diff --git a/modules/Bio/EnsEMBL/AlignStrainSlice.pm b/modules/Bio/EnsEMBL/AlignStrainSlice.pm
index 012fc7b1e3d10e7c8104252759089c4d442e0cb0..b3493a7c89912f73d979bb9ad6c8afa422ab22a1 100644
--- a/modules/Bio/EnsEMBL/AlignStrainSlice.pm
+++ b/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
diff --git a/modules/Bio/EnsEMBL/AssemblyMapper.pm b/modules/Bio/EnsEMBL/AssemblyMapper.pm
index df35c9a1503788b88f1282cb5a8074ae09ab490a..0f9994135a5b92128dbe4c859ef44b8684ae8ae8 100644
--- a/modules/Bio/EnsEMBL/AssemblyMapper.pm
+++ b/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);
diff --git a/modules/Bio/EnsEMBL/BaseAlignFeature.pm b/modules/Bio/EnsEMBL/BaseAlignFeature.pm
index 6fedb64366aecde6d3c53ed3d39f60d879faf897..2eba206c0e3518b4aa9102cb44ff94fa36b1ecac 100644
--- a/modules/Bio/EnsEMBL/BaseAlignFeature.pm
+++ b/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() != $self->length() )
diff --git a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
index 0086409497ef34cac2f7fd04aa0eca94d3977645..1a5fb87fae0de4172e01c7e67b5eedc546fb5016 100644
--- a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
@@ -88,7 +88,7 @@ use integer; #use proper arithmetic bitshifts
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Mapper::RangeRegistry;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
use Scalar::Util qw(weaken);
use Bio::EnsEMBL::Utils::Scalar qw( check_ref);
diff --git a/modules/Bio/EnsEMBL/CircularSlice.pm b/modules/Bio/EnsEMBL/CircularSlice.pm
index a87ad4031e63a2ec9d13708eba8fd5c1044b5f46..9b4991c3df7ed25b1f7ca18f9ea951c83b510d52 100644
--- a/modules/Bio/EnsEMBL/CircularSlice.pm
+++ b/modules/Bio/EnsEMBL/CircularSlice.pm
@@ -73,7 +73,7 @@ use Bio::PrimarySeqI;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception
- qw(throw deprecate warning stack_trace_dump);
+ qw(throw warning);
use Bio::EnsEMBL::RepeatMaskedSlice;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
@@ -151,15 +151,6 @@ sub new {
START END STRAND ADAPTOR EMPTY) ],
@_ );
- #empty is only for backwards compatibility
- if ($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');
}
diff --git a/modules/Bio/EnsEMBL/DBEntry.pm b/modules/Bio/EnsEMBL/DBEntry.pm
index 634f5527b71ccae5d7da1fabf875589a8a8ae318..7db525b8b1a38aa7ff535f6104169ffbbc1388d6 100644
--- a/modules/Bio/EnsEMBL/DBEntry.pm
+++ b/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);
diff --git a/modules/Bio/EnsEMBL/DBFile/CollectionAdaptor.pm b/modules/Bio/EnsEMBL/DBFile/CollectionAdaptor.pm
index 112353ea017f6666b5ef0ae3b7a718201fc303e1..3bf356e334fbf284bf1bce740db22616c9d075c3 100755
--- a/modules/Bio/EnsEMBL/DBFile/CollectionAdaptor.pm
+++ b/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);
diff --git a/modules/Bio/EnsEMBL/DBFile/FileAdaptor.pm b/modules/Bio/EnsEMBL/DBFile/FileAdaptor.pm
index aa5e0385caa02c991969472f9c2ce813199ea1a8..cb9fd28341a5722f0d9268735964ce4ffd432687 100755
--- a/modules/Bio/EnsEMBL/DBFile/FileAdaptor.pm
+++ b/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;
diff --git a/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
index 45f75b8171fec067b7b98cdb120b5ad3899ac186..e6ef61060b32bea38f680e9626e436e766a91a4a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
+++ b/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 );
diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
index 68a796179f116c33f0f47ed012a38e72635cdc12..58e6ba9dc41507ad2bb6b0dc169a4a0ca2a3b879 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+++ b/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
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index 60ebd94909eeb1a5c7098cc9571da17054d1ded4..7a537a781feb2753e0703adb9e3674c3faff94a9 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/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;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index 1c041a4c822d74bda1ee7020e4e1228dab77ba9e..b169d5de07f18c11a93d4d20c9f371d1bd130d01 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/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/;
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
index 6bd90c126c7a267cd4a7534dfc163894d6d0fff3..d278bea068a6cddc5a445c8a49a0f7754f5f7a41 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
+++ b/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);
diff --git a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
index 7b7e3b21b840ef3ff5650381bba049226317da6c..ebbb7648067a2ce74d441b20b7966c4e648f8285 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
+++ b/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);
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index ccbc8a5d4268317a3244d9df93b5fa42701a25b3..62000866518c51392f6c4d5c6c5ce559da7b2193 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/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
- : may 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
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
index ea58eb31290c6435784bd6e9669172ad93ed03c3..822b214126f7323939fe115001230f387ac17047 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+++ b/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);
