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ensembl-gh-mirror
ensembl
Commits
132666f5
Commit
132666f5
authored
21 years ago
by
Web Admin
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Added calls for assembly name/version to slice via DBAdaptor
parent
7beea4ad
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Changes
2
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2 changed files
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+89
-14
89 additions, 14 deletions
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
modules/Bio/EnsEMBL/Slice.pm
+47
-1
47 additions, 1 deletion
modules/Bio/EnsEMBL/Slice.pm
with
136 additions
and
15 deletions
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+
89
−
14
View file @
132666f5
...
...
@@ -815,24 +815,99 @@ sub assembly_type{
if
(
$value
)
{
$obj
->
{'
assembly
'}
=
$value
;
}
if
(
!
defined
$obj
->
{'
assembly
'})
{
my
$ass
;
eval
{
$ass
=
$obj
->
dnadb
->
get_MetaContainer
()
->
get_default_assembly
();
};
if
(
$@
)
{
$obj
->
throw
("
*** get_MetaContainer->get_default_assembly failed:
\n
$@
\n
"
.
"
assembly type must be set with assembly_type() first
");
}
elsif
(
!
$ass
)
{
$obj
->
throw
("
No default assembly defined in
"
.
$obj
->
dnadb
->
dbname
.
"
- must set with assembly_type() first
");
}
$obj
->
{'
assembly
'}
=
$ass
;
}
return
$obj
->
{'
assembly
'};
if
(
!
defined
$obj
->
{'
assembly
'})
{
my
$ass
;
eval
{
$ass
=
$obj
->
dnadb
->
get_MetaContainer
()
->
get_default_assembly
();
};
if
(
$@
)
{
$obj
->
throw
("
*** get_MetaContainer->get_default_assembly failed:
\n
$@
\n
"
.
"
assembly type must be set with assembly_type() first
");
}
elsif
(
!
$ass
)
{
$obj
->
throw
("
No default assembly defined in
"
.
$obj
->
dnadb
->
dbname
.
"
- must set with assembly_type() first
");
}
$obj
->
{'
assembly
'}
=
$ass
;
}
return
$obj
->
{'
assembly
'};
}
=head2 assembly_name
Arg [1] : (optional) string $value
the new assembly name value
Example : $db_adaptor->assembly_name($newval);
Description: Getter / Setter for the name of assembly used by
this database. If the value is not set then the
default value is obtained from the MetaContainer
Returntype : string
Exceptions : warn if there is no defined assembly name, and the default
assembly name cannot be obtained from the MetaContainer
Caller : ?
=cut
sub
assembly_name
{
my
(
$obj
,
$value
)
=
@_
;
if
(
$value
)
{
$obj
->
{'
assembly_name
'}
=
$value
;
}
if
(
!
defined
$obj
->
{'
assembly_name
'})
{
my
$ass
;
eval
{
$ass
=
$obj
->
dnadb
->
get_MetaContainer
()
->
get_default_assembly_name
();
};
if
(
$@
)
{
warn
("
*** get_MetaContainer->get_default_assembly_name failed ***
\n
$@
\n
");
}
elsif
(
!
$ass
)
{
warn
("
No default assembly name defined in
"
.
$obj
->
dnadb
->
dbname
.
"
!
");
}
$obj
->
{'
assembly_name
'}
=
$ass
;
}
return
$obj
->
{'
assembly_name
'};
}
=head2 assembly_version
Arg [1] : (optional) string $value
the new assembly version value
Example : $db_adaptor->assembly_version($newval);
Description: Getter / Setter for the version of assembly used by
this database. If the value is not set then the
default value is obtained from the MetaContainer
Returntype : string
Exceptions : warn if there is no defined assembly version, and the default
assembly version cannot be obtained from the MetaContainer
Caller : ?
=cut
sub
assembly_version
{
my
(
$obj
,
$value
)
=
@_
;
if
(
$value
)
{
$obj
->
{'
assembly_version
'}
=
$value
;
}
if
(
!
defined
$obj
->
{'
assembly_version
'})
{
my
$ass
;
eval
{
$ass
=
$obj
->
dnadb
->
get_MetaContainer
()
->
get_default_assembly_version
();
};
if
(
$@
)
{
warn
("
*** get_MetaContainer->get_default_assembly_version failed ***
\n
$@
\n
");
}
elsif
(
!
$ass
)
{
warn
("
No default assembly version defined in
"
.
$obj
->
dnadb
->
dbname
.
"
!
");
}
$obj
->
{'
assembly_version
'}
=
$ass
;
}
return
$obj
->
{'
assembly_version
'};
}
=head2 dnadb
Title : dnadb
...
...
This diff is collapsed.
Click to expand it.
modules/Bio/EnsEMBL/Slice.pm
+
47
−
1
View file @
132666f5
...
...
@@ -863,7 +863,7 @@ sub strand{
=cut
sub
assembly_type
{
sub
assembly_type
{
my
(
$self
,
$value
)
=
@_
;
if
(
defined
$value
)
{
$self
->
{'
assembly_type
'}
=
$value
;
...
...
@@ -874,6 +874,52 @@ sub assembly_type{
=head2 assembly_name
Arg [1] : string $value
Example : $slice->assembly_name();
Description: Gets/Sets the assembly name that this slice is constructed
from. This is generally set by the slice adaptor and probably
shouldnt be set outside of this context.
Returntype : string
Exceptions : none
Caller : general
=cut
sub
assembly_name
{
my
(
$self
,
$value
)
=
@_
;
if
(
defined
$value
)
{
$self
->
adaptor
->
db
->
assembly_name
(
$value
);
}
return
$self
->
adaptor
->
db
->
assembly_name
();
}
=head2 assembly_version
Arg [1] : string $value
Example : $slice->assembly_version();
Description: Gets/Sets the assembly version that this slice is constructed
from. This is generally set by the slice adaptor and probably
shouldnt be set outside of this context.
Returntype : string
Exceptions : none
Caller : general
=cut
sub
assembly_version
{
my
(
$self
,
$value
)
=
@_
;
if
(
defined
$value
)
{
$self
->
adaptor
->
db
->
assembly_version
(
$value
);
}
return
$self
->
adaptor
->
db
->
assembly_version
();
}
=head2 get_all_KaryotypeBands
Arg [1] : none
...
...
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