remove unused imports

modules/Bio/EnsEMBL/AlignStrainSlice.pm

@@ -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
 

modules/Bio/EnsEMBL/AssemblyMapper.pm

@@ -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);
 

modules/Bio/EnsEMBL/BaseAlignFeature.pm

@@ -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() )

modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm

@@ -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);
 

modules/Bio/EnsEMBL/CircularSlice.pm

@@ -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');
   }

modules/Bio/EnsEMBL/DBEntry.pm

@@ -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);
 

modules/Bio/EnsEMBL/DBFile/CollectionAdaptor.pm

@@ -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);
 

modules/Bio/EnsEMBL/DBFile/FileAdaptor.pm

@@ -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;
 

modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm

@@ -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 );
 

modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm

@@ -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;
   }
 

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -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/;

modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm

@@ -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);
 

modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm

@@ -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);

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/DBConnection.pm

@@ -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);

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -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;

modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm

@@ -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;

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -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 );

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -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