From f58532e4c4ae0a21fcc3febf050896226dd665d1 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 22 Nov 2002 17:24:16 +0000
Subject: [PATCH] removed deprecated methods
---
modules/Bio/EnsEMBL/Analysis.pm | 26 ---
modules/Bio/EnsEMBL/Clone.pm | 119 ----------
.../EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm | 25 +-
modules/Bio/EnsEMBL/Exon.pm | 217 ------------------
modules/Bio/EnsEMBL/Gene.pm | 159 -------------
5 files changed, 1 insertion(+), 545 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Analysis.pm b/modules/Bio/EnsEMBL/Analysis.pm
index 94662e6d0c..438701fe67 100755
--- a/modules/Bio/EnsEMBL/Analysis.pm
+++ b/modules/Bio/EnsEMBL/Analysis.pm
@@ -522,32 +522,6 @@ sub compare {
return 0;
}
-
-
-=head2 id
-
- Arg : none
- Example : none
- Description: deprecated function, use dbID instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub id {
- my ($self,$arg) = @_;
- $self->warn( "Analysis->id is deprecated. Use dbID!" );
- print STDERR caller;
-
- if (defined($arg)) {
- $self->{_dbid} = $arg;
- }
- return $self->{_dbid};
-}
-
-
-
1;
diff --git a/modules/Bio/EnsEMBL/Clone.pm b/modules/Bio/EnsEMBL/Clone.pm
index 01755874ea..047b8b86aa 100644
--- a/modules/Bio/EnsEMBL/Clone.pm
+++ b/modules/Bio/EnsEMBL/Clone.pm
@@ -455,125 +455,6 @@ sub adaptor {
}
-
-
-
-=head2 delete
-
- Args : none
- Example : none
- Description: deprecated, use object adaptor for deletion
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub delete {
- my ($self)=shift;
- $self->warn("delete is now deprecated, use delete_by_dbID instead");
- $self->delete_by_dbID;
-}
-
-
-=head2 seq_date
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use created instead
- All contig sequences should have been created at the
- same time as this clone anyway, and seq_date is no longer
- accessable from RawContig.
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub seq_date {
- my ($self) = @_;
-
- $self->warn("Call to deprecated method Bio::EnsEMBL::Clone::seq_date" .
- "Calling created method instead");
- return $self->created();
-
- # my $id = $self->id();
-# my ($seq_date,$old_seq_date);
-
-# foreach my $contig ($self->get_all_Contigs) {
-# $seq_date = $contig->seq_date;
-# if ($old_seq_date) {
-# if ($seq_date != $old_seq_date) {
-# $self->warn ("The created date of the DNA sequence from contig
-# $contig is different from that of the sequence
-# from other contigs on the same clone!");
-# }
-# }
-# $old_seq_date = $seq_date;
-# }
-
-# return $seq_date;
-}
-
-=head2 is_golden
-
- Args : none
- Example : none
- Description: deprecated, use assembly_mapper->in_assembly( $clone )
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub is_golden{
- my ($self,@args) = @_;
-
- $self->warn("Clone::is_golden is deprecated. " .
- "Use \$assembly_mapper->in_assembly(\$clone)");
-
- my $asma = $self->adaptor()->db()->get_AssemblyMapperAdaptor();
- my $am = $asma->fetch_by_type($self->db()->assembly_type());
- return $am->in_assembly($self);
-
-# foreach my $contig ($self->get_all_Contigs) {
-# if ($contig->is_golden) {
-# return 1;
-# }
-# }
-# return 0;
-}
-
-
-
-=head2 get_Contig
-
- Args : none
- Example : none
- Description: deprecated, use ContigAdaptor to get Contig
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-
-sub get_Contig {
- my ($self,$contigid) = @_;
-
- $self->throw("Clone::get_Contig is deprecated, " .
