From 6ad9f7a8072d1c4c107ea9c9139b5ff13d0c369e Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 22 Nov 2002 17:10:55 +0000
Subject: [PATCH] removed more deprecated methods
---
.../DBSQL/ProxyDnaAlignFeatureAdaptor.pm | 10 +----
modules/Bio/EnsEMBL/DBSQL/ProxyGeneAdaptor.pm | 22 ----------
.../DBSQL/ProxyRepeatFeatureAdaptor.pm | 19 ---------
modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm | 22 ----------
modules/Bio/EnsEMBL/DBSQL/RawContigAdaptor.pm | 41 -------------------
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm | 27 ------------
6 files changed, 1 insertion(+), 140 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProxyDnaAlignFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProxyDnaAlignFeatureAdaptor.pm
index cd3bb199ed..ef56055cca 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProxyDnaAlignFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProxyDnaAlignFeatureAdaptor.pm
@@ -154,12 +154,4 @@ sub remove {
return $self->{'_primary_adaptor'}->remove($feature);
}
-
-
-
-
-
-
-
-
-
+1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProxyGeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProxyGeneAdaptor.pm
index 58560a1915..64ab53bcd6 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProxyGeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProxyGeneAdaptor.pm
@@ -74,28 +74,6 @@ sub fetch_all_by_Slice {
-=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 $self->fetch_all_by_Slice(@args);
-}
-
-
-
-
=head2 fetch_by_transcript_stable_id
Arg [1] : list of arbitrary args @args
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProxyRepeatFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProxyRepeatFeatureAdaptor.pm
index 26c52d4f92..9788ac122a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProxyRepeatFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProxyRepeatFeatureAdaptor.pm
@@ -68,24 +68,5 @@ sub fetch_all_by_Slice {
}
-=head2 fetch_by_Slice
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use fetch_all_by_Slice instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub fetch_by_Slice {
- my ($self, @args) = @_;
-
- $self->warn("fetch_by_Slice has been renamed fetch_all_by_Slice\n" . caller);
-
- return $self->fetch_all_by_Slice(@args);
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm
index 983b8d80fb..9956afa9d8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm
@@ -76,28 +76,6 @@ sub fetch_all_by_Slice {
}
-
-=head2 fetch_by_Slice
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use fetch_all_by_Slice instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub fetch_by_Slice {
- my ($self, @args) = @_;
-
- $self->warn("fetch_by_Slice has been renamed fetch_all_by_Slice\n" . caller);
-
- return $self->fetch_all_by_Slice(@args);
-}
-
-
-
=head2 fetch_by_SNP_id
Arg [1] : list of arbitrary args @args
diff --git a/modules/Bio/EnsEMBL/DBSQL/RawContigAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RawContigAdaptor.pm
index 274152c0d1..7128292f3b 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RawContigAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RawContigAdaptor.pm
@@ -535,47 +535,6 @@ sub deleteObj {
-
-=head2 fetch_by_clone
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use fetch_all_by_Clone instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub fetch_by_clone {
- my ($self, @args) = @_;
-
- print STDERR "fetch_by_clone has been renamed fetch_all_by_Clone\n" . caller;
-
- return $self->fetch_by_Clone(@args);
-}
-
-
-=head2 fetch_by_Clone
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use fetch_all_by_Clone instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub fetch_by_Clone {
- my ($self, @args) = @_;
-
- $self->warn("fetch_by_Clone has been renamed fetch_all_by_Clone\n" . caller);
-
- return $self->fetch_all_by_Clone(@args);
-}
-
-
=head2 remove
Arg [1] : Bio::EnsEMBL::RawContig $contig
diff --git a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
index f1f26e6ba1..32f92b5d54 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
@@ -305,31 +305,4 @@ sub _reverse_comp {
}
-
-
-
-
-=head2 fetch_by_Contig_start_end_strand
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use fetch_by_RawContig_start_end_strand instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub fetch_by_Contig_start_end_strand {
- my ($self, @args) = @_;
-
- $self->warn("fetch_by_Contig_start_end_strand has been renamed fetch_by_RawContig_start_end_strand\n" . caller);
-
- return $self->fetch_by_RawContig_start_end_strand(@args);
-}
-
-
-
-
-
1;
--
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