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ensembl-gh-mirror
ensembl
Commits
08daed32
Commit
08daed32
authored
Sep 09, 2011
by
Monika Komorowska
Browse files
circular reference fix
parent
b3616e19
Changes
32
Expand all
Hide whitespace changes
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Showing
20 changed files
with
150 additions
and
108 deletions
+150
-108
modules/Bio/EnsEMBL/AlignStrainSlice.pm
modules/Bio/EnsEMBL/AlignStrainSlice.pm
+1
-1
modules/Bio/EnsEMBL/ArchiveStableId.pm
modules/Bio/EnsEMBL/ArchiveStableId.pm
+7
-5
modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
+4
-1
modules/Bio/EnsEMBL/AssemblyMapper.pm
modules/Bio/EnsEMBL/AssemblyMapper.pm
+3
-2
modules/Bio/EnsEMBL/Attribute.pm
modules/Bio/EnsEMBL/Attribute.pm
+4
-1
modules/Bio/EnsEMBL/BaseAlignFeature.pm
modules/Bio/EnsEMBL/BaseAlignFeature.pm
+4
-2
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
+2
-1
modules/Bio/EnsEMBL/CircularSlice.pm
modules/Bio/EnsEMBL/CircularSlice.pm
+60
-56
modules/Bio/EnsEMBL/DBEntry.pm
modules/Bio/EnsEMBL/DBEntry.pm
+9
-9
modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+2
-2
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
+4
-2
modules/Bio/EnsEMBL/Feature.pm
modules/Bio/EnsEMBL/Feature.pm
+9
-4
modules/Bio/EnsEMBL/IndividualSliceFactory.pm
modules/Bio/EnsEMBL/IndividualSliceFactory.pm
+23
-6
modules/Bio/EnsEMBL/Map/Ditag.pm
modules/Bio/EnsEMBL/Map/Ditag.pm
+2
-2
modules/Bio/EnsEMBL/Map/DitagFeature.pm
modules/Bio/EnsEMBL/Map/DitagFeature.pm
+1
-1
modules/Bio/EnsEMBL/Map/Marker.pm
modules/Bio/EnsEMBL/Map/Marker.pm
+5
-4
modules/Bio/EnsEMBL/Map/MarkerFeature.pm
modules/Bio/EnsEMBL/Map/MarkerFeature.pm
+6
-4
modules/Bio/EnsEMBL/Map/Qtl.pm
modules/Bio/EnsEMBL/Map/Qtl.pm
+1
-2
modules/Bio/EnsEMBL/Map/QtlFeature.pm
modules/Bio/EnsEMBL/Map/QtlFeature.pm
+1
-1
modules/Bio/EnsEMBL/MappedSlice.pm
modules/Bio/EnsEMBL/MappedSlice.pm
+2
-2
No files found.
modules/Bio/EnsEMBL/AlignStrainSlice.pm
View file @
08daed32
...
...
@@ -296,7 +296,7 @@ sub get_all_Slices {
-
START
=>
$self
->
Slice
->
{'
start
'},
-
END
=>
$self
->
Slice
->
{'
end
'},
-
STRAND
=>
$self
->
Slice
->
{'
strand
'},
-
ADAPTOR
=>
$self
->
Slice
->
{'
adaptor
'}
,
-
ADAPTOR
=>
$self
->
Slice
->
adaptor
()
,
-
SEQ
=>
$self
->
Slice
->
{'
seq
'},
-
SEQ_REGION_NAME
=>
$self
->
Slice
->
{'
seq_region_name
'},
-
SEQ_REGION_LENGTH
=>
$self
->
Slice
->
{'
seq_region_length
'},
...
...
modules/Bio/EnsEMBL/ArchiveStableId.pm
View file @
08daed32
...
...
@@ -84,7 +84,7 @@ use Bio::EnsEMBL::Root;
our
@ISA
=
qw(Bio::EnsEMBL::Root)
;
use
Bio::EnsEMBL::Utils::
Argument
qw(rearrange)
;
use
Scalar::
Util
qw(weaken isweak)
;
=head2 new
...
...
@@ -124,7 +124,7 @@ sub new {
$self
->
{'
release
'}
=
$release
;
$self
->
{'
assembly
'}
=
$assembly
;
$self
->
{'
type
'}
=
$type
;
$self
->
{'
adaptor
'}
=
$adaptor
;
$self
->
adaptor
(
$adaptor
)
;
return
$self
;
}
...
