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ensembl-gh-mirror
ensembl
Commits
b762e22e
Commit
b762e22e
authored
Jan 28, 2008
by
Ian Longden
Browse files
removed regulatory method calls (now moved to own database)
parent
077ec5b4
Changes
4
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4 changed files
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1 addition
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93 deletions
+1
-93
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+1
-2
modules/Bio/EnsEMBL/Gene.pm
modules/Bio/EnsEMBL/Gene.pm
+0
-26
modules/Bio/EnsEMBL/Transcript.pm
modules/Bio/EnsEMBL/Transcript.pm
+0
-43
modules/Bio/EnsEMBL/Translation.pm
modules/Bio/EnsEMBL/Translation.pm
+0
-22
No files found.
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
View file @
b762e22e
...
...
@@ -264,8 +264,7 @@ sub get_available_adaptors{
Gene KaryotypeBand MiscSet
MiscFeature OligoArray OligoFeature
OligoProbe PredictionTranscript PredictionExon
ProteinFeature ProteinAlignFeature RegulatoryFeature
RegulatoryFactor RegulatorySearchRegion RepeatConsensus
ProteinFeature ProteinAlignFeature RepeatConsensus
RepeatFeature Sequence SimpleFeature
Slice SupportingFeature Transcript
TranscriptSupportingFeature Translation UnmappedObject
...
...
modules/Bio/EnsEMBL/Gene.pm
View file @
b762e22e
...
...
@@ -1037,32 +1037,6 @@ sub get_all_DAS_Features{
}
=head2 get_all_regulatory_features
Arg [1] : Boolean $recursive
If set, regulatory features on transcripts belonging to this
gene are returned as well
Example : @features = $gene->get_all_regulatory_features(1);
Description: Gets all the regulatory features associated with a particular
gene, and (optionally) its transcripts. Each feature only
appears once.
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature objects
Exceptions : If arg is not of correct type.
Caller : general
Status : At Risk
: regulatory features are under development
=cut
sub
get_all_regulatory_features
{
my
(
$self
,
$recursive
)
=
@_
;
my
$rfa
=
$self
->
adaptor
->
db
->
get_RegulatoryFeatureAdaptor
();
return
$rfa
->
fetch_all_by_gene
(
$self
,
$recursive
);
}
=head2 add_unconventional_transcript_association
...
...
modules/Bio/EnsEMBL/Transcript.pm
View file @
b762e22e
...
...
@@ -2149,49 +2149,6 @@ sub get_all_DAS_Features {
}
=head2 fetch_all_regulatory_features
Arg [1] : none
Example : @features = $transcript->fetch_all_regulatory_features();
Description: Gets all the regulatory features associated with this transcript.
Each feature only appears once.
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : ?
Status : At Risk
=cut
sub
fetch_all_regulatory_features
{
my
(
$self
)
=
@_
;
my
$rfa
=
$self
->
adaptor
->
db
->
get_RegulatoryFeatureAdaptor
();
return
$rfa
->
fetch_all_by_transcript
(
$self
);
}
=head2 fetch_coded_for_regulatory_factors
Arg [1] : none
Example : $transcript->fetch_coded_for_regualtory_factors()
Description: Fetches any regulatory_factors that are coded for by this transcript
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_transcript
(
$self
);
}
=head2 _compare_xrefs
...
...
modules/Bio/EnsEMBL/Translation.pm
View file @
b762e22e
...
...
@@ -1008,27 +1008,5 @@ sub get_all_DAS_Features{
return
$self
->
SUPER::
get_all_DAS_Features
(
$slice
);
}
=head2 get_all_regulatory_features
Example : @features = $translation->get_all_regulatory_features();
Description: Gets all the regulatory features associated with this
translation.
Each feature only appears once.
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : general
Status : At Risk
: Regulatory features are currently under development and are
: likely to change.
=cut
sub
get_all_regulatory_features
{
my
(
$self
)
=
@_
;
my
$rfa
=
$self
->
adaptor
->
db
->
get_RegulatoryFeatureAdaptor
();
return
$rfa
->
fetch_all_by_translation
(
$self
);
}
1
;
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