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ensembl-gh-mirror
ensembl
Commits
9aed91b8
Commit
9aed91b8
authored
Sep 29, 2016
by
Magali Ruffier
Browse files
remove deprecated methods for release 87
parent
af33ebd3
Changes
44
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+0
-1101
DEPRECATED.md
DEPRECATED.md
+0
-1
modules/Bio/EnsEMBL/AssemblyMapper.pm
modules/Bio/EnsEMBL/AssemblyMapper.pm
+0
-94
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
+0
-92
modules/Bio/EnsEMBL/DBEntry.pm
modules/Bio/EnsEMBL/DBEntry.pm
+0
-17
modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
+0
-58
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
+0
-30
modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+0
-56
modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
+0
-29
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+0
-54
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+0
-124
modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+0
-34
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+0
-39
modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
+0
-18
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+0
-112
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+0
-183
modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
+0
-28
modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
+0
-65
modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+0
-25
modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
+0
-6
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+0
-36
No files found.
DEPRECATED.md
View file @
9aed91b8
...
...
@@ -168,7 +168,6 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP
-
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()*
...
...
modules/Bio/EnsEMBL/AssemblyMapper.pm
View file @
9aed91b8
...
...
@@ -737,98 +737,4 @@ sub adaptor {
return
$self
->
{'
adaptor
'};
}
=head2 in_assembly
Description: DEPRECATED, use map() or list_ids() instead.
=cut
sub
in_assembly
{
my
(
$self
,
$object
)
=
@_
;
deprecate
('
in_assembly is deprecated and will be removed in e87. Use map() or list_ids() instead.
');
my
$csa
=
$self
->
db
->
get_CoordSystemAdaptor
();
my
$top_level
=
$csa
->
fetch_top_level
();
my
$asma
=
$self
->
adaptor
->
fetch_by_CoordSystems
(
$object
->
coord_system
(),
$top_level
);
my
@list
=
$asma
->
list_ids
(
$object
->
seq_region
(),
$object
->
start
(),
$object
->
end
(),
$object
->
coord_system
()
);
return
(
@list
>
0
);
}
=head2 map_coordinates_to_assembly
Description: DEPRECATED, use map() instead.
=cut
sub
map_coordinates_to_assembly
{
my
(
$self
,
$contig_id
,
$start
,
$end
,
$strand
)
=
@_
;
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
,
$self
->
contig_CoordSystem
()
);
}
=head2 fast_to_assembly
Description: DEPRECATED, use map() instead.
=cut
sub
fast_to_assembly
{
my
(
$self
,
$contig_id
,
$start
,
$end
,
$strand
)
=
@_
;
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
,
$self
->
contig_CoordSystem
()
);
}
=head2 map_coordinates_to_rawcontig
Description: DEPRECATED, use map() instead.
=cut
sub
map_coordinates_to_rawcontig
{
my
(
$self
,
$chr_name
,
$start
,
$end
,
$strand
)
=
@_
;
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
()
);
}
=head2 list_contig_ids
Description: DEPRECATED, use list_ids() instead.
=cut
sub
list_contig_ids
{
my
(
$self
,
$chr_name
,
$start
,
$end
)
=
@_
;
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
()
);
}
1
;
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
View file @
9aed91b8
...
...
@@ -733,96 +733,4 @@ sub adaptor {
}
=head2 in_assembly
Deprecated. Use map() or list_ids() instead
=cut
sub
in_assembly
{
my
(
$self
,
$object
)
=
@_
;
deprecate
('
in_assembly is deprecated and will be removed in e87. Use map() or list_ids() instead.
');
my
$csa
=
$self
->
db
->
get_CoordSystemAdaptor
();
my
$top_level
=
$csa
->
fetch_top_level
();
my
$asma
=
$self
->
adaptor
->
fetch_by_CoordSystems
(
$object
->
coord_system
(),
$top_level
);
my
@list
=
$asma
->
list_ids
(
$object
->
seq_region
(),
$object
->
start
(),
$object
->
end
(),
$object
->
coord_system
());
return
(
@list
>
0
);
}
=head2 map_coordinates_to_assembly
DEPRECATED use map() instead
=cut
sub
map_coordinates_to_assembly
{
my
(
$self
,
$contig_id
,
$start
,
$end
,
$strand
)
=
@_
;
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
,
$self
->
contig_CoordSystem
());
}
=head2 fast_to_assembly
DEPRECATED use map() instead
=cut
sub
fast_to_assembly
{
my
(
$self
,
$contig_id
,
$start
,
$end
,
$strand
)
=
@_
;
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
,
$self
->
contig_CoordSystem
());
}
=head2 map_coordinates_to_rawcontig
DEPRECATED use map() instead
=cut
sub
map_coordinates_to_rawcontig
{
my
(
$self
,
$chr_name
,
$start
,
$end
,
$strand
)
=
@_
;
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
());
}
=head2 list_contig_ids
DEPRECATED Use list_ids instead
=cut
sub
list_contig_ids
{
my
(
$self
,
$chr_name
,
$start
,
$end
)
=
@_
;
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
());
}
1
;
modules/Bio/EnsEMBL/DBEntry.pm
View file @
9aed91b8
...