...
@@ -166,6 +166,8 @@ sub new_fast {
'
current_version
'
=>
$_
[
7
],
},
$class
;
weaken
(
$self
->
{
adaptor
})
if
(
!
isweak
(
$self
->
{
adaptor
})
);
return
$self
;
}
...
...
@@ -395,9 +397,9 @@ sub current_version {
if
(
@
_
)
{
$self
->
{'
current_version
'}
=
shift
;
}
elsif
(
!
defined
$self
->
{'
current_version
'})
{
if
(
defined
$self
->
{'
adaptor
'}
)
{
if
(
defined
$self
->
adaptor
()
)
{
# lazy load
$self
->
{'
adaptor
'}
->
lookup_current
(
$self
);
$self
->
adaptor
()
->
lookup_current
(
$self
);
}
}
...
...
@@ -522,7 +524,7 @@ sub type {
sub
adaptor
{
my
$self
=
shift
;
$self
->
{'
adaptor
'}
=
shift
if
(
@
_
);
weaken
(
$self
->
{'
adaptor
'}
=
shift
)
if
(
@
_
);
return
$self
->
{'
adaptor
'};
}
...
...
modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
View file @
08daed32
...
...
@@ -52,6 +52,7 @@ use vars qw(@ISA);
use
Bio::EnsEMBL::
Feature
;
use
Bio::EnsEMBL::Utils::
Argument
qw(rearrange)
;
use
Scalar::
Util
qw(weaken isweak)
;
@ISA
=
qw(Bio::EnsEMBL::Feature)
;
...
...
@@ -105,7 +106,9 @@ sub new {
sub
new_fast
{
my
$class
=
shift
;
my
$hashref
=
shift
;
return
bless
$hashref
,
$class
;
my
$self
=
bless
$hashref
,
$class
;
weaken
(
$self
->
{
adaptor
})
if
(
!
isweak
(
$self
->
{
adaptor
})
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/AssemblyMapper.pm
View file @
08daed32
...
...
@@ -75,6 +75,7 @@ use warnings;
use
Bio::EnsEMBL::
Mapper
;
use
Bio::EnsEMBL::Utils::
Exception
qw(throw deprecate)
;
use
Scalar::
Util
qw(weaken)
;
my
$ASSEMBLED
=
'
assembled
';
my
$COMPONENT
=
'
component
';
...
...
@@ -340,7 +341,7 @@ sub fastmap {
my
$mapper
=
$self
->
{'
mapper
'};
my
$asm_cs
=
$self
->
{'
asm_cs
'};
my
$cmp_cs
=
$self
->
{'
cmp_cs
'};
my
$adaptor
=
$self
->
{'
adaptor
'}
;
my
$adaptor
=
$self
->
adaptor
()
;
my
$frm
;
my
@tmp
;
...
...
@@ -777,7 +778,7 @@ sub adaptor {
my
(
$self
,
$value
)
=
@_
;
if
(
defined
(
$value
)
)
{
$self
->
{'
adaptor
'}
=
$value
;
weaken
(
$self
->
{'
adaptor
'}
=
$value
)
;
}
return
$self
->
{'
adaptor
'};
...
...
modules/Bio/EnsEMBL/Attribute.pm
View file @
08daed32
...
...
@@ -55,6 +55,7 @@ use strict;
use
warnings
;
use
Bio::EnsEMBL::Utils::
Argument
qw(rearrange)
;
use
Scalar::
Util
qw(weaken isweak)
;
=head2 new
...
...
@@ -106,7 +107,9 @@ sub new {
sub
new_fast
{
my
$class
=
shift
;
my
$hashref
=
shift
;
return
bless
$hashref
,
$class
;
my
$self
=
bless
$hashref
,
$class
;
weaken
(
$self
->
{
adaptor
})
if
(
!
isweak
(
$self
->
{
adaptor
})
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/BaseAlignFeature.pm
View file @
08daed32
...
...
@@ -102,6 +102,7 @@ package Bio::EnsEMBL::BaseAlignFeature;
use
Bio::EnsEMBL::
FeaturePair
;
use
Bio::EnsEMBL::Utils::
Argument
qw(rearrange)
;
use
Bio::EnsEMBL::Utils::
Exception
qw(throw warning)
;
use
Scalar::
Util
qw(weaken isweak)
;
use
vars
qw(@ISA)
;
use
strict
;
...
