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ensembl-gh-mirror
ensembl-hive
Commits
15940b3a
Commit
15940b3a
authored
Mar 17, 2006
by
Abel Ureta-Vidal
Browse files
Clean up a bit the runnable and output subroutines
parent
00cf9984
Changes
1
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1 changed file
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16 additions
and
43 deletions
+16
-43
modules/Bio/EnsEMBL/Hive/Process.pm
modules/Bio/EnsEMBL/Hive/Process.pm
+16
-43
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modules/Bio/EnsEMBL/Hive/Process.pm
View file @
15940b3a
...
...
@@ -427,10 +427,6 @@ sub parameters {
return
$self
->
analysis
->
parameters
;
}
#FIXME kfb 11.01.2006 added runnable method from Pipeline/RunnableDB. Required by
#PairAligner.
=head2 runnable
Title : runnable
...
...
@@ -445,30 +441,20 @@ sub parameters {
sub
runnable
{
my
(
$self
,
$arg
)
=
@_
;
if
(
!
defined
(
$self
->
{'
_
runnable
s
'}))
{
$self
->
{'
_
runnable
s
'}
=
[]
;
if
(
!
defined
(
$self
->
{'
runnable
'}))
{
$self
->
{'
runnable
'}
=
[]
;
}
if
(
defined
(
$arg
))
{
#FIXME kfb 11.01.2006 use Analysis/Runnable object rather than Pipeline/RunnableI
# if ($arg->isa("Bio::EnsEMBL::Pipeline::RunnableI")) {
# push(@{$self->{'_runnables'}},$arg);
# } else {
# &throw("[$arg] is not a Bio::EnsEMBL::Pipeline::RunnableI");
# }
if
(
$arg
->
isa
("
Bio::EnsEMBL::Analysis::Runnable
"))
{
push
(
@
{
$self
->
{'
_runnables
'}},
$arg
);
}
else
{
&throw
("
[
$arg
] is not a Bio::EnsEMBL::Analysis::Runnable
");
}
if
(
$arg
->
isa
("
Bio::EnsEMBL::Analysis::Runnable
"))
{
push
(
@
{
$self
->
{'
runnable
'}},
$arg
);
}
else
{
&throw
("
[
$arg
] is not a Bio::EnsEMBL::Analysis::Runnable
");
}
return
@
{
$self
->
{'
_
runnable
s
'}};
}
return
@
{
$self
->
{'
runnable
'}};
}
#FIXME kfb 11.01.2006 added output method from Pipeline/RunnableDB. Required by
#PairAligner.
=head2 output
Title : output
...
...
@@ -478,32 +464,19 @@ sub runnable {
Args : None
=cut
sub
output
{
my
(
$self
)
=
@_
;
$self
->
{'
_output
'}
=
[]
;
my
@r
=
$self
->
runnable
;
if
(
@r
&&
scalar
(
@r
)){
foreach
my
$r
(
$self
->
runnable
){
#FIXME debug
print
STDERR
"
Process output
"
.
scalar
(
@
{
$r
->
output
})
.
"
\n
";
sub
output
{
my
(
$self
)
=
@_
;
#FIXME kfb 12.01.2006
#push(@{
$self->{'
_
output'}
}, $r->output)
;
push
(
@
{
$self
->
{'
_output
'}},
@
{
$r
->
output
})
;
}
unless
(
defined
$self
->
{'
output
'})
{
$self
->
{'
output
'}
=
[]
;
foreach
my
$r
(
@
{
$self
->
runnable
})
{
push
(
@
{
$self
->
{'
output
'}},
@
{
$r
->
output
});
}
}
#FIXME debug
print
STDERR
"
_output
"
.
scalar
(
@
{
$self
->
{'
_output
'}})
.
"
\n
";
return
@
{
$self
->
{'
_output
'}};
return
@
{
$self
->
{'
output
'}};
}
1
;
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