- "use \$contig_adaptor->fetch_by_dbID(\$contig_id) instead\n");
-
- return undef;
-
-# my $contig = $self->adaptor->get_Contig($contigid);
-
-# return $contig->fetch();
-}
-
-
-
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
index 7f08455a7b..17612dca81 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
@@ -98,28 +98,5 @@ sub fetch_all_by_Exon {
return $out;
}
-
-
-=head2 fetch_by_Exon
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use fetch_all_by_Exon instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub fetch_by_Exon {
- my ($self, @args) = @_;
-
- $self->warn("fetch_by_Exon has been renamed fetch_all_by_Exon\n" . caller);
-
- return $self->fetch_all_by_Exon(@args);
-}
-
-
-
-
1;
+
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index f6fd2e49f4..9bf37ec7cb 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -1767,223 +1767,6 @@ triplets (start, stop, strand) from which new ranges could be built.
###############################################################################
-=head2 id
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use dbID or stable_id instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub id{
- my ($self) = shift;
- my $value = shift;
-
- my ($p,$f,$l) = caller;
- $self->warn("$f:$l id deprecated. Please choose from stable_id or dbID");
-
- if( defined $value ) {
- $self->warn("$f:$l stable ids are loaded separately and dbIDs are generated on writing. Ignoring set value $value");
- return;
- }
-
- if( defined $self->stable_id ) {
- return $self->stable_id();
- } else {
- return $self->dbID;
- }
-}
-
-
-
-=head2 clone_id
-
- Args : none
- Example : none
- Description: deprecated, exons can have more than one clone.
- StickyExons dont support this call
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub clone_id{
- my $self = shift;
-
- $self->warn("Exon->clone_id method deprecated\n");
- return undef;
-
- if( @_ ) {
- my $value = shift;
- $self->{'clone_id'} = $value;
- }
-
- if( defined $self->{'clone_id'} ) {
- return $self->{'clone_id'};
- } elsif( defined $self->contig() ) {
- return $self->contig->cloneid();
- } else {
- return undef;
- }
-}
-
-=head2 contig_id
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use Bio::EnsEMBL::Exon::contig instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub contig_id{
- my $self = shift;
- $self->warn("Bio::EnsEMBL::Exon::contig_id is deprecated. \n" .
- "Use exon->contig->dbID instead $!");
-
-# if($contig_id) {
-# my $contig =
-# $self->adaptor->db->get_RawContigAdaptor->fetch_by_dbID($contig_id);
-# $self->contig($contig);
-# }
-
-# return $self->contig()->dbID();
-
- if( @_ ) {
- my $value = shift;
- #print "setting contig_id = ".$value."\n";
- $self->{'contigid'} = $value;
- }
- if( defined $self->{'contigid'} ) {
- return $self->{'contigid'};
- } elsif( defined $self->contig() ) {
- return $self->contig->dbID();
- } else {
- return undef;
- }
-}
-
-
-
-=head2 each_Supporting_Feature
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use get_all_supporting_features instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub each_Supporting_Feature {
- my ($self, @args) = @_;
-
- $self->warn("Exon::each_Supporting_Feature has been renamed " .
- "get_all_supporting_features" . caller);
-
- return $self->get_all_supporting_features(@args);
-}
-
-
-=head2 add_Supporting_Feature
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use add_supporting_features instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub add_Supporting_Feature {
- my ($self, @args) = @_;
-
- $self->warn("Exon::add_Supporting_Feature has been renamed " .
