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ensembl-gh-mirror
ensembl
Commits
a64aa50e
Commit
a64aa50e
authored
Nov 22, 2002
by
Graham McVicker
Browse files
removed deprecated methods
parent
f132ef2a
Changes
13
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13 changed files
with
7 additions
and
2733 deletions
+7
-2733
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
+0
-40
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
+5
-8
modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
+0
-42
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+0
-190
modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm
+0
-129
modules/Bio/EnsEMBL/DBSQL/CloneAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/CloneAdaptor.pm
+0
-32
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+1
-1994
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+0
-66
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+0
-78
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+0
-64
modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
+0
-68
modules/Bio/EnsEMBL/DBSQL/MapFragAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/MapFragAdaptor.pm
+0
-21
modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+1
-1
No files found.
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
View file @
a64aa50e
...
...
@@ -437,44 +437,4 @@ sub db {
}
=head2 fetch_by_newest_logic_name
Description: DEPRECATED Logic names should now be unique and should not
need to use this method. Use fetch_by_logic_name instead.
=cut
sub
fetch_by_newest_logic_name
{
my
$self
=
shift
;
my
$logic_name
=
shift
;
$self
->
warn
("
logic_names should now be unique should not
"
.
"
need to use this method use fetch_by_logic_name
\n
");
return
$self
->
fetch_by_logic_name
(
$logic_name
);
}
=head2 mysql2Unixtime
Description: DEPRECATED do not use
=cut
sub
mysql2Unixtime
{
my
$sqltime
=
shift
;
my
(
$package
,
$file
,
$line
)
=
caller
();
warn
("
AnalysisAdaptor::mysql2Unixtime is deprecated.
\n
"
.
"
package:
$package
: file:
$file
line:
$line
\n
");
require
"
Time::Local
";
my
(
$year
,
$month
,
$mday
,
$hour
,
$min
,
$sec
)
=
(
$sqltime
=~
/(\d+)-(\d+)-(\d+)\s+(\d+):(\d+):(\d+)/
);
my
$time
=
timelocal
(
$sec
,
$min
,
$hour
,
$mday
,
$month
,
$year
);
}
1
;
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
View file @
a64aa50e
...
...
@@ -126,15 +126,12 @@ sub new {
}
if
(
$dbobj
->
isa
('
Bio::EnsEMBL::Container
'))
{
$self
->
throw
("
The base adaptor constructor argument should not be
"
.
"
a Bio::EnsEMBL::Container. This will create a circular
"
.
"
reference loop and result in memory leaks. You should
"
.
"
use the DBAdaptor::get_XxxxAdaptor methods to create
"
.
"
your object adaptors instead
");
#avoid a circular reference loop!
$self
->
db
(
$dbobj
->
_obj
);
}
else
{
$self
->
db
(
$dbobj
);
}
$self
->
db
(
$dbobj
);
return
$self
;
}
...
...
@@ -207,4 +204,4 @@ sub deleteObj {
}
1
;
modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
View file @
a64aa50e
...
...
@@ -130,46 +130,4 @@ sub fetch_all_by_Slice_and_pid {
=head2 fetch_by_Contig_and_pid
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_and_pid instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Contig_and_pid
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Contig_and_pid has been renamed fetch_all_by_RawContig_and_pid
\n
"
.
caller
);
return
$self
->
fetch_all_by_RawContig_and_pid
(
@args
);
}
=head2 fetch_by_Slice_and_pid
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice_and_pid instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Slice_and_pid
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Slice_and_pid has been renamed fetch_all_by_Slice_and_pid
\n
"
.
caller
);
return
$self
->
fetch_all_by_Slice_and_pid
(
@args
);
}
1
;
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
View file @
a64aa50e
...
...
@@ -670,196 +670,6 @@ sub deleteObj {
%
{
$self
->
{'
_slice_feature_cache
'}}
=
();
}
=head2 fetch_by_Contig_constraint
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Contig_constraint
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Contig_constraint has been renamed fetch_all_by_RawContig_constraint
\n
"
.
caller
);
return
$self
->
fetch_all_by_RawContig_constraint
(
@args
);
}
=head2 fetch_by_Contig
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Contig
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Contig has been renamed fetch_all_by_RawContig
\n
"
.
caller
);
return
$self
->
fetch_all_by_RawContig
(
@args
);
}
=head2 fetch_by_Contig_and_score
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_and_score instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Contig_and_score
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Contig_and_score has been renamed fetch_all_by_RawContig_and_score
\n
"
.
