Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
ensembl-gh-mirror
ensembl
Commits
67709b92
Commit
67709b92
authored
Nov 11, 2015
by
Magali Ruffier
Browse files
planned retirement of deprecated methods
parent
bc190300
Changes
23
Hide whitespace changes
Inline
Side-by-side
Showing
20 changed files
with
173 additions
and
110 deletions
+173
-110
DEPRECATED.md
DEPRECATED.md
+89
-0
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+2
-2
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+7
-7
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+3
-3
modules/Bio/EnsEMBL/Exon.pm
modules/Bio/EnsEMBL/Exon.pm
+5
-5
modules/Bio/EnsEMBL/Feature.pm
modules/Bio/EnsEMBL/Feature.pm
+2
-2
modules/Bio/EnsEMBL/FeaturePair.pm
modules/Bio/EnsEMBL/FeaturePair.pm
+8
-8
modules/Bio/EnsEMBL/Gene.pm
modules/Bio/EnsEMBL/Gene.pm
+5
-6
modules/Bio/EnsEMBL/IdentityXref.pm
modules/Bio/EnsEMBL/IdentityXref.pm
+6
-6
modules/Bio/EnsEMBL/KaryotypeBand.pm
modules/Bio/EnsEMBL/KaryotypeBand.pm
+1
-1
modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
+1
-1
modules/Bio/EnsEMBL/Map/DitagFeature.pm
modules/Bio/EnsEMBL/Map/DitagFeature.pm
+3
-2
modules/Bio/EnsEMBL/Map/MapLocation.pm
modules/Bio/EnsEMBL/Map/MapLocation.pm
+1
-1
modules/Bio/EnsEMBL/OperonTranscript.pm
modules/Bio/EnsEMBL/OperonTranscript.pm
+1
-1
modules/Bio/EnsEMBL/PredictionTranscript.pm
modules/Bio/EnsEMBL/PredictionTranscript.pm
+3
-3
modules/Bio/EnsEMBL/Registry.pm
modules/Bio/EnsEMBL/Registry.pm
+1
-1
modules/Bio/EnsEMBL/Root.pm
modules/Bio/EnsEMBL/Root.pm
+7
-32
modules/Bio/EnsEMBL/SeqFeatureI.pm
modules/Bio/EnsEMBL/SeqFeatureI.pm
+11
-8
modules/Bio/EnsEMBL/Slice.pm
modules/Bio/EnsEMBL/Slice.pm
+16
-20
modules/Bio/EnsEMBL/StrainSlice.pm
modules/Bio/EnsEMBL/StrainSlice.pm
+1
-1
No files found.
DEPRECATED.md
View file @
67709b92
...
...
@@ -71,9 +71,98 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP
-
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()*
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
View file @
67709b92
...
...
@@ -511,7 +511,7 @@ sub fetch_by_assembly_location {
my
(
$self
,
$chrStart
,
$chrEnd
,
$strand
,
$chrName
,
$assemblyType
)
=
@_
;
deprecate
('
U
se fetch_by_Slice_start_end_strand() instead
');
deprecate
('
fetch_by_assembly_location is deprecated and will be removed in e87. Please u
se fetch_by_Slice_start_end_strand() instead
');
my
$csa
=
$self
->
db
->
get_CoordSystem
();
my
$top_cs
=
@
{
$csa
->
fetch_all
};
...
...
@@ -532,7 +532,7 @@ sub fetch_by_assembly_location {
=cut
sub
fetch_by_RawContig_start_end_strand
{
deprecate
('
U
se fetch_by_Slice_start_end_strand instead.
');
deprecate
('
fetch_by_RawContig_start_end_strand is deprecated and will be removed in e87. Please u
se fetch_by_Slice_start_end_strand instead.
');
fetch_by_Slice_start_end_strand
(
@
_
);
}
...
...
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
View file @
67709b92
...
...
@@ -2749,7 +2749,7 @@ sub _build_circular_slice_cache {
sub
fetch_by_mapfrag
{
my
(
$self
,
$mymapfrag
,
$flag
,
$size
)
=
@_
;
deprecate
('
U
se fetch_by_misc_feature_attribute instead
');
deprecate
('
fetch_by_mapfrag is deprecated and will be removed in e87. Please u
se fetch_by_misc_feature_attribute instead
');
$flag
||=
'
fixed-width
';
# alt.. 'context'
$size
||=
$flag
eq
'
fixed-width
'
?
