Commit a92c4755 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

Merge pull request #96 from Ensembl/feature/deprecate

Feature/deprecate
parents 1343d1ca 18965a81
Ensembl Deprecated Methods
===================
This file contains the list of methods deprecated in the Ensembl core API.
A method is deprecated when it is not functional any more (schema/data change) or has been replaced by a better one.
Backwards compatibility is provided whenever possible.
When a method is deprecated, a deprecation warning is thrown whenever the method is used.
The warning also contains instructions on replacing the deprecated method and when it will be removed.
A year after deprecation (4 Ensembl releases), the method is removed from the API.
### Removed in Ensembl Release 87 ###
- Bio::EnsEMBL::**AssemblyMapper**::*in_assembly()*
- Bio::EnsEMBL::**AssemblyMapper**::*map_coordinates_to_assembly()*
- Bio::EnsEMBL::**AssemblyMapper**::*fast_to_assembly()*
- Bio::EnsEMBL::**AssemblyMapper**::*map_coordinates_to_rawcontig()*
- Bio::EnsEMBL::**AssemblyMapper**::*list_contig_ids()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*in_assembly()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*map_coordinates_to_assembly()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*fast_to_assembly()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*map_coordinates_to_rawcontig()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*list_contig_ids()*
- Bio::EnsEMBL::**DBEntry**::*get_synonyms()*
- Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*register_region()*
- Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*register_contig()*
- Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*fetch_by_type()*
- Bio::EnsEMBL::DBSQL::**KaryotypeBandAdaptor**::*fetch_by_chr_band()*
- Bio::EnsEMBL::DBSQL::**TranslationAdaptor**::*fetch_all_by_**DBEntry**()*
- Bio::EnsEMBL::DBSQL::**TranslationAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_all_Groups()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_all_Groups_by_type()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_Group_by_id()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_Group_by_Gene_dbID()*
- Bio::EnsEMBL::DBSQL::**AnalysisAdaptor**::*feature_classes()*
- Bio::EnsEMBL::DBSQL::**BaseAlignFeatureAdaptor**::*fetch_all_by_RawContig_and_pid()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig_constraint()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig_and_score()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*remove_by_RawContig()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*db_handle()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*port()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*driver()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*password()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*username()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*host()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*reconnect_when_lost()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*disconnect_when_inactive()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*dbname()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*prepare()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*list_supported_assemblies()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*assembly_type()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*db()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*source()*
- Bio::EnsEMBL::DBSQL::**DBConnection**::*group()*
- Bio::EnsEMBL::DBSQL::**DBConnection**::*species()*
- Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*geneids_by_extids()*
- Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*translationids_by_extids()*
- Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*transcriptids_by_extids()*
- Bio::EnsEMBL::DBSQL::**DataFileAdaptor**::*DataFile_to_extension()*
- Bio::EnsEMBL::DBSQL::**ExonAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**ExonAdaptor**::*fetch_all_by_gene_id()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_nearest_Gene_by_Feature()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_by_maximum_DBLink()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_display_xref()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_description()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_all_by_**DBEntry**()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_by_Peptide_id()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_Species()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_default_assembly()*
- Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_by_translation_id()*
- Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_all_by_feature_and_dbID()*
- Bio::EnsEMBL::DBSQL::**RepeatConsensusAdaptor**::*fetch_by_class_seq()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_mapfrag()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_chr_start_end()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_contig_name()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_clone_accession()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_supercontig_name()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*list_overlapping_supercontigs()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_chr_name()*
- Bio::EnsEMBL::DBSQL::**TranscriptAdaptor**::*get_display_xref()*
- Bio::EnsEMBL::DBSQL::**TranscriptAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**TranscriptAdaptor**::*fetch_all_by_DBEntry()*
- Bio::EnsEMBL::DBSQL::**SequenceAdaptor**::*fetch_by_assembly_location()*
- Bio::EnsEMBL::DBSQL::**SequenceAdaptor**::*fetch_by_RawContig_start_end_strand()*
- Bio::EnsEMBL::**Exon**::*temporary_id()*
- Bio::EnsEMBL::**Exon**::*created()*
- Bio::EnsEMBL::**Exon**::*modified()*
- Bio::EnsEMBL::**Exon**::*type()*
- Bio::EnsEMBL::**FeaturePair**::*feature1()*
- Bio::EnsEMBL::**FeaturePair**::*feature2()*
- Bio::EnsEMBL::**FeaturePair**::*set_featurepair_fields()*
- Bio::EnsEMBL::**FeaturePair**::*gffstring()*
- Bio::EnsEMBL::**FeaturePair**::*hphase()*
- Bio::EnsEMBL::**FeaturePair**::*hend_phase()*
- Bio::EnsEMBL::**Feature**::*contig()*
- Bio::EnsEMBL::**Feature**::*id()*
- Bio::EnsEMBL::**Gene**::*add_DBLink()*
- Bio::EnsEMBL::**Gene**::*temporary_id()*
- Bio::EnsEMBL::**Gene**::*chr_name()*
- Bio::EnsEMBL::**Gene**::*type()*
- Bio::EnsEMBL::**Gene**::*confidence()*
- Bio::EnsEMBL::**IdentityXref**::*query_identity()*
- Bio::EnsEMBL::**IdentityXref**::*target_identity()*
- Bio::EnsEMBL::**IdentityXref**::*translation_start()*
- Bio::EnsEMBL::**IdentityXref**::*translation_end()*
- Bio::EnsEMBL::**IdentityXref**::*query_start()*
- Bio::EnsEMBL::**IdentityXref**::*query_end()*
- Bio::EnsEMBL::**KaryotypeBand**::*chr_name()*
- Bio::EnsEMBL::Map::DBSQL::**MarkerFeatureAdaptor**::*fetch_all_by_RawContig_and_priority()*
- Bio::EnsEMBL::Map::**DitagFeature**::*fetch_ditag()*
- Bio::EnsEMBL::Map::**MapLocation**::*chromosome()*
- Bio::EnsEMBL::**OperonTranscript**::*add_gene()*
- Bio::EnsEMBL::**PredictionTranscript**::*get_exon_count()*
- Bio::EnsEMBL::**PredictionTranscript**::*set_exon_count()*
- Bio::EnsEMBL::**PredictionTranscript**::*get_cdna()*
- Bio::EnsEMBL::**Registry**::*load_registry_with_web_adaptors()*
- Bio::EnsEMBL::**Root**::*throw()*
- Bio::EnsEMBL::**Root**::*warn()*
- Bio::EnsEMBL::**Root**::*verbose()*
- Bio::EnsEMBL::**Root**::*stack_trace_dump()*
- Bio::EnsEMBL::**Root**::*stack_trace()*
- Bio::EnsEMBL::**Slice**::*get_all_SNPs()*