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index ee800396604e924ff81a6652bd8ef090789e5d89..29942c95f527c835297540eab15329469ab66bdd 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/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;
diff --git a/modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
index 8e009bcafa69799905410c76d77c8231601ba629..bd95e3878f17f79a87f2f5672bf232fbaca014f0 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
+++ b/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;
diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index 3e6252428d43bd782e1fffe9635d86e88d99a15f..d54e6c38680a1ec5437e08c20ccdfeb39c0a3ee8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/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 );
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 8eb469721b708de92175dd04d18b114b91b0b113..73015b24cb00d243f8a42a2241d5a34b0e0f0422 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/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
diff --git a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
index edb71365b5b85491c168955f882ae99f9d4d1b21..d5721db3bd92164048166f5f79b50f89fd8ec243 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
@@ -72,7 +72,7 @@ use warnings;
use Bio::EnsEMBL::Genome;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
-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 vars qw(@ISA);
diff --git a/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
index 4fa9de806ec4f44307aa827b7043c962d1517d62..5758cb9b1aaed4ade4882bb8bab6c1731ef57597 100644
--- a/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
@@ -61,7 +61,7 @@ use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::KaryotypeBand;
-use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
diff --git a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
index 53713ba154e14a47e21980320acbaff6621d879c..b709b7567e1c0870f7ad7c88bb729e4398772240 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
@@ -56,7 +56,6 @@ package Bio::EnsEMBL::DBSQL::MetaContainer;
use strict;
use warnings;
-use Bio::EnsEMBL::Utils::Exception qw/deprecate/;
use Bio::Species;
diff --git a/modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
index c6c42e4ec1b3f51b59167317056dbf0d29e71f43..8d41e5afcef4df9b11b97d6a58af7a75463461f8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
@@ -50,8 +50,6 @@ use base qw ( Bio::EnsEMBL::DBSQL::DBAdaptor );
sub get_available_adaptors {
return {
- 'GOTerm' => 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor', #deprecated
- 'SOTerm' => 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor', #deprecated
'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer',
'OntologyTerm' => 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor' };
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
index 5ada52f80d9d98dad0876ccfab047efbd274560b..e5b22047897100b25b778fccd010c385126a8685 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
@@ -53,7 +53,7 @@ package Bio::EnsEMBL::DBSQL::OperonAdaptor;
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;
diff --git a/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
index 267521d8743d25f1a800028009b2c035e3361787..dd31e840fc459fdee28f4ebe9860a75d0b6772fc 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
@@ -55,7 +55,7 @@ package Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor;
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;
diff --git a/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
index 8eb15e878e30177d40e31818c353bd16e2701c49..c34ceae3b39013b34ab60483034d28cc2be68fc7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
@@ -55,7 +55,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::PredictionExon;
-use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
+use Bio::EnsEMBL::Utils::Exception qw( warning throw );
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
diff --git a/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
index 22e1946935fe29d8e988c9495388807561f7d4c3..4c93b59f346e08bde48f16df37f444a031e1a8d4 100644
--- a/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
@@ -58,7 +58,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::DBSQL::AnalysisAdaptor;
use Bio::EnsEMBL::PredictionTranscript;
-use Bio::EnsEMBL::Utils::Exception qw(deprecate throw warning);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
index 16c9f3dd4997c23fbb47ead7ea9ddb228350ee43..5639bc0899e97f5948451562d0f0b033701c8579 100755
--- a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
@@ -59,7 +59,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::ProteinFeature;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
@@ -208,11 +208,6 @@ sub store {
throw("ProteinFeature argument is required");
}
- if (!$translation_id) {
- deprecate("Calling ProteinFeatureAdaptor without a translation_id is " . "deprecated. Pass a translation_id argument rather than " . "setting the ProteinFeature seqname to be the translation " . "id");
- $translation_id = $feature->seqname();
- }
-
my $db = $self->db();
if ($feature->is_stored($db)) {
diff --git a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
index bf8bad5e7fd48f7b7e25e411a18731ee9502728a..95440906b7416723669dee2bd60142e6d6969328 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