100000
:
0
;
return
$self
->
fetch_by_misc_feature_attribute
('
synonym
',
$mymapfrag
,
$size
);
...
...
@@ -2765,7 +2765,7 @@ sub fetch_by_mapfrag{
sub
fetch_by_chr_start_end
{
my
(
$self
,
$chr
,
$start
,
$end
)
=
@_
;
deprecate
('
U
se fetch_by_region() instead
');
deprecate
('
fetch_by_chr_start_end is deprecated and will be removed in e87. Please u
se fetch_by_region() instead
');
#assume that by chromosome the user actually meant top-level coord
#system since this is the old behaviour of this deprecated method
...
...
@@ -2787,7 +2787,7 @@ sub fetch_by_chr_start_end {
sub
fetch_by_contig_name
{
my
(
$self
,
$name
,
$size
)
=
@_
;
deprecate
('
U
se fetch_by_region(), Slice::project() and Slice::expand().
');
deprecate
('
fetch_by_contig_name is deprecated and will be removed in e87. Please u
se fetch_by_region(), Slice::project() and Slice::expand().
');
#previously wanted chromosomal slice on a given contig. Assume this means
#a top-level slice on a given seq_region in the seq_level coord system
...
...
@@ -2820,7 +2820,7 @@ sub fetch_by_contig_name {
sub
fetch_by_clone_accession
{
my
(
$self
,
$name
,
$size
)
=
@_
;
deprecate
('
U
se fetch_by_region(), Slice::project() and Slice::expand().
');
deprecate
('
fetch_by_clone_accession is deprecated and will be removed in e87. Please u
se fetch_by_region(), Slice::project() and Slice::expand().
');
my
$csa
=
$self
->
db
()
->
get_CoordSystemAdaptor
();
my
$clone_cs
=
$csa
->
fetch_by_name
('
clone
');
...
...
@@ -2876,7 +2876,7 @@ sub fetch_by_clone_accession{
sub
fetch_by_supercontig_name
{
my
(
$self
,
$name
,
$size
)
=
@_
;
deprecate
('
U
se fetch_by_region(), Slice::project() and Slice::expand().
');
deprecate
('
fetch_by_supercontig_name is deprecated and will be removed in e87. Please u
se fetch_by_region(), Slice::project() and Slice::expand().
');
my
$csa
=
$self
->
db
()
->
get_CoordSystemAdaptor
();
my
$sc_level
=
$csa
->
fetch_by_name
('
supercontig
');
...
...
@@ -2911,7 +2911,7 @@ sub fetch_by_supercontig_name {
sub
list_overlapping_supercontigs
{
my
(
$self
,
$slice
)
=
@_
;
deprecate
('
U
se Slice::project() instead.
');
deprecate
('
list_overlapping_supercontigs is deprecated and will be removed in e87. Please u
se Slice::project() instead.
');
my
$csa
=
$self
->
db
()
->
get_CoordSystemAdaptor
();
my
$sc_level
=
$csa
->
fetch_by_name
('
supercontig
');
...
...
@@ -2939,7 +2939,7 @@ sub list_overlapping_supercontigs {
sub
fetch_by_chr_name
{
my
(
$self
,
$chr_name
)
=
@_
;
deprecate
('
U
se fetch_by_region() instead.
');
deprecate
('
fetch_by_chr_name is deprecated and will be removed in e87. Please u
se fetch_by_region() instead.
');
my
$csa
=
$self
->
db
->
get_CoordSystemAdaptor
();
...
...
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
View file @
67709b92
...
...
@@ -2069,7 +2069,7 @@ sub fetch_all_by_transcript_supporting_evidence {
sub
get_display_xref
{
my
(
$self
,
$transcript
)
=
@_
;
deprecate
("
display_xref should be retrieved from Transcript object directly.
");
deprecate
("
get_display_xref is deprecated and will be removed in e87.
display_xref should be retrieved from Transcript object directly.
");
if
(
!
defined
$transcript
)
{
throw
("
Must call with a Transcript object
");
...