...
@@ -174,8 +175,9 @@ sub new {
sub
new_fast
{
my
(
$class
,
$hashref
)
=
@_
;
return
bless
$hashref
,
$class
;
my
$self
=
bless
$hashref
,
$class
;
weaken
(
$self
->
{
adaptor
})
if
(
!
isweak
(
$self
->
{
adaptor
})
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
View file @
08daed32
...
...
@@ -84,6 +84,7 @@ use integer; #use proper arithmetic bitshifts
use
Bio::EnsEMBL::
Mapper
;
use
Bio::EnsEMBL::Mapper::
RangeRegistry
;
use
Bio::EnsEMBL::Utils::
Exception
qw(throw deprecate)
;
use
Scalar::
Util
qw(weaken)
;
#2^20 = approx 10^6
my
$CHUNKFACTOR
=
20
;
...
...
@@ -719,7 +720,7 @@ sub component_CoordSystem {
sub
adaptor
{
my
$self
=
shift
;
$self
->
{'
adaptor
'}
=
shift
if
(
@
_
);
weaken
(
$self
->
{'
adaptor
'}
=
shift
)
if
(
@
_
);
return
$self
->
{'
adaptor
'};
}
...
...
modules/Bio/EnsEMBL/CircularSlice.pm
View file @
08daed32
This diff is collapsed.
Click to expand it.
modules/Bio/EnsEMBL/DBEntry.pm
View file @
08daed32
...
...
@@ -45,6 +45,7 @@ use Bio::Annotation::DBLink;
use
Bio::EnsEMBL::Utils::
Argument
qw(rearrange)
;
use
Bio::EnsEMBL::Utils::
Exception
qw(deprecate)
;
use
Scalar::
Util
qw(weaken isweak)
;
our
@ISA
=
qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink)
;
...
...
@@ -65,10 +66,9 @@ our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink);
sub
new_fast
{
my
$class
=
shift
;
my
$hashref
=
shift
;
bless
$hashref
,
$class
;
return
$hashref
;
my
$self
=
bless
$hashref
,
$class
;
weaken
(
$self
->
{
adaptor
})
if
(
!
isweak
(
$self
->
{
adaptor
})
);
return
$self
;
}
...
...
@@ -120,7 +120,7 @@ sub new {
'
DB_DISPLAY_NAME
',
'
INFO_TYPE
',
'
INFO_TEXT
',
'
TYPE
',
'
SECONDARY_DB_NAME
',
'
SECONDARY_DB_TABLE
',
'
LINKAGE_ANNOTATION
',
'
ANALYSIS
'],
@args
);
$self
->
{'
adaptor
'}
=
$adaptor
;
$self
->
adaptor
(
$adaptor
)
;
$self
->
{'
dbID
'}
=
$dbID
;
if
(
defined
$primary_id
)
{
$self
->
primary_id
(
$primary_id
)
}
...
...
@@ -569,8 +569,8 @@ sub get_all_synonyms {
my
$self
=
shift
;
# lazy-load synonyms if required
if
(
!
$self
->
{
synonyms
}
&&
$self
->
{
adaptor
}
)
{
$self
->
{
synonyms
}
=
$self
->
{
adaptor
}
->
fetch_all_synonyms
(
$self
->
dbID
());
if
(
!
$self
->
{
synonyms
}
&&
$self
->
adaptor
()
)
{
$self
->
{
synonyms
}
=
$self
->
adaptor
()
->
fetch_all_synonyms
(
$self
->
dbID
());
}
return
$self
->
{
synonyms
};
...
...
@@ -595,7 +595,7 @@ sub get_all_dependents {
my
$self
=
shift
;
my
$ensembl_object
=
shift
;
return
$self
->
{
adaptor
}
->
get_all_dependents
(
$self
->
dbID
(),
$ensembl_object
);
return
$self
->
adaptor
()
->
get_all_dependents
(
$self
->
dbID
(),
$ensembl_object
);
}
=head2 get_all_masters
...
...
@@ -616,7 +616,7 @@ sub get_all_masters {
my
$self
=
shift
;
my
$ensembl_object
=
shift
;
return
$self
->
{
adaptor
}
->
get_all_masters
(
$self
->
dbID
(),
$ensembl_object
);
return
$self
->
adaptor
()
->
get_all_masters
(
$self
->
dbID
(),
$ensembl_object
);
}
...