...
@@ -666,22 +666,5 @@ sub status{
return
$self
->
{
status
};
}
=head1 DEPRECATED METHODS
=cut
=head2 get_synonyms
DEPRECATED use get_all_synonyms instead
=cut
sub
get_synonyms
{
my
$self
=
shift
;
deprecate
("
get_synonyms is deprecated and will be removed in e87. Use get_all_synonyms instead.
");
return
$self
->
get_all_synonyms
;
}
1
;
modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
View file @
9aed91b8
...
...
@@ -73,20 +73,6 @@ use Bio::EnsEMBL::Utils::Exception qw/throw deprecate warning/;
use
Bio::EnsEMBL::Utils::
Scalar
qw/assert_ref/
;
use
DBI
qw( :sql_types )
;
=head2 fetch_all_Groups
Arg[1] : (optional) String - type of group
Description : DEPRECATED. Please use fetch_all()
Returntype : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
=cut
sub
fetch_all_Groups
{
my
(
$self
,
$type
)
=
@_
;
deprecate
('
fetch_all_Groups is deprecate and will be removed in e87. Please use fetch_all()
');
return
$self
->
fetch_all
(
$type
);
}
=head2 fetch_all
Arg[1] : (optional) String - type of group
...
...
@@ -176,35 +162,6 @@ sub fetch_all {
return
\
@group_list
;
}
=head2 fetch_all_Groups_by_type
Arg[1] : String - type of group
Description : DEPRECATED. Please use fetch_all()
Returntype : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
=cut
sub
fetch_all_Groups_by_type
{
my
(
$self
,
$type
)
=
@_
;
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
;
}
=head2 fetch_Group_by_id
Arg[1] : AltAlleleGroup dbID.
Description : DEPRECATED. Please use fetch_by_dbID
Returntype : Bio::EnsEMBL::AltAlleleGroup
=cut
sub
fetch_Group_by_id
{
my
(
$self
,
$group_id
)
=
@_
;
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
);
}
=head2 fetch_by_dbID
Arg[1] : AltAlleleGroup dbID.
...
...
@@ -262,21 +219,6 @@ sub fetch_by_dbID {
return
;
}
=head2 fetch_Group_by_Gene_dbID
Arg[1] : Integer Gene ID of the member to query by
Description : DEPRECATED. Please use fetch_by_gene_id
Returntype : Bio::EnsEMBL::AltAlleleGroup
=cut
sub
fetch_Group_by_Gene_dbID
{
my
(
$self
,
$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
);
}
=head2 fetch_by_gene_id
Arg[1] : Integer Gene ID of the member to query by
...
...
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
View file @
9aed91b8
...
...
@@ -203,36 +203,6 @@ SELECT DISTINCT analysis_id FROM %s |;
return
[
@analyses
];
}
=head2 feature_classes
Arg [1] : NONE
Example : my @fclasses = $analysis_adaptor->feature_classes;
Description: Returns a list of the different classes of Ensembl feature
object that have an analysis
Returntype : List of feature classes
Exceptions : none
Caller : general
Status : Stable
=cut
sub
feature_classes
{
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
DnaAlignFeature
Gene
MarkerFeature
PredictionTranscript
ProteinAlignFeature
ProteinFeature
RepeatFeature
SimpleFeature
)
;
}
=head2 fetch_by_dbID
Arg [1] : int $internal_analysis_id - the database id of the analysis
...
...
modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
View file @
9aed91b8
...
...