...
@@ -2119,7 +2119,7 @@ sub get_display_xref {
sub
get_stable_entry_info
{
my
(
$self
,
$transcript
)
=
@_
;
deprecate
("
Stable ids should be loaded directly
now
");
deprecate
("
get_stable_entry_info is deprecated and will be removed in e87.
Stable ids should be loaded directly
instead
");
unless
(
defined
$transcript
&&
ref
$transcript
&&
$transcript
->
isa
('
Bio::EnsEMBL::Transcript
')
)
{
...
...
@@ -2151,7 +2151,7 @@ sub get_stable_entry_info {
sub
fetch_all_by_DBEntry
{
my
$self
=
shift
;
deprecate
('
U
se fetch_all_by_external_name instead.
');
deprecate
('
fetch_all_by_DBEntry is deprecated and will be removed in e87. Please u
se fetch_all_by_external_name instead.
');
return
$self
->
fetch_all_by_external_name
(
@
_
);
}
...
...
modules/Bio/EnsEMBL/Exon.pm
View file @
67709b92
...
...
@@ -1612,7 +1612,7 @@ sub summary_as_hash {
sub
_get_stable_entry_info
{
my
$self
=
shift
;
deprecate
(
"
This function shouldnt be called any more
"
);
deprecate
(
"
_get_stable_entry_info is deprecated and will be removed in e84. Please use stable_id instead.
"
);
if
(
!
defined
$self
->
adaptor
)
{
return
undef
;
}
...
...
@@ -1628,7 +1628,7 @@ sub _get_stable_entry_info {
sub
temporary_id
{
my
$self
=
shift
;
deprecate
('
It should not be necessary to use this method
.
');
deprecate
('
temporary_id is deprecated and will be removed in e87
.
');
$self
->
{'
tempID
'}
=
shift
if
(
@
_
);
return
$self
->
{'
tempID
'};
}
...
...
@@ -1642,7 +1642,7 @@ sub temporary_id {
sub
created
{
my
(
$self
,
$value
)
=
@_
;
deprecate
(
"
C
reated
attribute not supported any more
.
"
);
deprecate
(
"
c
reated
is deprecated and will be removed in e87
.
"
);
if
(
defined
$value
)
{
$self
->
{'
_created
'}
=
$value
;
}
...
...
@@ -1658,7 +1658,7 @@ sub created {
sub
modified
{
my
(
$self
,
$value
)
=
@_
;
deprecate
(
"
Modified
attribute not supported any more
.
"
);
deprecate
(
"
Modified
is deprecated and will be removed in e87
.
"
);
if
(
defined
$value
)
{
$self
->
{'
_modified
'}
=
$value
;
}
...
...
@@ -1674,7 +1674,7 @@ sub modified {
sub
type
{
my
(
$self
,
$value
)
=
@_
;
deprecate
("
Type
attribute not supported anymore
.
");
deprecate
("
Type
is deprecated and will be removed in e87
.
");
if
(
defined
(
$value
))
{
$self
->
{'
type
'}
=
$value
;
}
...
...
modules/Bio/EnsEMBL/Feature.pm
View file @
67709b92
...
...
@@ -1502,7 +1502,7 @@ sub species {
Use slice() instead
=cut
sub
contig
{
deprecate
('
U
se slice() instead
');
deprecate
('
contig is deprecated and will be removed in e87. Please u
se slice() instead
');
slice
(
@
_
);
}
...
...
@@ -1603,7 +1603,7 @@ Use display_id, hseqname, dbID or stable_id instead
sub
id
{
my
$self
=
shift
;
deprecate
("
id method is
not used -
use display_id instead
");
deprecate
("
id method is
deprecated and will be removed in e87. Please
use display_id instead
");
return
$self
->
{'
stable_id
'}
if
(
$self
->
{'
stable_id
'});
return
$self
->
{'
hseqname
'}
if
(
$self
->
{'
hseqname
'});
return
$self
->
{'
seqname
'}
if
(
$self
->
{'
seqname
'});
...
...
modules/Bio/EnsEMBL/FeaturePair.pm
View file @
67709b92
...
...
@@ -729,7 +729,7 @@ sub level_id {
sub
feature1
{
my
(
$self
,
$arg
)
=
@_
;
deprecate
('
U
se start(), end(), strand(), slice(), etc. methods instead.