- Bio::EnsEMBL::**Slice**::*get_all_genotyped_SNPs()*
- Bio::EnsEMBL::**Slice**::*get_all_OligoFeatures_by_type()*
- Bio::EnsEMBL::**Slice**::*get_all_supercontig_Slices()*
- Bio::EnsEMBL::**Slice**::*get_Chromosome()*
- Bio::EnsEMBL::**Slice**::*chr_name()*
- Bio::EnsEMBL::**Slice**::*chr_start()*
- Bio::EnsEMBL::**Slice**::*chr_end()*
- Bio::EnsEMBL::**Slice**::*assembly_type()*
- Bio::EnsEMBL::**Slice**::*dbID()*
- Bio::EnsEMBL::**Slice**::*get_all_MapFrags()*
- Bio::EnsEMBL::**Slice**::*has_MapSet()*
- Bio::EnsEMBL::**StrainSlice**::*get_all_differences_Slice()*
- Bio::EnsEMBL::**Transcript**::*created()*
- Bio::EnsEMBL::**Transcript**::*modified()*
- Bio::EnsEMBL::**Transcript**::*temporary_id()*
- Bio::EnsEMBL::**Transcript**::*type()*
- Bio::EnsEMBL::**Transcript**::*confidence()*
- Bio::EnsEMBL::**Translation**::*temporary_id()*
- Bio::EnsEMBL::Utils::**ConversionSupport**::*user_confirm()*
### Removed in Ensembl Release 84 ###
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_by_attrib()*
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_all_by_attrib()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_short_name()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_max_assembly_contig()*
- Bio::EnsEMBL::**Exon**::*_get_stable_entry_info()*
- Bio::EnsEMBL::**FeaturePair**::*validate()*
- Bio::EnsEMBL::**FeaturePair**::*validate_prot_feature()*
- Bio::EnsEMBL::**Root**::*rearrange()*
- Bio::EnsEMBL::**SeqFeatureI**::*analysis()*
- Bio::EnsEMBL::**SeqFeatureI**::*validate()*
- Bio::EnsEMBL::**SeqFeatureI**::*id()*
- Bio::EnsEMBL::**SeqFeatureI**::*percent_id()*
- Bio::EnsEMBL::**SeqFeatureI**::*e_value()*
- Bio::EnsEMBL::**SeqFeatureI**::*phase()*
- Bio::EnsEMBL::**SeqFeatureI**::*end_phase()*
- Bio::EnsEMBL::**SeqFeatureI**::*location()*
- Bio::EnsEMBL::**Slice**::*get_all_SNPs_transcripts()*
- Bio::EnsEMBL::**Slice**::*get_all_AffyFeatures()*
- Bio::EnsEMBL::**Slice**::*get_all_OligoFeatures()*
- Bio::EnsEMBL::**Slice**::*get_all_OligoFeatures_by_type()*
- Bio::EnsEMBL::**Slice**::*get_tiling_path()*
- Bio::EnsEMBL::**Transcript**::*sort()*
- Bio::EnsEMBL::**Transcript**::*_translation_id()*
......@@ -745,7 +745,7 @@ sub adaptor {
sub in_assembly {
my ( $self, $object ) = @_;
deprecate('Use map() or list_ids() instead.');
deprecate('in_assembly is deprecated and will be removed in e87. Use map() or list_ids() instead.');
my $csa = $self->db->get_CoordSystemAdaptor();
......@@ -772,7 +772,7 @@ sub in_assembly {
sub map_coordinates_to_assembly {
my ( $self, $contig_id, $start, $end, $strand ) = @_;
deprecate('Use map() instead.');
deprecate('map_coordinates_to_assembly is deprecated and will be removed in e87. Use map() instead.');
# Not sure if contig_id is seq_region_id or name...
return
......@@ -790,7 +790,7 @@ sub map_coordinates_to_assembly {
sub fast_to_assembly {
my ( $self, $contig_id, $start, $end, $strand ) = @_;
deprecate('Use map() instead.');
deprecate('fast_to_assembly is deprecated and will be removed in e87. Use map() instead.');
# Not sure if contig_id is seq_region_id or name...
return
......@@ -807,7 +807,7 @@ sub fast_to_assembly {
sub map_coordinates_to_rawcontig {
my ( $self, $chr_name, $start, $end, $strand ) = @_;
deprecate('Use map() instead.');
deprecate('map_coordinates_to_rawcontig is deprecated and will be removed in e87. Use map() instead.');
return
$self->map( $chr_name, $start, $end, $strand,
......@@ -823,7 +823,7 @@ sub map_coordinates_to_rawcontig {
sub list_contig_ids {
my ( $self, $chr_name, $start, $end ) = @_;
deprecate('Use list_ids() instead.');
deprecate('list_contig_ids is deprecated and will be removed in e87. Use list_ids() instead.');
return
$self->list_ids( $chr_name, $start, $end,
......