@@ -1804,60 +1804,4 @@ sub delete_cache{
}
=head2 register_region
Description: DEPRECATED use register_assembled instead
=cut
sub
register_region
{
my
(
$self
,
$assmapper
,
$type
,
$chr_name
,
$start
,
$end
)
=
@_
;
deprecate
('
register_region is deprecated and will be removed in e87. Use register_assembled instead
');
$self
->
register_assembled
(
$assmapper
,
$chr_name
,
$start
,
$end
);
}
=head2 register_contig
Description: DEPRECATED use register_component instead
=cut
sub
register_contig
{
my
(
$self
,
$assmapper
,
$type
,
$contig_id
)
=
@_
;
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...
register_component
(
$assmapper
,
$contig_id
);
}
=head2 fetch_by_type
Description: DEPRECATED use fetch_by_CoordSystems instead
=cut
sub
fetch_by_type
{
my
(
$self
,
$type
)
=
@_
;
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
my
$csa
=
$self
->
db
()
->
get_CoordSystemAdaptor
();
my
$cs1
=
$csa
->
fetch_top_level
(
$type
);
my
$cs2
=
$csa
->
fetch_sequence_level
();
return
$self
->
fetch_by_CoordSystems
(
$cs1
,
$cs2
);
}
1
;
modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
View file @
9aed91b8
...
...
@@ -297,35 +297,6 @@ sub fetch_all_by_hit_name_unversioned {
}
=head2 fetch_all_by_RawContig_and_pid
Description: DEPRECATED use fetch_all_by_Slice_and_pid instead
=cut
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
;
#get the primary table alias
my
@tabs
=
$self
->
_tables
;
my
$alias
=
$tabs
[
0
]
->
[
1
];
if
(
defined
$pid
)
{
$constraint
=
"
${alias}
.perc_ident >
$pid
";
}
return
$self
->
fetch_all_by_RawContig_constraint
(
$contig
,
$constraint
,
$logic_name
);
}
##implemented by subclasses:
# store
# _tables
...
...
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
View file @
9aed91b8
...
...
@@ -1331,60 +1331,6 @@ sub _list_seq_region_ids {
}
=head1 DEPRECATED METHODS
=cut
=head2 fetch_all_by_RawContig_constraint
Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
=cut
sub
fetch_all_by_RawContig_constraint
{
my
$self
=
shift
;
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
(
@
_
);
}
=head2 fetch_all_by_RawContig
Description: DEPRECATED use fetch_all_by_Slice instead
=cut
sub
fetch_all_by_RawContig
{
my
$self
=
shift
;
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
(
@
_
);
}
=head2 fetch_all_by_RawContig_and_score
Description: DEPRECATED use fetch_all_by_Slice_and_score instead
=cut
sub
fetch_all_by_RawContig_and_score
{
my
$self
=
shift
;
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
(
@
_
);
}
=head2 remove_by_RawContig
Description: DEPRECATED use remove_by_Slice instead
=cut
sub
remove_by_RawContig
{
my
$self
=
shift
;
deprecate
("
fetch_by_RawContig is deprecated and will be removed in e87. Use remove_by_Slice instead
");
return
$self
->
remove_by_Slice
(
@
_
);
}
sub
remove_by_analysis_id
{
my
(
$self
,
$analysis_id
)
=
@_
;
...
...
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
View file @
9aed91b8
...
...
@@ -1109,129 +1109,5 @@ sub revert_adaptor {
return
$deleted_adaptor
;
}
#########################
# sub DEPRECATED METHODS
#########################
=head2 db
Description: DEPRECATED
=cut
sub
db
{
my
(
$self
,
$arg
)
=
@_
;
deprecate
("
DBAdaptor->db is deprecated and will be removed in e87. Please use DBConnection->db instead.
");
return
$self
->
dbc
(
$arg
);
}
=head2 assembly_type
Description: DEPRECATED - Use CoordSystemAdaptor to obtain default coordinate
system instead.
=cut
sub
assembly_type
{
my
$self
=
shift
;
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
()};
return
(
$cs
)
?
$cs
->
version
()
:
undef
;
}
=head2 list_supported_assemblies
Description: DEPRECATED - Use CoordSystemAdaptor to obtain list of top-level
coordinate systems instead
=cut
sub
list_supported_assemblies
{
my
(
$self
)
=
@_
;
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
;
foreach
my
$cs
(
@
{
$csa
->
fetch_all
()})
{
$versions
{
$cs
->
version
()}
=
1
;
}
return
keys
%versions
;
}
sub
prepare
{
my
(
$self
,
@args
)
=
@_
;
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
("
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
("
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
("
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
);
}
sub
host
{
my
(
$self
,
@args
)
=
@_
;
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
("
DBAdaptor->username is deprecated and will be removed in e87. Please use DBConnection->username instead.
");
$self
->
dbc
->
username
(
@args
);
}