');
deprecate
('
feature1 is deprecated and will be removed in e87. Please u
se start(), end(), strand(), slice(), etc. methods instead.
');
if
(
$arg
)
{
$self
->
start
(
$arg
->
start
());
...
...
@@ -756,7 +756,7 @@ sub feature1 {
sub
feature2
{
my
(
$self
,
$arg
)
=
@_
;
deprecate
('
U
se hstart(),hend(),hstrand(),hseqname() methods instead.
');
deprecate
('
feature2 is deprecated and will be removed in e87. Please u
se hstart(),hend(),hstrand(),hseqname() methods instead.
');
if
(
defined
(
$arg
))
{
$self
->
hstart
(
$arg
->
start
());
...
...
@@ -837,7 +837,7 @@ sub invert {
sub
validate
{
my
(
$self
)
=
@_
;
deprecate
('
This method does nothing and should not be used
.
');
deprecate
('
validate is deprecated and will be removed in e84
.
');
}
=head2 validate_prot_feature
...
...
@@ -849,7 +849,7 @@ sub validate {
sub
validate_prot_feature
{
my
(
$self
)
=
@_
;
deprecate
('
This method does nothing and should not be used
.
');
deprecate
('
validate is deprecated and will be removed in e84
.
');
}
=head2 set_featurepair_fields
...
...
@@ -861,7 +861,7 @@ sub validate_prot_feature {
sub
set_featurepair_fields
{
my
(
$self
,
$start
,
$end
,
$strand
,
$score
,
$seqname
,
$hstart
,
$hend
,
$hstrand
,
$hseqname
,
$analysis
,
$e_value
,
$perc_id
,
$phase
,
$end_phase
)
=
@_
;
deprecate
("
Use individual Getter/Setters or Constructor arguments
"
.
"
instead.
\n
There is no advantage to using this metho
d.
");
deprecate
("
set_featurepair_fields is deprecated and will be removed in e87. Please use individual Getter/Setters or Constructor arguments instea
d.
");
throw
('
interface fault
')
if
(
@
_
<
12
or
@
_
>
15
);
...
...
@@ -890,7 +890,7 @@ sub set_featurepair_fields {
sub
gffstring
{
my
(
$self
)
=
@_
;
deprecate
('
Do not use
');
deprecate
('
gffstring is deprecated and will be removed in e87.
');
my
$str
.=
(
defined
$self
->
slice
)
?
$self
->
slice
->
name
()
.
"
\t
"
:
"
\t
";
$str
.=
"
\t
";
#source tag
...
...
@@ -927,7 +927,7 @@ sub gffstring {
sub
hphase
{
my
(
$self
,
$value
)
=
@_
;
deprecate
('
This method does nothing useful
.
');
deprecate
('
hphase is deprecated and will be removed in e87
.
');
if
(
defined
(
$value
))
{
$self
->
{
_hphase
}
=
$value
;
...
...
@@ -945,7 +945,7 @@ sub hphase {
sub
hend_phase
{
my
(
$self
,
$value
)
=
@_
;
deprecate
('
This method does nothing useful
.
');
deprecate
('
hend_phase is deprecated and will be removed in e87
.
');
if
(
defined
(
$value
))
{
$self
->
{
_hend_phase
}
=
$value
;
...
...
modules/Bio/EnsEMBL/Gene.pm
View file @
67709b92
...
...
@@ -1530,7 +1530,7 @@ sub havana_gene {
sub
add_DBLink
{
my
(
$self
,
$value
)
=
@_
;
throw
("
add_DBLink is deprecated
. You probably want
add_DBEntry.
");
throw
("
add_DBLink is deprecated
and will be removed in e87. Please use
add_DBEntry
instead
.
");
# unless(defined $value && ref $value
# && $value->isa('Bio::Annotation::DBLink') ) {
...
...
@@ -1553,8 +1553,7 @@ sub add_DBLink{
sub
temporary_id
{
my
(
$obj
,
$value
)
=
@_
;
deprecate
(
"
I cant see what a temporary_id is good for, please use
"
.
"
dbID or stableID or
\n
try without an id.