......@@ -741,7 +741,7 @@ sub adaptor {
sub in_assembly {
my ($self, $object) = @_;
deprecate('Use map() or list_ids() instead.');
deprecate('in_assembly is deprecated and will be removed in e87. Use map() or list_ids() instead.');
my $csa = $self->db->get_CoordSystemAdaptor();
......@@ -766,7 +766,7 @@ sub in_assembly {
sub map_coordinates_to_assembly {
my ($self, $contig_id, $start, $end, $strand) = @_;
deprecate('Use map() instead.');
deprecate('map_coordinates_to_assembly is deprecated and will be removed in e87. Use map() instead.');
#not sure if contig_id is seq_region_id or name...
return $self->map($contig_id, $start, $end, $strand,
......@@ -784,7 +784,7 @@ sub map_coordinates_to_assembly {
sub fast_to_assembly {
my ($self, $contig_id, $start, $end, $strand) = @_;
deprecate('Use map() instead.');
deprecate('fast_to_assembly is deprecated and will be removed in e87. Use map() instead.');
#not sure if contig_id is seq_region_id or name...
return $self->map($contig_id, $start, $end, $strand,
......@@ -801,7 +801,7 @@ sub fast_to_assembly {
sub map_coordinates_to_rawcontig {
my ($self, $chr_name, $start, $end, $strand) = @_;
deprecate('Use map() instead.');
deprecate('map_coordinates_to_rawcontig is deprecated and will be removed in e87. Use map() instead.');
return $self->map($chr_name, $start, $end, $strand,
$self->assembled_CoordSystem());
......@@ -816,7 +816,7 @@ sub map_coordinates_to_rawcontig {
sub list_contig_ids {
my ($self, $chr_name, $start, $end) = @_;
deprecate('Use list_ids() instead.');
deprecate('list_contig_ids is deprecated and will be removed in e87. Use list_ids() instead.');
return $self->list_ids($chr_name, $start, $end,
$self->assembled_CoordSystem());
......
......@@ -707,7 +707,7 @@ sub ensembl_id{
sub get_synonyms {
my $self = shift;
deprecate("get_synonyms has been renamed get_all_synonyms.");
deprecate("get_synonyms is deprecated and will be removed in e87. Use get_all_synonyms instead.");
return $self->get_all_synonyms;
}
......
......@@ -82,7 +82,7 @@ use DBI qw( :sql_types );
sub fetch_all_Groups {
my ($self, $type) = @_;
deprecate('Please use fetch_all()');
deprecate('fetch_all_Groups is deprecate and will be removed in e87. Please use fetch_all()');
return $self->fetch_all($type);
}
......@@ -185,7 +185,7 @@ sub fetch_all {
sub fetch_all_Groups_by_type {
my ($self, $type) = @_;
deprecate('Please use fetch_all()');
deprecate('fetch_all_Groups_by_type is deprecated and will be removed in e87. Please use fetch_all()');
my $group_list = $self->fetch_all($type);
return $group_list;
}
......@@ -200,7 +200,7 @@ sub fetch_all_Groups_by_type {
sub fetch_Group_by_id {
my ($self, $group_id) = @_;
deprecate('Please use fetch_by_dbID()');
deprecate('fetch_Group_by_id is deprecated and will be removed in e87. Please use fetch_by_dbID()');
return $self->fetch_by_dbID($group_id);
}
......@@ -272,7 +272,7 @@ sub fetch_by_dbID {
sub fetch_Group_by_Gene_dbID {
my ($self, $gene_id) = @_;
deprecate('Please use fetch_by_gene_id()');
deprecate('fetch_Group_by_Gene_dbID is deprecated and will be removed in e87. Please use fetch_by_gene_id()');
return $self->fetch_by_gene_id($gene_id);
}
......
......@@ -217,7 +217,7 @@ SELECT DISTINCT analysis_id FROM %s |;
=cut
sub feature_classes{
deprecate("Deprecated. Hard-coded logic is not supported");
deprecate("feature_classes is deprecated and will be removed in e87. Hard-coded logic is not supported");
# Can't think of a way to do this programatically, so hard-coded
return qw(
DensityFeature
......