...
modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
View file @
08daed32
...
...
@@ -827,7 +827,6 @@ sub fetch_all_by_Transcript_list {
my
$tl
=
Bio::EnsEMBL::
Translation
->
new
(
-
dbID
=>
$tl_id
,
-
adaptor
=>
$self
,
-
seq_start
=>
$seq_start
,
-
seq_end
=>
$seq_end
,
-
start_exon
=>
$start_exon
,
...
...
@@ -836,7 +835,8 @@ sub fetch_all_by_Transcript_list {
-
version
=>
$version
,
-
created_date
=>
$created_date
||
undef
,
-
modified_date
=>
$modified_date
||
undef
);
$tl
->
adaptor
(
$self
);
$tr
->
translation
(
$tl
);
push
@out
,
$tl
;
...
...
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
View file @
08daed32
...
...
@@ -35,6 +35,7 @@ package Bio::EnsEMBL::DnaPepAlignFeature;
use
strict
;
use
Bio::EnsEMBL::
BaseAlignFeature
;
use
Scalar::
Util
qw(weaken isweak)
;
use
vars
qw(@ISA)
;
...
...
@@ -62,8 +63,9 @@ use vars qw(@ISA);
sub
new_fast
{
my
(
$class
,
$hashref
)
=
@_
;
return
bless
$hashref
,
$class
;
my
$self
=
bless
$hashref
,
$class
;
weaken
(
$self
->
{
adaptor
})
if
(
!
isweak
(
$self
->
{
adaptor
})
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/Feature.pm
View file @
08daed32
...
...
@@ -74,6 +74,8 @@ use Bio::EnsEMBL::Slice;
use
Bio::EnsEMBL::
StrainSlice
;
use
vars
qw(@ISA)
;
use
Scalar::
Util
qw(weaken isweak)
;
@ISA
=
qw(Bio::EnsEMBL::Storable)
;
...
...
@@ -145,14 +147,16 @@ sub new {
}
}
return
bless
({'
start
'
=>
$start
,
my
$self
=
bless
({'
start
'
=>
$start
,
'
end
'
=>
$end
,
'
strand
'
=>
$strand
,
'
slice
'
=>
$slice
,
'
analysis
'
=>
$analysis
,
'
adaptor
'
=>
$adaptor
,
'
seqname
'
=>
$seqname
,
'
dbID
'
=>
$dbID
},
$class
);
$self
->
adaptor
(
$adaptor
);
return
$self
;
}
...
...
@@ -171,7 +175,9 @@ sub new {
sub
new_fast
{
my
$class
=
shift
;
my
$hashref
=
shift
;
return
bless
$hashref
,
$class
;
my
$self
=
bless
$hashref
,
$class
;
weaken
(
$self
->
{
adaptor
})
if
(
!
isweak
(
$self
->
{
adaptor
})
);
return
$self
;
}
=head2 start
...
...
@@ -1544,5 +1550,4 @@ sub id {
return
$self
->
{'
dbID
'};
}
1
;
modules/Bio/EnsEMBL/IndividualSliceFactory.pm
View file @
08daed32
...
...
@@ -26,6 +26,7 @@ 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
Scalar::
Util
qw(weaken)
;
=head2 new
=cut
...
...
@@ -38,26 +39,42 @@ sub new{
my
(
$population_name
,
$coord_system
,
$start
,
$end
,
$strand
,
$seq_region_name
,
$seq_region_length
,
$adaptor
)
=
rearrange
(['
POPULATION
',
'
COORD_SYSTEM
','
START
','
END
','
STRAND
','
SEQ_REGION_NAME
','
SEQ_REGION_LENGTH
',
'
ADAPTOR
'],
@
_
);
return
bless
{
my
$self
=
bless
{
population_name
=>
$population_name
,
coord_system
=>
$coord_system
,
start
=>
$start
,
end
=>
$end
,
strand
=>
$strand
,
seq_region_name
=>
$seq_region_name
,
seq_region_length
=>
$seq_region_length
,
adaptor
=>
$adaptor
},
$class
;
seq_region_length
=>
$seq_region_length
},
$class
;
$self
->
adaptor
(
$adaptor
);
return
$self
;
}
sub
adaptor
{
my
$self
=
shift
;
if
(
@
_
)
{
my
$ad
=
shift
;
if
(
$ad
&&
(
!
ref
(
$ad
)
||
!