@@ -56,7 +56,7 @@ use strict;
use warnings;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::RepeatConsensus;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
use base qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
diff --git a/modules/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm
index d934303807ea3a268cb881b8c5afbce7630ce4ca..2bbf01b5fff3e4976434eed73992ed5ad8f811d2 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm
@@ -34,7 +34,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::SeqRegionSynonym;
@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
diff --git a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
index a693406dd320994a2df0976424cd9d242eb9d0cb..66032443f1942459f889d730e5aa9b05b42bde3d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
@@ -49,7 +49,7 @@ package Bio::EnsEMBL::DBSQL::SequenceAdaptor;
use strict;
use warnings;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use DBI qw/:sql_types/;
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 2d0a9c94a583bd091769d6f686320e9f99d76032..df305344b21d2533da9901dd271608f4aba75a63 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -110,7 +110,7 @@ use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::CircularSlice;
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::LRGSlice;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::ProjectionSegment;
use Scalar::Util qw/looks_like_number/;
use Bio::EnsEMBL::Utils::Scalar qw/assert_integer/;
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index bc09ca0754c971b309d588e5a305914d9717bd36..ce1f32e00205f79605bf7876c30165101f1ed5f3 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -77,7 +77,7 @@ use Bio::EnsEMBL::Gene;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
-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 vars qw(@ISA);
@@ -1064,15 +1064,6 @@ sub store {
} else {
$new_analysis_id = $db->get_AnalysisAdaptor->store($analysis);
}
- } elsif ($analysis_id) {
- # Fall back to analysis passed in (usually from gene) if analysis
- # wasn't set explicitely for the transcript. This is deprectated
- # though.
- warning( "You should explicitely attach "
- . "an analysis object to the Transcript. "
- . "Will fall back to Gene analysis, "
- . "but this behaviour is deprecated." );
- $new_analysis_id = $analysis_id;
} else {
throw("Need an analysis_id to store the Transcript.");
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index 2d28e4ec8306c4c35d673ddc62f2ba7d8194ab90..4b09dae62e2bd7d00a9023fb95f15648250e6c88 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -83,7 +83,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Translation;
-use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate );
+use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
@@ -308,8 +308,6 @@ sub fetch_by_Transcript {
Exceptions : none
Caller : general
Status : Medium Risk
- : At some time may be deprecated to instead use
- : TranscriptAdaptor::fetch_all_by_external_name
=cut
@@ -713,12 +711,6 @@ SQL
sub fetch_by_dbID {
my ( $self, $dbID, $transcript ) = @_;
- if ($transcript) {
- deprecate( "Use of fetch_by_dbID "
- . "with a Transcript argument is deprecated."
- . "Use fetch_by_Transcript instead." );
- }
-
if ( !defined($dbID) ) {
throw("dbID argument is required");
}
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index f6f964446dc7be9da7d4bb10777606e2509d8b9b..f613aa99a5da48bf3d877c96354ae028c475360d 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -72,7 +72,7 @@ use strict;
use Bio::EnsEMBL::Feature;
use Bio::Seq; # exons have to have sequences...
-use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
+use Bio::EnsEMBL::Utils::Exception qw( warning throw);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor;
@@ -925,14 +925,6 @@ sub move {
sub transform {
my $self = shift;
- # catch for old style transform calls
- if( !@_ || ( ref $_[0] &&
- ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" ))
- )) {
- deprecate('Calling transform without a coord system name is deprecated.');
- return $self->_deprecated_transform(@_);
- }
-
my $new_exon = $self->SUPER::transform( @_ );
if (not defined $new_exon or
$new_exon->length != $self->length) {
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index 5ec165008f83e6e33e37219c0c42b9467471ed50..5967319caf82ef1ee6e51638aca1498d16d2a033 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -79,7 +79,7 @@ use warnings;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Scalar qw(check_ref assert_ref);
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::StrainSlice;
@@ -514,14 +514,6 @@ sub transform {
my $cs_version = shift;
my $to_slice = shift;
- #
- # For backwards compatibility check if the arguments are old style args
- #
- if(!$cs_name || ref($cs_name)) {
- deprecate('Calling transform without a coord system name is deprecated.');
- return $self->_deprecated_transform($cs_name);
- }
-
my $slice = $self->{'slice'};
if(!$slice) {
@@ -1561,34 +1553,4 @@ sub flush_sub_SeqFeature {
}
-sub _deprecated_transform {
- my $self = shift;
- my $arg = shift;
-
- if(!$arg) {
- warning("Calling transform() with no arguments is deprecated.\n".