"
);
deprecate
('
temporary_id is deprecated and will be removed in e87.
');
if
(
defined
$value
)
{
$obj
->
{'
temporary_id
'}
=
$value
;
}
...
...
@@ -1574,7 +1573,7 @@ sub temporary_id {
sub
chr_name
{
my
$self
=
shift
;
deprecate
(
"
U
se project() to obtain other coordinate systems
"
);
deprecate
(
"
chr_name is deprecated and will be removed in e87. Please u
se project() to obtain other coordinate systems
"
);
my
$gene_slice
=
$self
->
slice
();
if
(
$gene_slice
->
coord_system
()
->
name
eq
"
chromosome
"
)
{
...
...
@@ -1621,7 +1620,7 @@ sub fetch_coded_for_regulatory_factors {
=cut
sub
type
{
deprecate
("
U
se biotype() instead
");
deprecate
("
type is deprecated and will be removed in e87. Please u
se biotype() instead
");
biotype
(
@
_
);
}
...
...
@@ -1633,7 +1632,7 @@ sub type {
=cut
sub
confidence
{
deprecate
("
U
se status() instead
");
deprecate
("
confidence is deprecated and will be removed in e87. Please u
se status() instead
");
status
(
@
_
);
}
...
...
modules/Bio/EnsEMBL/IdentityXref.pm
View file @
67709b92
...
...
@@ -452,7 +452,7 @@ sub map_feature {
=cut
sub
query_identity
{
deprecate
("
U
se xref_identity instead
");
deprecate
("
query_identity is deprecated and will be removed in e87. Please u
se xref_identity instead
");
xref_identity
(
@
_
);
}
...
...
@@ -465,7 +465,7 @@ sub query_identity{
=cut
sub
target_identity
{
deprecate
("
U
se ensembl_identity instead
");
deprecate
("
target_identity is deprecated and will be removed in e87. Please u
se ensembl_identity instead
");
ensembl_identity
(
@
_
);
}
...
...
@@ -479,7 +479,7 @@ sub target_identity{
=cut
sub
translation_start
{
deprecate
("
U
se ensembl_start instead
");
deprecate
("
translation_start is deprecated and will be removed in e87. Please u
se ensembl_start instead
");
ensembl_start
(
@
_
);
}
...
...
@@ -493,7 +493,7 @@ sub translation_start {
=cut
sub
translation_end
{
deprecate
("
U
se ensembl_end instead
");
deprecate
("
translation_end is deprecated and will be removed in e87. Please u
se ensembl_end instead
");
ensembl_end
(
@
_
);
}
...
...
@@ -507,7 +507,7 @@ sub translation_end {
=cut
sub
query_start
{
deprecate
("
U
se xref_start instead
");
deprecate
("
query_start is deprecated and will be removed in e87. Please u
se xref_start instead
");
xref_start
(
@
_
);
}
...
...
@@ -522,7 +522,7 @@ sub query_start {
=cut
sub
query_end
{
deprecate
("
U
se xref_end instead
");
deprecate
("
query_end is deprecated and will be removed in e87. Please u
se xref_end instead
");
xref_end
(
@
_
);
}
...
...
modules/Bio/EnsEMBL/KaryotypeBand.pm
View file @
67709b92
...
...
@@ -230,7 +230,7 @@ sub display_id {
sub
chr_name
{
my
$self
=
shift
;
deprecate
('
U
se $kary_band->slice()->seq_region_name() instead.
');
deprecate
('
chr_name is deprecated and will be removed in e87. Please u
se $kary_band->slice()->seq_region_name() instead.
');
if
(
!
$self
->
slice
)
{
warning
('
KaryotypeBand does not have Slice - cannot get seq_region_name.
');
return
'';
...
...
modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
View file @
67709b92
...
...
@@ -151,7 +151,7 @@ sub fetch_all_by_Slice_and_priority {
=cut
sub
fetch_all_by_RawContig_and_priority
{
deprecate
('
U
se fetch_all_by_Slice_and_priority() instead.
');
deprecate
('
fetch_all_by_RawContig_and_priority is deprecated and will be removed in e87. Please u
se fetch_all_by_Slice_and_priority() instead.
');
fetch_all_by_Slice_and_priority
(
@
_
);
}
...
