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Commit 67709b92 authored by Magali Ruffier's avatar Magali Ruffier
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planned retirement of deprecated methods

parent bc190300
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Showing with 173 additions and 110 deletions
DEPRECATED.md
View file @ 67709b92
......@@ -71,9 +71,98 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP
- Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_by_translation_id()*
- Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_all_by_feature_and_dbID()*
- Bio::EnsEMBL::DBSQL::**RepeatConsensusAdaptor**::*fetch_by_class_seq()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_mapfrag()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_chr_start_end()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_contig_name()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_clone_accession()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_supercontig_name()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*list_overlapping_supercontigs()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_chr_name()*
- Bio::EnsEMBL::DBSQL::**TranscriptAdaptor**::*get_display_xref()*
- Bio::EnsEMBL::DBSQL::**TranscriptAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**TranscriptAdaptor**::*fetch_all_by_DBEntry()*
- Bio::EnsEMBL::DBSQL::**SequenceAdaptor**::*fetch_by_assembly_location()*
- Bio::EnsEMBL::DBSQL::**SequenceAdaptor**::*fetch_by_RawContig_start_end_strand()*
- Bio::EnsEMBL::**Exon**::*temporary_id()*
- Bio::EnsEMBL::**Exon**::*created()*
- Bio::EnsEMBL::**Exon**::*modified()*
- Bio::EnsEMBL::**Exon**::*type()*
- Bio::EnsEMBL::**FeaturePair**::*feature1()*
- Bio::EnsEMBL::**FeaturePair**::*feature2()*
- Bio::EnsEMBL::**FeaturePair**::*set_featurepair_fields()*
- Bio::EnsEMBL::**FeaturePair**::*gffstring()*
- Bio::EnsEMBL::**FeaturePair**::*hphase()*
- Bio::EnsEMBL::**FeaturePair**::*hend_phase()*
- Bio::EnsEMBL::**Feature**::*contig()*
- Bio::EnsEMBL::**Feature**::*id()*
- Bio::EnsEMBL::**Gene**::*add_DBLink()*
- Bio::EnsEMBL::**Gene**::*temporary_id()*
- Bio::EnsEMBL::**Gene**::*chr_name()*
- Bio::EnsEMBL::**Gene**::*type()*
- Bio::EnsEMBL::**Gene**::*confidence()*
- Bio::EnsEMBL::**IdentityXref**::*query_identity()*
- Bio::EnsEMBL::**IdentityXref**::*target_identity()*
- Bio::EnsEMBL::**IdentityXref**::*translation_start()*
- Bio::EnsEMBL::**IdentityXref**::*translation_end()*
- Bio::EnsEMBL::**IdentityXref**::*query_start()*
- Bio::EnsEMBL::**IdentityXref**::*query_end()*
- Bio::EnsEMBL::**KaryotypeBand**::*chr_name()*
- Bio::EnsEMBL::Map::DBSQL::**MarkerFeatureAdaptor**::fetch_all_by_RawContig_and_priority()*
- Bio::EnsEMBL::Map::**DitagFeature**::*fetch_ditag()*
- Bio::EnsEMBL::Map::**MapLocation**::*chromosome()*
- Bio::EnsEMBL::**OperonTranscript**::*add_gene()*
- Bio::EnsEMBL::**PredictionTranscript**::*get_exon_count()*
- Bio::EnsEMBL::**PredictionTranscript**::*set_exon_count()*
- Bio::EnsEMBL::**PredictionTranscript**::*get_cdna()*
- Bio::EnsEMBL::**Registry**::*load_registry_with_web_adaptors()*
- Bio::EnsEMBL::**Root**::*throw()*
- Bio::EnsEMBL::**Root**::*warn()*
