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ensembl-gh-mirror
ensembl
Commits
9c9a1ce1
Commit
9c9a1ce1
authored
May 05, 2010
by
Andreas Kusalananda Kähäri
Browse files
Changes in store() to quieten the unit tests.
parent
8f65f33e
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1
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33 additions
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32 deletions
+33
-32
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+33
-32
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modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
View file @
9c9a1ce1
...
...
@@ -790,11 +790,9 @@ sub store {
# store translation
#
my
@translations
=
@
{
$db
->
get_TranslationAdaptor
()
->
fetch_all_by_Transcript
(
$transcript
)
};
my
$translation
=
shift
(
@translations
);
my
$alt_translations
=
$transcript
->
get_all_alternative_translations
();
my
$translation
=
$transcript
->
translation
();
if
(
defined
(
$translation
)
)
{
#make sure that the start and end exon are set correctly
...
...
@@ -865,42 +863,45 @@ sub store {
# Store the alternative translations, if there are any.
#
foreach
my
$alt_translation
(
@translations
)
{
my
$start_exon
=
$alt_translation
->
start_Exon
();
my
$end_exon
=
$alt_translation
->
end_Exon
();
if
(
defined
(
$alt_translations
)
)
{
foreach
my
$alt_translation
(
@
{
$alt_translations
}
)
{
my
$start_exon
=
$alt_translation
->
start_Exon
();
my
$end_exon
=
$alt_translation
->
end_Exon
();
if
(
!
defined
(
$start_exon
)
)
{
throw
("
Translation does not define a start exon.
");
}
elsif
(
!
defined
(
$end_exon
)
)
{
throw
("
Translation does not defined an end exon.
");
}
if
(
!
defined
(
$start_exon
)
)
{
throw
("
Translation does not define a start exon.
");
}
elsif
(
!
defined
(
$end_exon
)
)
{
throw
("
Translation does not defined an end exon.
");
}
if
(
!
defined
(
$start_exon
->
dbID
()
)
)
{
my
$key
=
$start_exon
->
hashkey
();
(
$start_exon
)
=
grep
{
$_
->
hashkey
()
eq
$key
}
@
{
$exons
};
if
(
!
defined
(
$start_exon
->
dbID
()
)
)
{
my
$key
=
$start_exon
->
hashkey
();
(
$start_exon
)
=
grep
{
$_
->
hashkey
()
eq
$key
}
@
{
$exons
};
if
(
defined
(
$start_exon
)
)
{
$alt_translation
->
start_Exon
(
$start_exon
);
}
else
{
throw
(
if
(
defined
(
$start_exon
)
)
{
$alt_translation
->
start_Exon
(
$start_exon
);
}
else
{
throw
(
"
Translation's start_Exon does not appear to be one of the
"
.
"
exons in its associated Transcript
"
);
}
}
elsif
(
!
defined
(
$end_exon
->
dbID
()
)
)
{
my
$key
=
$end_exon
->
hashkey
();
(
$end_exon
)
=
grep
{
$_
->
hashkey
()
eq
$key
}
@$exons
;
}
}
elsif
(
!
defined
(
$end_exon
->
dbID
()
)
)
{
my
$key
=
$end_exon
->
hashkey
();
(
$end_exon
)
=
grep
{
$_
->
hashkey
()
eq
$key
}
@$exons
;
if
(
defined
(
$end_exon
)
)
{
$translation
->
end_Exon
(
$end_exon
);
}
else
{
throw
("
Translation's end_Exon does not appear to be one of the
"
if
(
defined
(
$end_exon
)
)
{
$translation
->
end_Exon
(
$end_exon
);
}
else
{
throw
(
"
Translation's end_Exon does not appear to be one of the
"
.
"
exons in its associated Transcript.
"
);
}
}
}
$db
->
get_TranslationAdaptor
()
->
store
(
$alt_translation
,
$transc_dbID
);
}
## end foreach my $alt_translation...
$db
->
get_TranslationAdaptor
()
->
store
(
$alt_translation
,
$transc_dbID
);
}
## end foreach my $alt_translation...
}
## end if ( defined($alt_translations...))
#
# store the xrefs/object xref mapping
...
...
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