- "add_supporting_features" . caller);
-
- return $self->add_supporting_features(@args);
-}
-
-=head2 ori_start
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED not needed, do not use
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub ori_start{
- my $obj = shift;
-
- $obj->warn("Call to deprecated method ori_start " . caller);
-
- if( @_ ) {
- my $value = shift;
- $obj->{'ori_start'} = $value;
- }
- return $obj->{'ori_start'};
-
-}
-
-
-=head2 ori_end
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED not needed, do not use
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub ori_end{
- my $obj = shift;
-
- $obj->warn("Call to deprecated method ori_end " . caller);
-
- if( @_ ) {
- my $value = shift;
- $obj->{'ori_end'} = $value;
- }
- return $obj->{'ori_end'};
-
-}
-
-
-=head2 ori_strand
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED not needed, do not use
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub ori_strand{
- my $obj = shift;
-
- $obj->warn("Call to deprecated method ori_strand " . caller);
-
- if( @_ ) {
- my $value = shift;
- $obj->{'ori_strand'} = $value;
- }
- return $obj->{'ori_strand'};
-}
1;
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index b8076380ca..1762eda423 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -875,163 +875,4 @@ sub temporary_id {
}
-
-
-
-#############################
-#
-# DEPRECATED METHODS FOLLOW
-#
-#############################
-
-=head2 each_Transcript
-
- Title : each_Transcript
- Usage : DEPRECATED foreach $trans ( $gene->each_Transcript)
- Function: DEPRECATED
- Example : DEPRECATED
- Returns : DEPRECATED An array of Transcript objects
- Args : DEPRECATED
-
-
-=cut
-
-sub each_Transcript {
- my ($self) = @_;
-
- $self->warn("Gene->each_Transcript is deprecated. " .
- "Use get_all_Transcripts().\n" . $self->stack_trace_dump() ."\n");
-
-
-
- return $self->get_all_Transcripts();
-}
-
-=head2 id
-
- Title : id
- Usage : DEPRECATED $obj->id($newval)
- Function: DEPRECATED
- Returns : DEPRECATED value of id
- Args : DEPRECATED newvalue (optional)
-
-
-=cut
-
-sub id{
- my $self = shift;
- my $value = shift;
-
- my ($p,$f,$l) = caller;
- $self->warn("$f:$l id deprecated. Please choose from stable_id or dbID");
-
- if( defined $value ) {
- $self->warn("$f:$l stable ids are loaded separately and dbIDs are generated on writing. Ignoring set value $value");
- return;
- }
-
-
- if( defined $self->stable_id ) {
- return $self->stable_id();
- } else {
- return $self->dbID;
- }
-
-}
-
-
-sub each_unique_Exon{
- my ($self) = @_;
-
- my ($p,$f,$l) = caller;
- $self->warn("$f:$l each_unique_Exon deprecated. use get_all_Exons instead. Exon objects should be unique memory locations");
-
- return $self->get_all_Exons;
-}
-
-
-sub all_Exon_objects{
-
- my ($self) = @_;
-
- my ($p,$f,$l) = caller;
- $self->warn("$f:$l all_Exon_objects deprecated. use get_all_Exons instead. Exon objects should be unique memory locations");
-
- return $self->get_all_Exons;
-}
-
-
-=head2 refresh
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED no longer needed, do not call
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub refresh {
- my ($self) = @_;
-
- $self->warn("call to deprecated method refresh. This method is not needed "
- . "anymore and should not be called\n" );
-
-# foreach my $e ($self->get_all_Exons) {
-# $e->start($e->ori_start);
-# $e->end($e->ori_end);
-# $e->strand($e->ori_strand);
-# }
-}
-
-
-
-=head2 each_DBLink
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use Bio::EnsEMBL::get_all_DBLinks instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub each_DBLink {
- my $self = shift;
-
- $self->warn("each_DBLink has been renamed get_all_DBLinks\n" .
- caller);
-
- return $self->get_all_DBLinks();
-}
-
-
-=head2 get_Exon_by_id
-
- Arg [1] : none
- Example : none
- Description: DEPRECATED use get_all_Exons instead
- Returntype : none
- Exceptions : none
- Caller : none
-
-=cut
-
-sub get_Exon_by_id {
- my ($self, $id) = @_;
-
- $self->warn("Get Exon by id is deprecated use get_all_Exons and " .
- "sort through them yourself\n");
-
- # perhaps not ideal
- foreach my $exon ( $self->get_all_Exons ) {
- # should this be stable_id
- if( $exon->dbID eq $id ) {
- return $exon;
- }
- }
-}
-
1;
--
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