...
modules/Bio/EnsEMBL/Map/DitagFeature.pm
View file @
67709b92
...
...
@@ -65,8 +65,9 @@ package Bio::EnsEMBL::Map::DitagFeature;
use
strict
;
use
vars
qw(@ISA)
;
use
Bio::EnsEMBL::
Feature
;
use
Bio::EnsEMBL::Utils::
Exception
qw( throw )
;
use
Bio::EnsEMBL::Utils::
Exception
qw( throw
deprecate
)
;
use
Bio::EnsEMBL::Utils::
Argument
qw( rearrange )
;
@ISA
=
qw(Bio::EnsEMBL::Feature)
;
...
...
@@ -170,7 +171,7 @@ sub new {
=cut
sub
fetch_ditag
{
throw
("
Deprecated method, p
lease use ditag() instead.
\n
")
deprecate
("
fetch_ditag is deprecated and will be removed in e87. P
lease use ditag() instead.
")
}
...
...
modules/Bio/EnsEMBL/Map/MapLocation.pm
View file @
67709b92
...
...
@@ -195,7 +195,7 @@ sub lod_score {
sub
chromosome
{
my
$self
=
shift
;
deprecate
('
use chromosome_name instead
');
deprecate
('
chromosome is deprecated and will be removed in e87. Please
use chromosome_name instead
');
if
(
@
_
)
{
my
$chr
=
shift
;
...
...
modules/Bio/EnsEMBL/OperonTranscript.pm
View file @
67709b92
...
...
@@ -274,7 +274,7 @@ sub add_Gene {
=cut
sub
add_gene
{
my
(
$self
,
$gene
)
=
@_
;
deprecate
('
Call
is deprecated
. U
se $self->add_Gene()
');
deprecate
('
add_gene
is deprecated
and will be removed in e87. Please u
se $self->add_Gene()
');
return
$self
->
add_Gene
(
$gene
);
}
=head2 add_DBEntry
...
...
modules/Bio/EnsEMBL/PredictionTranscript.pm
View file @
67709b92
...
...
@@ -574,7 +574,7 @@ sub get_all_Attributes {
sub
get_exon_count
{
my
$self
=
shift
;
deprecate
('
U
se scalar(@{$transcript->get_all_Exon()s}) instead
');
deprecate
('
get_exon_count is deprecated and will be removed in e87. Please u
se scalar(@{$transcript->get_all_Exon()s}) instead
');
return
scalar
(
@
{
$self
->
get_all_Exons
}
);
}
...
...
@@ -586,7 +586,7 @@ sub get_exon_count {
=cut
sub
set_exon_count
{
deprecate
('
This method no longer does anything
.
');
deprecate
('
set_exon_count is deprecated and will be removed in e84
.
');
}
...
...
@@ -599,7 +599,7 @@ sub set_exon_count {
sub
get_cdna
{
my
$self
=
shift
;
deprecate
('
use spliced_seq instead
');
deprecate
('
get_cdna is deprecated and will be removed in e87. Please
use spliced_seq instead
');
return
$self
->
spliced_seq
();
}
...
...
modules/Bio/EnsEMBL/Registry.pm
View file @
67709b92
...
...
@@ -2649,7 +2649,7 @@ sub load_registry_from_multiple_dbs {
sub
load_registry_with_web_adaptors
{
my
$class
=
shift
;
deprecate
('
U
se the load_registry_from_db instead
');
deprecate
('
load_registry_with_web_adaptors is deprecated and will be removed in e87. Please u
se the load_registry_from_db instead
');
my
$site_eval
=
eval
{
require
SiteDefs
};
if
(
$@
or
(
!
defined
(
$site_eval
))){
die
"
Can't use SiteDefs.pm - $@
\n
";
}
SiteDefs
->
import
(
qw(:ALL)
);
...
...
modules/Bio/EnsEMBL/Root.pm
View file @
67709b92
...
...
@@ -92,11 +92,7 @@ sub new{
sub
throw
{
my
(
$self
,
$string
)
=
@_
;
Bio::EnsEMBL::Utils::
Exception
->
warning
("
\n
------------------ DEPRECATED ---------------------
\n
"
.
"
Bio::EnsEMBL::Root::throw has been deprecated
\n
"
.
