mey get deprecated, use remove_db instead from the Registry
=cut
......@@ -350,7 +348,6 @@ sub remove_db_adaptor {
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::ProxyAdaptor
Status : At Risk
: may get deprecated soon
: please use Bio::EnsEMBL::Registry->get_all_db_adaptors
=cut
......@@ -373,7 +370,6 @@ sub get_all_db_adaptors {
Exceptions : none
Caller : ?
Status : At Risk
: may get deprecated soon
: please use Bio::EnsEMBL::Registry->get_db_adaptors
=cut
......
......@@ -75,7 +75,7 @@ use DBI;
use Bio::EnsEMBL::DBSQL::StatementHandle;
use Bio::EnsEMBL::Utils::Exception qw/deprecate throw info warning/;
use Bio::EnsEMBL::Utils::Exception qw/deprecate throw warning/;
use Bio::EnsEMBL::Utils::Argument qw/rearrange/;
use Bio::EnsEMBL::Utils::Scalar qw/assert_ref wrap_array/;
use Bio::EnsEMBL::Utils::SqlHelper;
......@@ -159,7 +159,7 @@ sub new {
my $driver = $dbconn ? $dbconn->driver() : $driver_arg;
$driver ||= 'mysql';
if ($driver eq 'pgsql') {
warning("Using 'pgsql' as an alias for the 'Pg' driver is deprecated.");
deprecate("Using 'pgsql' as an alias for the 'Pg' driver is deprecated.");
$driver = 'Pg';
}
$self->driver($driver);
......
......@@ -59,7 +59,7 @@ use Bio::EnsEMBL::DBEntry;
use Bio::EnsEMBL::IdentityXref;
use Bio::EnsEMBL::OntologyXref;
use Bio::EnsEMBL::Utils::Exception qw(deprecate throw warning);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
use strict;
......
......@@ -64,7 +64,7 @@ use base qw/Bio::EnsEMBL::DBSQL::BaseAdaptor/;
use Bio::EnsEMBL::DataFile;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw/throw warning deprecate/;
use Bio::EnsEMBL::Utils::Exception qw/throw/;
use Bio::EnsEMBL::Utils::Scalar qw/:assert/;
my $GLOBAL_BASE_PATH;
......
......@@ -55,7 +55,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
use Bio::EnsEMBL::Utils::Exception qw( warning throw );
use vars qw( @ISA );
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
......
......@@ -72,7 +72,7 @@ package Bio::EnsEMBL::DBSQL::GeneAdaptor;
use strict;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use Bio::EnsEMBL::DBSQL::SliceAdaptor;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
......@@ -1158,10 +1158,7 @@ sub is_ref {
Arg [1] : reference to list of Bio::EnsEMBL::Genes $genes
Example : $gene_adaptor->store_alt_alleles([$gene1, $gene2, $gene3]);
Description: DEPRECATED. Switch to using AltAlleleGroup and the
AltAlleleGroupAdaptor which supports more complex queries
This method creates a group of alternative alleles (i.e. locus)
Description: This method creates a group of alternative alleles (i.e. locus)
from a set of genes. The genes should be genes from alternate
haplotypes which are similar. The genes must already be stored
in this database. WARNING - now that more fine-grained support
......
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