- Bio::EnsEMBL::**Root**::*verbose()*
- Bio::EnsEMBL::**Root**::*stack_trace_dump()*
- Bio::EnsEMBL::**Root**::*stack_trace()*
- Bio::EnsEMBL::**Slice**::*get_all_SNPs()*
- Bio::EnsEMBL::**Slice**::*get_all_genotyped_SNPs()*
- Bio::EnsEMBL::**Slice**::*get_all_OligoFeatures_by_type()*
- Bio::EnsEMBL::**Slice**::*get_all_supercontig_Slices()*
- Bio::EnsEMBL::**Slice**::*get_Chromosome()*
- Bio::EnsEMBL::**Slice**::*chr_name()*
- Bio::EnsEMBL::**Slice**::*chr_start()*
- Bio::EnsEMBL::**Slice**::*chr_end()*
- Bio::EnsEMBL::**Slice**::*assembly_type()*
- Bio::EnsEMBL::**Slice**::*dbID()*
- Bio::EnsEMBL::**Slice**::*get_all_MapFrags()*
- Bio::EnsEMBL::**Slice**::*has_MapSet()*
- Bio::EnsEMBL::**StrainSlice**::*get_all_differences_Slice()*
- Bio::EnsEMBL::**Transcript**::*created()*
- Bio::EnsEMBL::**Transcript**::*modified()*
- Bio::EnsEMBL::**Transcript**::*temporary_id()*
- Bio::EnsEMBL::**Transcript**::*type()*
- Bio::EnsEMBL::**Transcript**::*confidence()*
- Bio::EnsEMBL::**Translation**::*temporary_id()*
- Bio::EnsEMBL::Utils::**ConversionSupport**::*user_confirm()*
### Removed in Ensembl Release 84 ###
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_by_attrib()*
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_all_by_attrib()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_short_name()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_max_assembly_contig()*
- Bio::EnsEMBL::**Exon**::*_get_stable_entry_info()*
- Bio::EnsEMBL::**FeaturePair**::*validate()*
- Bio::EnsEMBL::**FeaturePair**::*validate_prot_feature()*
- Bio::EnsEMBL::**Root**::*rearrange()*
- Bio::EnsEMBL::**SeqFeatureI**::*analysis()*
- Bio::EnsEMBL::**SeqFeatureI**::*validate()*
- Bio::EnsEMBL::**SeqFeatureI**::*id()*
- Bio::EnsEMBL::**SeqFeatureI**::*percent_id()*
- Bio::EnsEMBL::**SeqFeatureI**::*e_value()*
- Bio::EnsEMBL::**SeqFeatureI**::*phase()*
- Bio::EnsEMBL::**SeqFeatureI**::*end_phase()*
- Bio::EnsEMBL::**SeqFeatureI**::*location()*
- Bio::EnsEMBL::**Slice**::*get_all_SNPs_transcripts()*
- Bio::EnsEMBL::**Slice**::*get_all_AffyFeatures()*
- Bio::EnsEMBL::**Slice**::*get_all_OligoFeatures()*
- Bio::EnsEMBL::**Slice**::*get_all_OligoFeatures_by_type()*
- Bio::EnsEMBL::**Slice**::*get_tiling_path()*
- Bio::EnsEMBL::**Transcript**::*sort()*
- Bio::EnsEMBL::**Transcript**::*_translation_id()*
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
View file @ 67709b92
......@@ -511,7 +511,7 @@ sub fetch_by_assembly_location {
my ( $self, $chrStart, $chrEnd,
$strand, $chrName, $assemblyType ) = @_;
deprecate('Use fetch_by_Slice_start_end_strand() instead');
deprecate('fetch_by_assembly_location is deprecated and will be removed in e87. Please use fetch_by_Slice_start_end_strand() instead');
my $csa = $self->db->get_CoordSystem();
my $top_cs = @{$csa->fetch_all};
......@@ -532,7 +532,7 @@ sub fetch_by_assembly_location {
=cut
sub fetch_by_RawContig_start_end_strand {
deprecate('Use fetch_by_Slice_start_end_strand instead.');
deprecate('fetch_by_RawContig_start_end_strand is deprecated and will be removed in e87. Please use fetch_by_Slice_start_end_strand instead.');
fetch_by_Slice_start_end_strand(@_);
}
......