"
use Bio::EnsEMBL::Utils::Exception qw(throw);
\n
"
.
"
throw('message'); #instead
\n
"
.
"
\n
---------------------------------------------------
\n
");
deprecate
('
Root->throw has been deprecated and will be removed in e87. Please use Exception->throw instead
');
Bio::EnsEMBL::Utils::
Exception
->
throw
(
$string
);
...
...
@@ -112,14 +108,8 @@ sub throw{
sub
warn
{
my
(
$self
,
$string
)
=
@_
;
deprecate
('
Root->warn has been deprecated and will be removed in e87. Please use Exception->warning instead
');
Bio::EnsEMBL::Utils::
Exception
->
warning
("
\n
------------------ DEPRECATED ---------------------
\n
"
.
"
Bio::EnsEMBL::Root::warn has been deprecated
\n
"
.
"
use Bio::EnsEMBL::Utils::Exception qw(warning);
\n
"
.
"
warning('message'); #instead
\n
"
.
"
\n
---------------------------------------------------
\n
");
Bio::EnsEMBL::Utils::
Exception
->
warning
(
$string
);
}
...
...
@@ -136,12 +126,8 @@ sub warn{
sub
verbose
{
my
(
$self
,
$value
)
=
@_
;
Bio::EnsEMBL::Utils::
Exception
->
warning
("
\n
------------------ DEPRECATED ---------------------
\n
"
.
"
Bio::EnsEMBL::Root::verbose has been deprecated
\n
"
.
"
use Bio::EnsEMBL::Utils::Exception qw(verbose);
\n
"
.
"
verbose(value); #instead
\n
"
.
"
\n
---------------------------------------------------
\n
");
deprecate
('
Root->verbose has been deprecated and will be removed in e87. Please use Exception->verbose instead
');
Bio::EnsEMBL::Utils::
Exception
->
verbose
(
$value
);
}
...
...
@@ -155,11 +141,7 @@ sub verbose{
sub
stack_trace_dump
{
my
(
$self
)
=
@_
;
Bio::EnsEMBL::Utils::
Exception
->
warning
("
\n
------------------ DEPRECATED ---------------------
\n
"
.
"
Bio::EnsEMBL::Root::stack_trace_dump has been deprecated
\n
"
.
"
use Bio::EnsEMBL::Utils::Exception qw(stack_trace_dump);
\n
"
.
"
stack_trace_dump(); #instead
\n
"
.
"
\n
---------------------------------------------------
\n
");
deprecate
('
Root->stack_trace_dump has been deprecated and will be removed in e87. Please use Exception->stack_trace_dump instead
');
Bio::EnsEMBL::Utils::
Exception
->
stack_trace_dump
();
...
...
@@ -175,11 +157,7 @@ sub stack_trace_dump{
sub
stack_trace
{
my
(
$self
)
=
@_
;
Bio::EnsEMBL::Utils::
Exception
->
warning
("
\n
------------------ DEPRECATED ---------------------
\n
"
.
"
Bio::EnsEMBL::Root::stack_trace has been deprecated
\n
"
.
"
use Bio::EnsEMBL::Utils::Exception qw(stack_trace);
\n
"
.
"
stack_trace(); #instead
\n
"
.
"
\n
---------------------------------------------------
\n
");
deprecate
('
Root->stack_trace has been deprecated and will be removed in e87. Please use Exception->stack_trace instead
');
Bio::EnsEMBL::Utils::
Exception
->
stack_trace
();
...
...
@@ -197,10 +175,7 @@ sub _rearrange {
#----------------
my
(
$self
,
$order
,
@param
)
=
@_
;
my
$mess
=
"
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
\n
";
$mess
.=
"
rearrange(order, list); #instead
\n
";
Bio::EnsEMBL::Utils::
Exception
->
deprecate
(
$mess
);
deprecate
('
Root->_rearrange is deprecated and will be removed in e84. Please use Argument->rearrange instead
');
return
Bio::EnsEMBL::Utils::
Argument
->
rearrange
(
$order
,
@param
);
...
...
modules/Bio/EnsEMBL/SeqFeatureI.pm
View file @
67709b92
...
...
@@ -52,6 +52,7 @@ use Carp;