- "A coordinate system name argument should be used instead.\n".
- "You probably wanted transform('seqlevel') or transform('contig').");
- return $self->transform('seqlevel');
- }
-
- if(ref($arg) eq 'Bio::EnsEMBL::Slice') {
- if($arg->{'empty'}) {
- warning("Calling transform with an empty slice is deprecated.\n" .
- "A coordinate system name argument should be used instead.\n".
- "You probably wanted transform('chromosome') or " .
- "transform('toplevel')");
- return $self->transform('toplevel');
- }
- warning("Calling transform with a slice is deprecated.\n" .
- "Use the transfer method instead");
- return $self->transfer($arg);
- }
-
- warning("Calling transform with a [".ref($arg)."] arg is no longer " .
- "(or never was) supported. Doing nothing instead.");
-
- return $self;
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/FeaturePair.pm b/modules/Bio/EnsEMBL/FeaturePair.pm
index 7c5205f2bac269f4acfdbd1005a83f510710dc72..96890bb609b25792a1f85d981cf15521e4348700 100755
--- a/modules/Bio/EnsEMBL/FeaturePair.pm
+++ b/modules/Bio/EnsEMBL/FeaturePair.pm
@@ -92,7 +92,7 @@ use strict;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::Feature);
@@ -166,34 +166,7 @@ sub new {
$self->{'dbname'} = $external_db_name;
$self->{'db_display_name'} = $external_display_db_name;
$self->{'hdescription'} = $hdescription;
- #
- # Feature1 and Feature2 arg handling for backwards compatibility
- #
- if ($f1) {
- deprecate("Using FEATURE1 arg to construct FeaturePairs" . " is deprecated.\nUse the args START,END,STRAND,SLICE instead");
-
- #eval because we are not exactly sure what f1 arg will look like
- eval {
- $self->{'start'} = $f1->start();
- $self->{'end'} = $f1->end();
- $self->{'strand'} = $f1->strand();
- $self->{'slice'} = $f1->contig();
- $self->{'analysis'} = $f1->analysis() if ($f1->analysis());
- };
- }
- if ($f2) {
- deprecate("Using FEATURE2 arg to construct FeaturePairs is deprecated" . "\nUse the args HSTART,HEND,HSTRAND,HSEQNAME instead");
-
- #eval because we are not exactly sure what f2 arg will look like
- eval {
- $self->{'hseqname'} = $f2->seqname();
- $self->{'hstart'} = $f2->start();
- $self->{'hend'} = $f2->end();
- $self->{'hstrand'} = $f2->strand();
- $self->{'analysis'} = $f2->analysis() if ($f2->analysis());
- };
- }
return $self;
} ## end sub new
@@ -716,8 +689,6 @@ sub level_id {
return $self->{'level_id'};
}
-=head1 DEPRECATED METHODS
-
=head2 invert
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 6b34d3e7959c4cdcff718481568c264c21eef8cf..17045ec1a40f6336a3211c8d5b7a9f44295acf75 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -68,7 +68,7 @@ use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Intron;
use Bio::EnsEMBL::Biotype;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
use parent qw(Bio::EnsEMBL::Feature);
@@ -1143,12 +1143,6 @@ sub modified_date {
sub transform {
my $self = shift;
- # catch for old style transform calls
- if( !@_ || ( ref $_[0] && ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" )) )) {
- deprecate('Calling transform without a coord system name is deprecated.');
- return $self->_deprecated_transform(@_);
- }
-
my $new_gene = $self->SUPER::transform(@_);
if ( !defined($new_gene) ) {
@@ -1553,35 +1547,4 @@ sub biotype {
return $self->{'biotype'} ;
}
-
-
-###########################
-# DEPRECATED METHODS FOLLOW
-###########################
-
-=head2 fetch_coded_for_regulatory_factors
-
- Arg [1] : none
- Example : $gene->fetch_coded_for_regulatory_factors()
- Description: DEPRECATED: Fetches any regulatory_factors that are coded for by
- this gene.