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
View file @ 67709b92
......@@ -2749,7 +2749,7 @@ sub _build_circular_slice_cache {
sub fetch_by_mapfrag{
my ($self,$mymapfrag,$flag,$size) = @_;
deprecate('Use fetch_by_misc_feature_attribute instead');
deprecate('fetch_by_mapfrag is deprecated and will be removed in e87. Please use fetch_by_misc_feature_attribute instead');
$flag ||= 'fixed-width'; # alt.. 'context'
$size ||= $flag eq 'fixed-width' ? 100000 : 0;
return $self->fetch_by_misc_feature_attribute('synonym',$mymapfrag,$size);
......@@ -2765,7 +2765,7 @@ sub fetch_by_mapfrag{
sub fetch_by_chr_start_end {
my ($self,$chr,$start,$end) = @_;
deprecate('Use fetch_by_region() instead');
deprecate('fetch_by_chr_start_end is deprecated and will be removed in e87. Please use fetch_by_region() instead');
#assume that by chromosome the user actually meant top-level coord
#system since this is the old behaviour of this deprecated method
......@@ -2787,7 +2787,7 @@ sub fetch_by_chr_start_end {
sub fetch_by_contig_name {
my ($self, $name, $size) = @_;
deprecate('Use fetch_by_region(), Slice::project() and Slice::expand().');
deprecate('fetch_by_contig_name is deprecated and will be removed in e87. Please use fetch_by_region(), Slice::project() and Slice::expand().');
#previously wanted chromosomal slice on a given contig. Assume this means
#a top-level slice on a given seq_region in the seq_level coord system
......@@ -2820,7 +2820,7 @@ sub fetch_by_contig_name {
sub fetch_by_clone_accession{
my ($self,$name,$size) = @_;
deprecate('Use fetch_by_region(), Slice::project() and Slice::expand().');
deprecate('fetch_by_clone_accession is deprecated and will be removed in e87. Please use fetch_by_region(), Slice::project() and Slice::expand().');
my $csa = $self->db()->get_CoordSystemAdaptor();
my $clone_cs = $csa->fetch_by_name('clone');
......@@ -2876,7 +2876,7 @@ sub fetch_by_clone_accession{
sub fetch_by_supercontig_name {
my ($self,$name, $size) = @_;
deprecate('Use fetch_by_region(), Slice::project() and Slice::expand().');
deprecate('fetch_by_supercontig_name is deprecated and will be removed in e87. Please use fetch_by_region(), Slice::project() and Slice::expand().');
my $csa = $self->db()->get_CoordSystemAdaptor();
my $sc_level = $csa->fetch_by_name('supercontig');
......@@ -2911,7 +2911,7 @@ sub fetch_by_supercontig_name {
sub list_overlapping_supercontigs {
my ($self,$slice) = @_;
deprecate('Use Slice::project() instead.');
deprecate('list_overlapping_supercontigs is deprecated and will be removed in e87. Please use Slice::project() instead.');
my $csa = $self->db()->get_CoordSystemAdaptor();
my $sc_level = $csa->fetch_by_name('supercontig');
......@@ -2939,7 +2939,7 @@ sub list_overlapping_supercontigs {
sub fetch_by_chr_name{
my ($self,$chr_name) = @_;
deprecate('Use fetch_by_region() instead.');
deprecate('fetch_by_chr_name is deprecated and will be removed in e87. Please use fetch_by_region() instead.');
my $csa = $self->db->get_CoordSystemAdaptor();
......
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
View file @ 67709b92
......@@ -2069,7 +2069,7 @@ sub fetch_all_by_transcript_supporting_evidence {
sub get_display_xref {
my ($self, $transcript) = @_;
deprecate("display_xref should be retrieved from Transcript object directly.");
deprecate("get_display_xref is deprecated and will be removed in e87. display_xref should be retrieved from Transcript object directly.");
if ( !defined $transcript ) {
throw("Must call with a Transcript object");
......@@ -2119,7 +2119,7 @@ sub get_display_xref {
sub get_stable_entry_info {
my ($self, $transcript) = @_;
deprecate("Stable ids should be loaded directly now");
deprecate("get_stable_entry_info is deprecated and will be removed in e87. Stable ids should be loaded directly instead");
unless ( defined $transcript && ref $transcript &&
$transcript->isa('Bio::EnsEMBL::Transcript') ) {
......@@ -2151,7 +2151,7 @@ sub get_stable_entry_info {
sub fetch_all_by_DBEntry {
my $self = shift;
deprecate('Use fetch_all_by_external_name instead.');
deprecate('fetch_all_by_DBEntry is deprecated and will be removed in e87. Please use fetch_all_by_external_name instead.');
return $self->fetch_all_by_external_name(@_);
}
......
modules/Bio/EnsEMBL/Exon.pm
View file @ 67709b92
......@@ -1612,7 +1612,7 @@ sub summary_as_hash {
sub _get_stable_entry_info {
my $self = shift;
deprecate( "This function shouldnt be called any more" );
deprecate( "_get_stable_entry_info is deprecated and will be removed in e84. Please use stable_id instead." );
if( !defined $self->adaptor ) {
return undef;
}
......@@ -1628,7 +1628,7 @@ sub _get_stable_entry_info {
sub temporary_id {
my $self = shift;
deprecate('It should not be necessary to use this method.');
deprecate('temporary_id is deprecated and will be removed in e87.');
$self->{'tempID'} = shift if(@_);
return $self->{'tempID'};
}
......@@ -1642,7 +1642,7 @@ sub temporary_id {
sub created {
my ($self,$value) = @_;
deprecate( "Created attribute not supported any more." );
deprecate( "created is deprecated and will be removed in e87." );
if(defined $value ) {
$self->{'_created'} = $value;
}
......@@ -1658,7 +1658,7 @@ sub created {
sub modified {
my ($self,$value) = @_;
deprecate( "Modified attribute not supported any more." );
deprecate( "Modified is deprecated and will be removed in e87." );
if( defined $value ) {
$self->{'_modified'} = $value;
}
......@@ -1674,7 +1674,7 @@ sub modified {
sub type {
my ($self,$value) = @_;
deprecate("Type attribute not supported anymore.");
deprecate("Type is deprecated and will be removed in e87.");
if (defined($value)) {
$self->{'type'} = $value;
}
......