......@@ -1812,7 +1812,7 @@ sub delete_cache{
sub register_region{
my ($self, $assmapper, $type, $chr_name, $start, $end) = @_;
deprecate('Use register_assembled instead');
deprecate('register_region is deprecated and will be removed in e87. Use register_assembled instead');
$self->register_assembled($assmapper, $chr_name, $start, $end);
}
......@@ -1827,7 +1827,7 @@ sub register_region{
sub register_contig {
my ($self, $assmapper, $type, $contig_id ) = @_;
deprecate('Use register_component instead');
deprecate('register_contig is deprecated and will be removed in e87. Use register_component instead');
#not sure if the use is passing in a seq_region_name or a
#seq_region_id...
......@@ -1844,7 +1844,7 @@ sub register_contig {
sub fetch_by_type{
my ($self,$type) = @_;
deprecate('Use fetch_by_CoordSystems instead');
deprecate('fetch_by_type is deprecated and will be removed in e87. Use fetch_by_CoordSystems instead');
#assume that what the user wanted was a mapper between the sequence coord
#level and the top coord level
......
......@@ -305,6 +305,7 @@ sub fetch_all_by_hit_name_unversioned {
sub fetch_all_by_RawContig_and_pid {
my($self, $contig, $pid, $logic_name) = @_;
deprecate('fetch_all_by_RawContig_and_pid is deprecated and will be removed in e87. Use fetch_all_by_Slice_and_pid instead.');
my $constraint;
......
......@@ -1391,7 +1391,7 @@ sub _list_seq_region_ids {
sub fetch_all_by_RawContig_constraint {
my $self = shift;
deprecate('Use fetch_all_by_Slice_constraint() instead.');
deprecate('fetch_all_by_RawContig_constraint is deprecated and will be removed in e87. Use fetch_all_by_Slice_constraint() instead.');
return $self->fetch_all_by_slice_constraint(@_);
}
......@@ -1403,7 +1403,7 @@ sub fetch_all_by_RawContig_constraint {
sub fetch_all_by_RawContig {
my $self = shift;
deprecate('Use fetch_all_by_Slice() instead.');
deprecate('fetch_all_by_RawContig is deprecated and will be removed in e87. Use fetch_all_by_Slice() instead.');
return $self->fetch_all_by_Slice(@_);
}
......@@ -1415,7 +1415,7 @@ sub fetch_all_by_RawContig {
sub fetch_all_by_RawContig_and_score{
my $self = shift;
deprecate('Use fetch_all_by_Slice_and_score() instead.');
deprecate('fetch_all_by_RawContig_and_score is deprecated and will be removed in e87. Use fetch_all_by_Slice_and_score() instead.');
return $self->fetch_all_by_Slice_and_score(@_);
}
......@@ -1427,7 +1427,7 @@ sub fetch_all_by_RawContig_and_score{
sub remove_by_RawContig {
my $self = shift;
deprecate("Use remove_by_Slice instead");
deprecate("fetch_by_RawContig is deprecated and will be removed in e87. Use remove_by_Slice instead");
return $self->remove_by_Slice(@_);
}
......
......@@ -1080,8 +1080,7 @@ sub _fetch_by_attrib{
my $attrib = shift;
my $version = shift;
deprecate("You should be using the public method fetch_by_attrib ".
"(without initial underscore) instead");
deprecate("_fetch_by_attrib is deprecated and will be removed in e84. Please use fetch_by_attrib instead.");
return $self->fetch_by_attrib($attrib,$version);
}
......@@ -1115,8 +1114,7 @@ sub _fetch_all_by_attrib{
my $self = shift;
my $attrib = shift;
deprecate("You should be using the public method fetch_all_by_attrib ".
"(without initial underscore) instead");
deprecate("_fetch_all_by_attrib is deprecated and will be removed in e84. Please use fetch_all_by_attrib instead.");
return $self->fetch_all_by_attrib($attrib);
}
......