- Returntype : Listref of Bio::Ensembl::RegulatoryFactor
- Exceptions :
- Caller : ?
- Status : At Risk
- : under development
-
-=cut
-
-sub fetch_coded_for_regulatory_factors {
-
- my ($self) = @_;
-
- my $rfa = $self->adaptor->db->get_RegulatoryFactorAdaptor();
-
- return $rfa->fetch_factors_coded_for_by_gene($self);
-
-}
-
-
1;
diff --git a/modules/Bio/EnsEMBL/IdentityXref.pm b/modules/Bio/EnsEMBL/IdentityXref.pm
index 29691f1615e68c387bf378f9361fbacf465c8a2c..0bc8f14e93d37041c8f1bd254e9748da91a01475 100644
--- a/modules/Bio/EnsEMBL/IdentityXref.pm
+++ b/modules/Bio/EnsEMBL/IdentityXref.pm
@@ -57,7 +57,6 @@ package Bio::EnsEMBL::IdentityXref;
use vars qw(@ISA $AUTOLOAD);
use strict;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
-use Bio::EnsEMBL::Utils::Exception qw( deprecate );
@ISA = qw( Bio::EnsEMBL::DBEntry );
diff --git a/modules/Bio/EnsEMBL/IndividualSlice.pm b/modules/Bio/EnsEMBL/IndividualSlice.pm
index 32da97d8ce7ba96c8faa0e51a45e856d8d61b0f1..8664b5c017fb56ce88df0da42d9f08a8f1e1561d 100644
--- a/modules/Bio/EnsEMBL/IndividualSlice.pm
+++ b/modules/Bio/EnsEMBL/IndividualSlice.pm
@@ -84,7 +84,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Mapper;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::Slice);
diff --git a/modules/Bio/EnsEMBL/IndividualSliceFactory.pm b/modules/Bio/EnsEMBL/IndividualSliceFactory.pm
index 7f4b49950f2d16ab54182cf3189484afe0967584..170a64c2959233c340823af7125fd6e5dcd88e52 100644
--- a/modules/Bio/EnsEMBL/IndividualSliceFactory.pm
+++ b/modules/Bio/EnsEMBL/IndividualSliceFactory.pm
@@ -35,7 +35,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Mapper;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Scalar::Util qw(weaken);
=head2 new
diff --git a/modules/Bio/EnsEMBL/KaryotypeBand.pm b/modules/Bio/EnsEMBL/KaryotypeBand.pm
index 2e7a22aa10969c8c02a08fc387e53c87bd6f9d0d..8c50e540b684728dd2fb832964a4d33849842511 100644
--- a/modules/Bio/EnsEMBL/KaryotypeBand.pm
+++ b/modules/Bio/EnsEMBL/KaryotypeBand.pm
@@ -78,7 +78,7 @@ use vars qw(@ISA);
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(deprecate warning);
+use Bio::EnsEMBL::Utils::Exception qw(warning);
@ISA = qw(Bio::EnsEMBL::Feature);
diff --git a/modules/Bio/EnsEMBL/Map/DitagFeature.pm b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
index cf880cfad4a4c6ba092dc7cdcefe7a05f5a4f6de..13453c7e18a1f46886dba4bed5d62efb5f573cb3 100644
--- a/modules/Bio/EnsEMBL/Map/DitagFeature.pm
+++ b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
@@ -68,7 +68,7 @@ use vars qw(@ISA);
use Bio::EnsEMBL::Feature;
-use Bio::EnsEMBL::Utils::Exception qw( throw deprecate);
+use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Feature);
diff --git a/modules/Bio/EnsEMBL/Map/MapLocation.pm b/modules/Bio/EnsEMBL/Map/MapLocation.pm
index d5e4ccfb86e78c85e30ae647d02d02b6f54f4701..54d8e6f64339843f50c284537509682fc3c6bf81 100644
--- a/modules/Bio/EnsEMBL/Map/MapLocation.pm
+++ b/modules/Bio/EnsEMBL/Map/MapLocation.pm
@@ -49,8 +49,6 @@ package Bio::EnsEMBL::Map::MapLocation;
use strict;
use vars qw(@ISA);
-use Bio::EnsEMBL::Utils::Exception qw(deprecate);
-
=head2 new
Arg [1] : (optional) string $name
diff --git a/modules/Bio/EnsEMBL/MappedSlice.pm b/modules/Bio/EnsEMBL/MappedSlice.pm
index d69f8014cbcec86a15cd34159fb7ea67e53f0ba3..98b56ce7ff1f61f677b76be0e23fe2803dc5a3ee 100644
--- a/modules/Bio/EnsEMBL/MappedSlice.pm
+++ b/modules/Bio/EnsEMBL/MappedSlice.pm
@@ -75,7 +75,6 @@ for a MappedSlice to do, or they are too complicated.
