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Commit f58532e4 authored by Graham McVicker's avatar Graham McVicker
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removed deprecated methods

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modules/Bio/EnsEMBL/Analysis.pm
+ 0
− 26
View file @ f58532e4
......@@ -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 $self->{_dbid};
}
1;
......
modules/Bio/EnsEMBL/Clone.pm
+ 0
− 119
View file @ f58532e4
......@@ -455,125 +455,6 @@ sub adaptor {
}
=head2 delete
Args : none
Example : none
Description: deprecated, use object adaptor for deletion
Returntype : none
Exceptions : none
Caller : none
=cut
sub delete {
my ($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;
......
modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
+ 1
− 24
View file @ f58532e4
......@@ -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 $self->fetch_all_by_Exon(@args);
}
1;
modules/Bio/EnsEMBL/Exon.pm
+ 0
− 217
View file @ f58532e4
......@@ -1767,223 +1767,6 @@ triplets (start, stop, strand) from which new ranges could be built.
###############################################################################
=head2 id
Arg [1] : none
Example : none
Description: DEPRECATED use dbID or stable_id instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub id{
my ($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;
modules/Bio/EnsEMBL/Gene.pm
+ 0
− 159
View file @ f58532e4
......@@ -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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