......@@ -1119,12 +1119,12 @@ sub revert_adaptor {
sub db{
my ($self, $arg ) = @_;
deprecate("db Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->db is deprecated and will be removed in e87. Please use DBConnection->db instead.");
return $self->dbc($arg);
}
sub source { deprecate('Do not use - this method does nothing'); }
sub source { deprecate('source is deprecated and will be removed in e84.'); }
=head2 assembly_type
......@@ -1137,7 +1137,7 @@ sub source { deprecate('Do not use - this method does nothing'); }
sub assembly_type{
my $self = shift;
deprecate('Use CoordSystemAdaptor $csa->fetch_all->[0]->version() instead');
deprecate('assembly_type is deprecated and will be removed in e87. Please use CoordSystemAdaptor $csa->fetch_all->[0]->version() instead');
my $csa = $self->get_CoordSystemAdaptor();
my ($cs) = @{$csa->fetch_all()};
......@@ -1155,7 +1155,7 @@ sub assembly_type{
sub list_supported_assemblies {
my($self) = @_;
deprecate('Use CoordSystemAdaptor::fetch_all instead');
deprecate('list_supported_assemblies is deprecated and will be removed in e87. Please use CoordSystemAdaptor::fetch_all instead');
my $csa = $self->get_CoordSystemAdaptor();
my %versions;
......@@ -1170,28 +1170,28 @@ sub list_supported_assemblies {
sub prepare{
my ($self, @args) = @_;
deprecate("prepare Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->prepare is deprecated and will be removed in e87. Please use DBConnection->prepare instead.");
$self->dbc->prepare(@args);
}
sub dbname{
my ($self, @args) = @_;
deprecate("dbname Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->dbname is deprecated and will be removed in e87. Please use DBConnection->dbname instead.");
$self->dbc->dbname(@args);
}
sub disconnect_when_inactive{
my ($self, @args) = @_;
deprecate("disconnect_when_inactive Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->disconnect_when_inactive is deprecated and will be removed in e87. Please use DBConnection->disconnect_when_inactive instead.");
$self->dbc->disconnect_when_inactive(@args);
}
sub reconnect_when_lost{
my ($self, @args) = @_;
deprecate("reconnect_when_lost Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->reconnect_when_lost is deprecated and will be removed in e87. Please use DBConnection->reconnect_when_lost instead.");
$self->dbc->reconnect_when_lost(@args);
}
......@@ -1199,31 +1199,31 @@ sub reconnect_when_lost{
sub host{
my ($self, @args) = @_;
deprecate("host Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->host is deprecated and will be removed in e87. Please use DBConnection->host instead.");
$self->dbc->host(@args);
}
sub username{
my ($self, @args) = @_;
deprecate("username Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->username is deprecated and will be removed in e87. Please use DBConnection->username instead.");
$self->dbc->username(@args);
}
sub password{
my ($self, @args) = @_;
deprecate("password Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->password is deprecated and will be removed in e87. Please use DBConnection->password instead.");
$self->dbc->password(@args);
}
sub driver{
my ($self, @args) = @_;
deprecate("driver Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->driver is deprecated and will be removed in e87. Please use DBConnection->driver instead.");
$self->dbc->driver(@args);
}
sub port{
my ($self, @args) = @_;
deprecate("port Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->port is deprecated and will be removed in e87. Please use DBConnection->port instead.");
$self->dbc->port(@args);
}
......@@ -1231,7 +1231,7 @@ sub db_handle{
my ($self, @args) = @_;
deprecate("db_handle Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
deprecate("DBAdaptor->db_handle is deprecated and will be removed in e87. Please use DBConnection->db_handle instead.");
$self->dbc->db_handle(@args);
}
......
......@@ -1089,7 +1089,7 @@ sub group {
my ($self, $arg ) = @_;
( defined $arg ) &&
( $self->{_group} = $arg );
deprecate "group should not be called from DBConnection but from an adaptor\n";
deprecate("DBConnection->group is deprecated and will be removed in e87. Please use adaptor->group instead.");
return $self->{_group};
}
......@@ -1104,7 +1104,7 @@ sub species {
my ($self, $arg ) = @_;
( defined $arg ) &&
( $self->{_species} = $arg );
deprecate "species should not be called from DBConnection but from an adaptor\n";
deprecate("DBConnection->species is deprecated and will be removed in e87. Please use adaptor->species instead.");
return $self->{_species};
}
......