Not supported Bio::EnsEMBL::Slice methods:
- All deprecated methods
All Bio::PrimarySeqI compliance methods
expand
get_generic_features
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index 29b6b043cc061ae466bc9f525b415e5ba2994c78..ac624fecd8e7688208bea4b40d0fa2b142460895 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -140,7 +140,7 @@ package Bio::EnsEMBL::Mapper;
use strict;
use integer;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Mapper::Pair;
use Bio::EnsEMBL::Mapper::IndelPair;
use Bio::EnsEMBL::Mapper::Unit;
diff --git a/modules/Bio/EnsEMBL/Operon.pm b/modules/Bio/EnsEMBL/Operon.pm
index 586e9f4d187781e5ea49cb4a50e46067a064df0d..0a612f8a80f1dc912e0911fbd2139939ed31a0a8 100755
--- a/modules/Bio/EnsEMBL/Operon.pm
+++ b/modules/Bio/EnsEMBL/Operon.pm
@@ -64,7 +64,7 @@ use warnings;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
use vars qw(@ISA);
diff --git a/modules/Bio/EnsEMBL/OperonTranscript.pm b/modules/Bio/EnsEMBL/OperonTranscript.pm
index ad7636bd702a5098746de9b20250e6474f9118c9..904162e21c95708d6aa1c2f34f8afd1a12f8755b 100755
--- a/modules/Bio/EnsEMBL/OperonTranscript.pm
+++ b/modules/Bio/EnsEMBL/OperonTranscript.pm
@@ -57,7 +57,7 @@ use warnings;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
use vars qw(@ISA);
diff --git a/modules/Bio/EnsEMBL/PredictionExon.pm b/modules/Bio/EnsEMBL/PredictionExon.pm
index 63a983c7a0d0517eda2bea9ca0bb20352bf96311..25d98a8dc0b0833f4e8ee0394612e340033955b6 100644
--- a/modules/Bio/EnsEMBL/PredictionExon.pm
+++ b/modules/Bio/EnsEMBL/PredictionExon.pm
@@ -71,7 +71,7 @@ use strict;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Exon;
-use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
+use Bio::EnsEMBL::Utils::Exception qw( warning throw );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
diff --git a/modules/Bio/EnsEMBL/PredictionTranscript.pm b/modules/Bio/EnsEMBL/PredictionTranscript.pm
index 0546ab810bc6cabc4b9ee414d7f0d2345506651a..e091ff8c5d0fd7118ce56511ad9de8427ca3931d 100644
--- a/modules/Bio/EnsEMBL/PredictionTranscript.pm
+++ b/modules/Bio/EnsEMBL/PredictionTranscript.pm
@@ -73,7 +73,7 @@ use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
-use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Transcript);
diff --git a/modules/Bio/EnsEMBL/SeqFeature.pm b/modules/Bio/EnsEMBL/SeqFeature.pm
index e2874490352d5ad20a35d3a6e8a88ec522a0e3c4..e68373c2478fc770e4b941c75c0602546ca77965 100755
--- a/modules/Bio/EnsEMBL/SeqFeature.pm
+++ b/modules/Bio/EnsEMBL/SeqFeature.pm
@@ -324,13 +324,6 @@ sub frame {
sub primary_tag{
my ($self,$arg) = @_;
- if (defined($arg)) {
- # throw warnings about setting primary tag
- my ($p,$f,$l) = caller;
- $self->warn("$f:$l setting primary_tag now deprecated." .
