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ensembl-gh-mirror
ensembl-hive
Commits
5655fa32
Commit
5655fa32
authored
May 22, 2013
by
Leo Gordon
Browse files
removed dependency on check_ref and assert_ref
parent
29fcfa6e
Changes
1
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1 changed file
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14 additions
and
15 deletions
+14
-15
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
+14
-15
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modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
View file @
5655fa32
...
...
@@ -27,8 +27,6 @@ See inline
use
strict
;
use
warnings
;
use
Bio::EnsEMBL::Utils::
Scalar
qw(check_ref assert_ref)
;
use
Bio::EnsEMBL::Hive::Utils::
GraphViz
;
use
Bio::EnsEMBL::Hive::Utils::
Config
;
...
...
@@ -93,12 +91,13 @@ sub graph {
=cut
sub
dba
{
my
(
$self
,
$dba
)
=
@_
;
if
(
defined
$dba
)
{
assert_ref
(
$dba
,
'
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
');
$self
->
{
dba
}
=
$dba
;
}
return
$self
->
{
dba
};
my
$self
=
shift
@_
;
if
(
@
_
)
{
$self
->
{
dba
}
=
shift
@_
;
}
return
$self
->
{
dba
};
}
...
...
@@ -205,12 +204,12 @@ sub _allocate_to_subgraph {
my
$target_object
=
$rule
->
to_analysis
();
my
$target_node_name
;
if
(
check_ref
(
$target_object
,
'
Bio::EnsEMBL::Hive::Analysis
'))
{
if
(
UNIVERSAL::
isa
(
$target_object
,
'
Bio::EnsEMBL::Hive::Analysis
'))
{
$target_node_name
=
_analysis_node_name
(
$rule
->
to_analysis
->
dbID
()
);
}
elsif
(
check_ref
(
$target_object
,
'
Bio::EnsEMBL::Hive::NakedTable
'))
{
}
elsif
(
UNIVERSAL::
isa
(
$target_object
,
'
Bio::EnsEMBL::Hive::NakedTable
'))
{
$target_node_name
=
_table_node_name
(
$target_object
->
table_name
())
.
'
_
'
.
(
$self
->
config_get
('
DuplicateTables
')
?
$rule
->
from_analysis_id
()
:
(
$source_analysis_allocation
||
''));
}
elsif
(
check_ref
(
$target_object
,
'
Bio::EnsEMBL::Hive::Accumulator
'))
{
}
elsif
(
UNIVERSAL::
isa
(
$target_object
,
'
Bio::EnsEMBL::Hive::Accumulator
'))
{
next
;
}
else
{
warn
('
Do not know how to handle the type
'
.
ref
(
$target_object
));
...
...
@@ -398,16 +397,16 @@ sub _dataflow_rules {
my
(
$from_node
,
$to_id
,
$to_node
)
=
(
_analysis_node_name
(
$from_analysis_id
)
);
# Different treatment for analyses and tables:
if
(
check_ref
(
$to
,
'
Bio::EnsEMBL::Hive::Analysis
'))
{
if
(
UNIVERSAL::
isa
(
$to
,
'
Bio::EnsEMBL::Hive::Analysis
'))
{
$to_id
=
$to
->
dbID
();
$to_node
=
_analysis_node_name
(
$to_id
);
}
elsif
(
check_ref
(
$to
,
'
Bio::EnsEMBL::Hive::NakedTable
'))
{
}
elsif
(
UNIVERSAL::
isa
(
$to
,
'
Bio::EnsEMBL::Hive::NakedTable
'))
{
$to_node
=
_table_node_name
(
$to
->
table_name
)
.
'
_
'
.
(
$self
->
config_get
('
DuplicateTables
')
?
$rule
->
from_analysis_id
()
:
(
$subgraph_allocation
->
{
$from_node
}
||
''));
$self
->
_add_table_node
(
$to_node
,
$to
->
table_name
);
}
elsif
(
check_ref
(
$to
,
'
Bio::EnsEMBL::Hive::Accumulator
'))
{
}
elsif
(
UNIVERSAL::
isa
(
$to
,
'
Bio::EnsEMBL::Hive::Accumulator
'))
{
$to_node
=
$subgraph_allocation
->
{
$from_node
};
}
else
{
...
...
@@ -445,7 +444,7 @@ sub _dataflow_rules {
arrowtail
=>
'
crow
',
);
}
}
elsif
(
check_ref
(
$to
,
'
Bio::EnsEMBL::Hive::Accumulator
'))
{
}
elsif
(
UNIVERSAL::
isa
(
$to
,
'
Bio::EnsEMBL::Hive::Accumulator
'))
{
# one-part dashed arrow:
$graph
->
add_edge
(
$from_node
=>
$to_node
,
color
=>
$accu_colour
,
...
...
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