caller
);
return
$self
->
fetch_all_by_RawContig_and_score
(
@args
);
}
=head2 fetch_all_by_Contig
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_all_by_Contig
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_all_by_Contig has been renamed fetch_all_by_RawContig
\n
"
.
caller
);
return
$self
->
fetch_all_by_RawContig
(
@args
);
}
=head2 fetch_all_by_Contig_and_score
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_and_score instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_all_by_Contig_and_score
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_all_by_Contig_and_score has been renamed fetch_all_by_RawContig_and_score
\n
"
.
caller
);
return
$self
->
fetch_all_by_RawContig_and_score
(
@args
);
}
=head2 fetch_all_by_Contig_constraint
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_all_by_Contig_constraint
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_all_by_Contig_constraint has been renamed fetch_all_by_RawContig_constraint
\n
"
.
caller
);
return
$self
->
fetch_all_by_RawContig_constraint
(
@args
);
}
=head2 fetch_by_Slice_and_score
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice_and_score instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Slice_and_score
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Slice_and_score has been renamed fetch_all_by_Slice_and_score
\n
"
.
caller
);
return
$self
->
fetch_all_by_Slice_and_score
(
@args
);
}
=head2 fetch_by_Slice_constraint
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice_constraint instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Slice_constraint
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Slice_constraint has been renamed fetch_all_by_Slice_constraint
\n
"
.
caller
);
return
$self
->
fetch_all_by_Slice_constraint
(
@args
);
}
=head2 fetch_by_Slice
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_Slice
{
my
(
$self
,
@args
)
=
@_
;
$self
->
warn
("
fetch_by_Slice has been renamed fetch_all_by_Slice
\n
"
.
caller
);
return
$self
->
fetch_all_by_Slice
(
@args
);
}
1
;
modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm
View file @
a64aa50e
...
...
@@ -268,135 +268,6 @@ sub get_dbID_by_chr_name {
=head2 get_landmark_MarkerFeatures
Arg [1] : none
Example : none
Description: DEPRECATED use Slice::get_landmark_MarkerFeatures instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
get_landmark_MarkerFeatures
{
my
(
$self
,
$chr_name
,
$glob
)
=
@_
;
$self
->
warn
("
ChromosomeAdaptor::get_landmark_MarkerFeatures is deprecated
"
.
"
use Slice::get_landmark_MarkerFeatures instead
\n
");
if
(
!
defined
$glob
)
{
$glob
=
500000
;
}
my
$statement
=
"
SELECT chr_start,
chr_end,
chr_strand,
name
FROM landmark_marker
WHERE chr_name = '
$chr_name
'
ORDER BY chr_start
";
$statement
=~
s/\s+/ /g
;
my
$sth
=
$self
->
prepare
(
$statement
);
$sth
->
execute
;
my
(
$start
,
$end
,
$strand
,
$name
);
my
$analysis
;
my
%analhash
;
$sth
->
bind_columns
(
undef
,
\
$start
,
\
$end
,
\
$strand
,
\
$name
);
my
@out
;
my
$prev
;
while
(
$sth
->
fetch
)
{
if
(
defined
$prev
&&
$prev
->
end
+
$glob
>
$start
&&
$prev
->
id
eq
$name
)
{
next
;
}
my
$sf
=
Bio::EnsEMBL::
SeqFeature
->
new
();
$sf
->
start
(
$start
);
$sf
->
end
(
$end
);
$sf
->
strand
(
$strand
);
$sf
->
id
(
$name
);
push
(
@out
,
$sf
);
$prev
=
$sf
;
}
return
@out
;
}
=head2 get_landmark_MarkerFeatures_old
Arg [1] : none
Example : none
Description: DEPRECATED do not use
Returntype : none
Exceptions : none
Caller : none
=cut
sub
get_landmark_MarkerFeatures_old
{
my
(
$self
,
$chr_name
)
=
@_
;
my
$glob
=
1000
;
$self
->
throw
(
"
Method deprecated.