- "Primary tag is delegated to analysis object");
- }
-
unless($self->analysis) {
return '';
}
@@ -354,13 +347,6 @@ sub primary_tag{
sub source_tag{
my ($self,$arg) = @_;
- if (defined($arg)) {
- # throw warnings about setting primary tag
- my ($p,$f,$l) = caller;
- $self->warn("$f:$l setting source_tag now deprecated. " .
- "Source tag is delegated to analysis object");
- }
-
unless($self->analysis) {
return "";
}
diff --git a/modules/Bio/EnsEMBL/SeqRegionSynonym.pm b/modules/Bio/EnsEMBL/SeqRegionSynonym.pm
index 0e7dc99ac2ecfaf77386be7121b32a1bb90d61d6..227780215a72133a7d2e58cedb175794a85e5451 100644
--- a/modules/Bio/EnsEMBL/SeqRegionSynonym.pm
+++ b/modules/Bio/EnsEMBL/SeqRegionSynonym.pm
@@ -54,7 +54,6 @@ 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);
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 5d7d64ed3e31c3d64971cd59a398e0f56d97ce4a..4172a02e58d156883a4754b3536279dec5430702 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -76,7 +76,7 @@ use Bio::PrimarySeqI;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
+use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use Bio::EnsEMBL::RepeatMaskedSlice;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::ProjectionSegment;
@@ -147,15 +147,6 @@ sub new {
rearrange([qw(SEQ COORD_SYSTEM SEQ_REGION_NAME SEQ_REGION_LENGTH
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');
}
@@ -188,7 +179,6 @@ sub new {
}
} else {
warning("Slice without coordinate system");
- #warn(stack_trace_dump());
}
$strand ||= 1;
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index d2a4dc1560cfb5496fd6b3d44809dc152c9907b7..c9fdc5c466d5ae310915a6c6eb725d92260a2524 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -72,7 +72,7 @@ use Bio::EnsEMBL::TranscriptMapper;
use Bio::EnsEMBL::SeqEdit;
use Bio::EnsEMBL::Biotype;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
-use Bio::EnsEMBL::Utils::Exception qw( deprecate warning throw );
+use Bio::EnsEMBL::Utils::Exception qw(warning throw );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use parent qw(Bio::EnsEMBL::Feature);
@@ -134,13 +134,6 @@ sub new {
$source
);
- # Catch for old style constructor calling:
- if ( ( @_ > 0 ) && ref( $_[0] ) ) {
- $exons = [@_];
- deprecate( "Transcript constructor should use named arguments.\n"
- . "Use Bio::EnsEMBL::Transcript->new(-EXONS => \@exons);\n"
- . "instead of Bio::EnsEMBL::Transcript->new(\@exons);" );
- } else {
(
$exons, $stable_id, $version,
$external_name, $external_db, $external_status,
@@ -161,7 +154,6 @@ sub new {
],
@_
);
- }
if ($exons) {
$self->{'_trans_exon_array'} = $exons;
@@ -2629,15 +2621,6 @@ sub equals {
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 $trans->transfer($slice) or ' .
- '$trans->transform("coordsysname") instead.');
- my (undef, $new_ex) = each(%{$_[0]});
- return $self->transfer($new_ex->slice);
- }
-
my $new_transcript = $self->SUPER::transform(@_);
if ( !defined($new_transcript) ) {
my @segments = @{ $self->project(@_) };
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index 278c852c1418afe8720414374a18a3b67749286d..919f82cd1ae8622638e6193ea5b81e07268ea2e5 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -62,7 +62,7 @@ package Bio::EnsEMBL::Translation;
use vars qw($AUTOLOAD @ISA);
use strict;
-use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::Utils::Exception qw(throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref wrap_array );
use Scalar::Util qw(weaken);
diff --git a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
index 642c90118580cc559dab1ef8b53633a129ddccb5..434bdf35379bb284a550ac7bc9d5c003dda8e035 100644
--- a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
@@ -58,7 +58,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Utils::Exception qw(warning throw deprecate stack_trace_dump);
+use Bio::EnsEMBL::Utils::Exception qw(warning throw);
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index 685b586f0c08855dfde324603d17c11d85b900d6..6657e4af704933176fcdcf17c8479cb2cfdb50fb 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -68,7 +68,7 @@ no warnings 'uninitialized';
use Getopt::Long;
use Text::Wrap;
-use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use FindBin qw($Bin $Script);
use POSIX qw(strftime);
use Cwd qw(abs_path);