......@@ -2341,7 +2341,7 @@ sub get_db_name_from_external_db_id{
sub geneids_by_extids{
my ($self,$name) = @_;
deprecate(" use 'list_gene_ids_by_extids instead");
deprecate("gene_ids_by_extids is deprecated and will be removed in e87. Please use 'list_gene_ids_by_extids instead");
return $self->list_gene_ids_by_extids( $name );
}
......@@ -2354,7 +2354,7 @@ sub geneids_by_extids{
sub translationids_by_extids{
my ($self,$name) = @_;
deprecate("Use list_translation_ids_by_extids instead");
deprecate("translationids_by_extids is deprecated and will be removed in e87. Please use list_translation_ids_by_extids instead");
return $self->list_translation_ids_by_extids( $name );
}
......@@ -2367,7 +2367,7 @@ sub translationids_by_extids{
sub transcriptids_by_extids{
my ($self,$name) = @_;
deprecate("Use list_transcript_ids_by_extids instead.");
deprecate("transcriptids_by_extids is deprecated and will be removed in e87. Please use list_transcript_ids_by_extids instead.");
return $self->list_transcript_ids_by_extids( $name );
}
......
......@@ -121,7 +121,7 @@ sub get_base_path {
sub DataFile_to_extension {
my ($self, $df) = @_;
deprecate("Use DataFile_to_extensions() instead");
deprecate("DataFile_to_extension is deprecated and will be removed in e87. Please use DataFile_to_extensions() instead");
my $extensions = $self->DataFile_to_extensions($df);
return $extensions->[0];
}
......
......@@ -747,7 +747,7 @@ sub _objs_from_sth {
sub get_stable_entry_info {
my ($self,$exon) = @_;
deprecated( "This method call shouldnt be necessary" );
deprecate( "get_stable_entry_info is deprecated and will be removed in e87. Please use object->stable_id instead." );
if( !$exon || !ref $exon || !$exon->isa('Bio::EnsEMBL::Exon') ) {
$self->throw("Needs a exon object, not a $exon");
......@@ -792,7 +792,7 @@ sub fetch_all_by_gene_id {
my $hashRef;
my ( $currentId, $currentTranscript );
deprecated( "Hopefully this method is not needed any more. Exons should be fetched by Transcript" );
deprecate("exon_adaptor->fetch_all_by_gene_id is deprecated and will be removed in e87. Please use transcript->get_all_Exons instead." );
if( !$gene_id ) {
$self->throw("Gene dbID not defined");
......
......@@ -2049,7 +2049,7 @@ sub fetch_nearest_Gene_by_Feature{
#This had no prime spec and was returning all overlaps regardless of strand
#else the first 10 from the stream with the first closest gene
deprecate( "use fetch_nearest_Genes_by_Feature instead");
deprecate( "fetch_neared_Gene_by_Feature is deprecated and will be removed in e87. Please use fetch_nearest_Genes_by_Feature instead");
#need to change params order here to account for new prime arg
return $_[0]->fetch_nearest_Genes_by_Feature($feat, undef, $stranded, $stream);
}
......@@ -2064,7 +2064,7 @@ sub fetch_nearest_Gene_by_Feature{
sub fetch_by_maximum_DBLink {
my ($self, $external_id) = @_;
deprecate("use fetch_all_by_external_name instead");
deprecate("fetch_by_maximum_DBLink is deprecated and will be removed in e87. Pleaseuse fetch_all_by_external_name instead");
my $genes = $self->fetch_all_by_external_name($external_id);
......@@ -2093,7 +2093,7 @@ sub fetch_by_maximum_DBLink {
sub get_display_xref {