"
);
return
();
# my $statement= " SELECT
# IF (sgp.raw_ori=1,(f.seq_start+sgp.chr_start-sgp.raw_start-1),
# (sgp.chr_start+sgp.raw_end-f.seq_end-1)),
# IF (sgp.raw_ori=1,(f.seq_end+sgp.chr_start-sgp.raw_start-1),
# (sgp.chr_start+sgp.raw_end-f.seq_start-1)),
# f.score,
# IF (sgp.raw_ori=1,f.strand,(-f.strand)),
# f.name, f.hstart, f.hend,
# f.hid, f.analysis, c.name
# FROM contig_landmarkMarker c,
# static_golden_path sgp,
# feature f
# WHERE f.contig = c.contig
# AND f.hid=c.marker
# AND sgp.raw_id=f.contig
# AND sgp.chr_name='$chr_name'";
# $statement =~ s/\s+/ /g;
# my $sth = $self->prepare($statement);
# $sth->execute;
# my ($start, $end, $score, $strand, $hstart,
# $name, $hend, $hid, $analysisid,$synonym);
# my $analysis;
# my %analhash;
# $sth->bind_columns
# ( undef, \$start, \$end, \$score, \$strand, \$name,
# \$hstart, \$hend, \$hid, \$analysisid,\$synonym);
# my @out;
# while( $sth->fetch ) {
# my $sf = Bio::EnsEMBL::SeqFeature->new();
# $sf->start($start);
# $sf->end($end);
# $sf->strand($strand);
# $sf->id($synonym);
# push(@out,$sf);
# }
# return @out;
}
sub
store
{
my
(
$self
,
$chromosome
)
=
@_
;
...
...
modules/Bio/EnsEMBL/DBSQL/CloneAdaptor.pm
View file @
a64aa50e
...
...
@@ -443,36 +443,4 @@ sub store{
}
=head2 fetch
Description: DEPRECATED use fetch_by_accession instead
=cut
sub
fetch
{
my
(
$self
,
$id
)
=
@_
;
$self
->
warn
("
fetch is now deprecated, use fetch_by_accession instead
");
$self
->
fetch_by_accession
(
$id
);
}
=head2 get_Contig
Description: DEPRECATED
use Bio::EnsEMBL::DBSQL::RawContigAdaptor::fetch_by_dbID instead
=cut
sub
get_Contig
{
my
(
$self
,
$contigid
)
=
@_
;
$self
->
throw
("
CloneAdaptor::get_Contig is deprecated,
"
.
"
use
\$
contig_adaptor->fetch_by_dbID(
\$
id) instead
");
return
undef
;
#my $contig = $self->db->get_Contig($contigid);
#return $contig->fetch();
}
1
;
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
View file @
a64aa50e
This diff is collapsed.
Click to expand it.
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
View file @
a64aa50e
...
...
@@ -740,72 +740,6 @@ sub create_tables {
}
=head2 fetch_by_translation
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Translation instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_translation
{
my
(
$self
,
$trans_id
)
=
@_
;
$self
->
warn
("
fetch_by_translation has been renamed fetch_all_by_Translation
");
my
$trans
=
$self
->
db
->
get_TranslationAdaptor
->
fetch_by_dbID
(
$trans_id
);
return
$self
->
fetch_all_by_Translation
(
$trans
);
}
=head2 fetch_all_by_rawContig
Arg [1] : none
Example : none
Description: DEPRECATED use Bio::EnsEMBL::fetch_all_by_RawContig instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_all_by_rawContig
{
my
(
$self
,
$rawContigId
)
=
@_
;
$self
->
warn
("
fetch_by_rawContig has been renamed fetch_by_RawContig
");
my
$contig
=
$self
->
db
->
get_RawContigAdaptor
->
fetch_by_dbID
(
$rawContigId
);
return
$self
->
fetch_by_RawContig
(
$contig
);
}
=head2 fetch_all_by_transcript
Arg [1] : none
Example : none
Description: DEPRECATED fetch_all_by_Transcript instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_transcript
{
my
(
$self
,
$trans
)
=
@_
;
$self
->
warn
("
fetch_by_transcript has been renamed fetch_all_by_Transcript
");
return
$self
->
fetch_all_by_Transcript
(
$trans
);
}
1
;
...
...
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
View file @
a64aa50e
...
...
@@ -595,83 +595,5 @@ sub remove {
}
=head2 fetch_by_geneId
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_by_gene_id instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_by_geneId
{
my
(
$self
,
$gene_id
)
=
@_
;
$self
->
warn
("
fetch_by_geneId has been renamed fetch_all_by_gene_id
\n
"
.
caller
);
return
$self
->
fetch_all_by_gene_id
(
$gene_id
);
}
=head2 fetch_frameshifts
Arg [1] : none
Example : none
Description: DEPRECATED do not use
Returntype : none
Exceptions : none
Caller : none
=cut
sub
fetch_frameshifts
{
my
(
$self
,
$exon
)
=
@_
;
$self
->
throw
("
call to deprecated method fetch_frameshifts
");
return
undef
;
# my @frameshifts;
# my $frameshift_sql = "
# SELECT frameshift_start, length
# FROM exon_frameshift
# WHERE exon_id = " . $exon->dbID;