$ad
->
isa
('
Bio::EnsEMBL::DBSQL::BaseAdaptor
')))
{
throw
('
Adaptor argument must be a Bio::EnsEMBL::DBSQL::BaseAdaptor
');
}
weaken
(
$self
->
{'
adaptor
'}
=
$ad
);
}
return
$self
->
{'
adaptor
'}
}
sub
get_all_IndividualSlice
{
my
$self
=
shift
;
my
$slice
;
if
(
!
$self
->
{'
adaptor
'}
)
{
if
(
!
$self
->
adaptor
)
{
warning
('
Cannot get IndividualSlice features without attached adaptor
');
return
'';
}
my
$variation_db
=
$self
->
{'
adaptor
'}
->
db
->
get_db_adaptor
('
variation
');
my
$variation_db
=
$self
->
adaptor
->
db
->
get_db_adaptor
('
variation
');
unless
(
$variation_db
)
{
warning
("
Variation database must be attached to core database to
"
.
...
...
@@ -80,7 +97,7 @@ sub get_all_IndividualSlice{
-
strand
=>
$self
->
{'
strand
'},
-
seq_region_name
=>
$self
->
{'
seq_region_name
'},
-
seq_region_length
=>
$self
->
{'
seq_region_length
'},
-
adaptor
=>
$self
->
{'
adaptor
'}
-
adaptor
=>
$self
->
adaptor
);
my
$population
=
$population_adaptor
->
fetch_by_name
(
$self
->
{'
population_name
'});
#check that there is such population in the database
...
...
modules/Bio/EnsEMBL/Map/Ditag.pm
View file @
08daed32
...
...
@@ -100,10 +100,10 @@ sub new {
'
name
'
=>
$name
,
'
type
'
=>
$type
,
'
tag_count
'
=>
$tag_count
,
'
sequence
'
=>
$sequence
,
'
adaptor
'
=>
$adaptor
,
'
sequence
'
=>
$sequence
},
$class
);
$self
->
adaptor
(
$adaptor
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/Map/DitagFeature.pm
View file @
08daed32
...
...
@@ -134,7 +134,6 @@ sub new {
my
$self
=
bless
(
{'
dbID
'
=>
$dbID
,
'
analysis
'
=>
$analysis
,
'
adaptor
'
=>
$adaptor
,
'
slice
'
=>
$slice
,
'
start
'
=>
$start
,
'
end
'
=>
$end
,
...
...
@@ -150,6 +149,7 @@ sub new {
'
ditag
'
=>
$ditag
,
},
$class
);
$self
->
adaptor
(
$adaptor
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/Map/Marker.pm
View file @
08daed32
...
...
@@ -78,7 +78,6 @@ sub new {
my
$class
=
ref
(
$caller
)
||
$caller
;
my
$self
=
bless
(
{'
dbID
'
=>
$dbID
,
'
adaptor
'
=>
$adaptor
,
'
left_primer
'
=>
$left_primer
,
'
right_primer
'
=>
$right_primer
,
'
min_primer_dist
'
=>
$min_primer_dist
,
...
...
@@ -88,6 +87,8 @@ sub new {
'
display_marker_synonym
'
=>
$display_synonym
},
$class
);
$self
->
adaptor
(
$adaptor
);
#only load the marker synononyms if they were supplied, otherwise they
# will be lazy-loaded
if
(
$syns
&&
@$syns
)
{
...
...
@@ -275,7 +276,7 @@ sub get_all_MarkerSynonyms {
#lazy-load the marker synonyms if they haven't been retrieved
if
(
!
exists
$self
->
{'
marker_synonyms
'}
&&
$self
->
{'
adaptor
'}
&&
$self
->
{'
dbID
'})
{
$self
->
adaptor
&&
$self
->
{'
dbID
'})
{
$self
->
adaptor
->
fetch_attributes
(
$self
);
}
...
...
@@ -404,7 +405,7 @@ sub get_all_MapLocations {
#lazy-load the map locations if they have not been fetched yet
if
(
!
exists
$self
->
{'
map_locations
'}
&&
$self
->
{'
adaptor
'}
&&
$self
->
{'
dbID
'})
{
$self
->
adaptor
&&
$self
->
{'
dbID
'})
{
$self
->
adaptor
->
fetch_attributes
(
$self
);
}
...
...
@@ -435,7 +436,7 @@ sub get_MapLocation {
#lazy-load the map locations if they have not been fetched yet
if
(
!
exists
$self
->
{'
map_locations
'}
&&
$self
->
{'
adaptor
'}
&&
$self
->
{'
dbID
'})
{
$self
->
adaptor
&&
$self
->
{'
dbID
'})
{
$self
->
adaptor
->
fetch_attributes
(
$self
);
}
...
...
modules/Bio/EnsEMBL/Map/MarkerFeature.pm
View file @
08daed32
...
...
@@ -73,9 +73,8 @@ sub new {
my
$class
=
ref
(
$caller
)
||
$caller
;
return
bless
(
{
my
$self
=
bless
(
{
'
dbID
'
=>
$dbID
,
'
adaptor
'
=>
$adaptor
,
'
start
'
=>
$start
,
'
end
'
=>
$end
,
'
strand
'
=>
0
,
...
...
@@ -84,6 +83,9 @@ sub new {
'
marker_id
'
=>
$marker_id
,
'
marker
'
=>
$marker
,
'
map_weight
'
=>
$map_weight
},
$class
);
$self
->
adaptor
(
$adaptor
);
return
$self
;
}
...
...
@@ -132,9 +134,9 @@ sub marker {
if
(
@
_
)
{
$self
->
{'
marker
'}
=
shift
;
}
elsif
(
!
$self
->
{'
marker
'}
&&
$self
->
{'
adaptor
'}
&&
$self
->
{'
marker_id
'})
{
}
elsif
(
!
$self
->
{'
marker
'}
&&
$self
->
adaptor
&&
$self
->
{'
marker_id
'})
{
#lazy load the marker if it is not already loaded
my
$ma
=
$self
->
{'
adaptor
'}
->
db
->
get_MarkerAdaptor
;
my
$ma
=
$self
->
adaptor
->
db
->
get_MarkerAdaptor
;
$self
->
{'
marker
'}
=
$ma
->
fetch_by_dbID
(
$self
->
{'
marker_id
'});
}
...
...
modules/Bio/EnsEMBL/Map/Qtl.pm
View file @
08daed32
...
...
@@ -75,7 +75,6 @@ sub new {
$class
=
ref
(
$class
)
||
$class
;
my
$self
=
bless
(
{
'
dbID
'
=>
$dbID
,
'
adaptor
'
=>
$adaptor
,
'
flank_marker_1
'
=>
$flank_marker_1
,
'
flank_marker_2
'
=>
$flank_marker_2
,
'
peak_marker
'
=>
$peak_marker
,
...
...
@@ -83,7 +82,7 @@ sub new {
'
lod_score
'
=>
$lod_score
,
'
synonyms
'
=>
$synonyms
},
$class
);
$self
->
adaptor
(
$adaptor
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/Map/QtlFeature.pm
View file @
08daed32
...
...
@@ -62,7 +62,6 @@ sub new {
$class
=
ref
(
$class
)
||
$class
;
my
$self
=
bless
(
{
'
adaptor
'
=>
$adaptor
,
'
slice
'
=>
$slice
,
'
start
'
=>
$start
,
'
end
'
=>
$end
,
...
...
@@ -71,6 +70,7 @@ sub new {
'
strand
'
=>
0
},
$class
);
$self
->
adaptor
(
$adaptor
);
return
$self
;
}
...
...
modules/Bio/EnsEMBL/MappedSlice.pm
View file @
08daed32
...
...
@@ -181,7 +181,7 @@ sub new {
# need to weaken reference to prevent circular reference
weaken
(
$self
->
{'
container
'}
=
$container
);
$self
->
{'
adaptor
'}
=
$adaptor
if
(
defined
(
$adaptor
));
$self
->
adaptor
(
$adaptor
)
if
(
defined
(
$adaptor
));
$self
->
{'
name
'}
=
$name
if
(
defined
(
$name
));
$self
->
{'
slice_mapper_pairs
'}
=
[]
;
...
...
@@ -275,7 +275,7 @@ sub get_all_Slice_Mapper_pairs {
sub
adaptor
{
my
$self
=
shift
;
$self
->
{'
adaptor
'}
=
shift
if
(
@
_
);
weaken
(
$self
->
{'
adaptor
'}
=
shift
)
if
(
@
_
);
return
$self
->
{'
adaptor
'};
}
...
...
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