modules/Bio/EnsEMBL/Feature.pm
View file @ 67709b92
......@@ -1502,7 +1502,7 @@ sub species {
Use slice() instead
=cut
sub contig {
deprecate('Use slice() instead');
deprecate('contig is deprecated and will be removed in e87. Please use slice() instead');
slice(@_);
}
......@@ -1603,7 +1603,7 @@ Use display_id, hseqname, dbID or stable_id instead
sub id {
my $self = shift;
deprecate("id method is not used - use display_id instead");
deprecate("id method is deprecated and will be removed in e87. Please use display_id instead");
return $self->{'stable_id'} if($self->{'stable_id'});
return $self->{'hseqname'} if($self->{'hseqname'});
return $self->{'seqname'} if($self->{'seqname'});
......
modules/Bio/EnsEMBL/FeaturePair.pm
View file @ 67709b92
......@@ -729,7 +729,7 @@ sub level_id {
sub feature1 {
my ($self, $arg) = @_;
deprecate('Use start(), end(), strand(), slice(), etc. methods instead.');
deprecate('feature1 is deprecated and will be removed in e87. Please use start(), end(), strand(), slice(), etc. methods instead.');
if ($arg) {
$self->start($arg->start());
......@@ -756,7 +756,7 @@ sub feature1 {
sub feature2 {
my ($self, $arg) = @_;
deprecate('Use hstart(),hend(),hstrand(),hseqname() methods instead.');
deprecate('feature2 is deprecated and will be removed in e87. Please use hstart(),hend(),hstrand(),hseqname() methods instead.');
if (defined($arg)) {
$self->hstart($arg->start());
......@@ -837,7 +837,7 @@ sub invert {
sub validate {
my ($self) = @_;
deprecate('This method does nothing and should not be used.');
deprecate('validate is deprecated and will be removed in e84.');
}
=head2 validate_prot_feature
......@@ -849,7 +849,7 @@ sub validate {
sub validate_prot_feature {
my ($self) = @_;
deprecate('This method does nothing and should not be used.');
deprecate('validate is deprecated and will be removed in e84.');
}
=head2 set_featurepair_fields
......@@ -861,7 +861,7 @@ sub validate_prot_feature {
sub set_featurepair_fields {
my ($self, $start, $end, $strand, $score, $seqname, $hstart, $hend, $hstrand, $hseqname, $analysis, $e_value, $perc_id, $phase, $end_phase) = @_;
deprecate("Use individual Getter/Setters or Constructor arguments " . " instead.\nThere is no advantage to using this method.");
deprecate("set_featurepair_fields is deprecated and will be removed in e87. Please use individual Getter/Setters or Constructor arguments instead.");
throw('interface fault') if (@_ < 12 or @_ > 15);
......@@ -890,7 +890,7 @@ sub set_featurepair_fields {
sub gffstring {
my ($self) = @_;
deprecate('Do not use');
deprecate('gffstring is deprecated and will be removed in e87.');
my $str .= (defined $self->slice) ? $self->slice->name() . "\t" : "\t";
$str .= "\t"; #source tag
......@@ -927,7 +927,7 @@ sub gffstring {
sub hphase {
my ($self, $value) = @_;
deprecate('This method does nothing useful.');
deprecate('hphase is deprecated and will be removed in e87.');
if (defined($value)) {
$self->{_hphase} = $value;
......@@ -945,7 +945,7 @@ sub hphase {
sub hend_phase {
my ($self, $value) = @_;
deprecate('This method does nothing useful.');
deprecate('hend_phase is deprecated and will be removed in e87.');
if (defined($value)) {
$self->{_hend_phase} = $value;
......
modules/Bio/EnsEMBL/Gene.pm
View file @ 67709b92
......@@ -1530,7 +1530,7 @@ sub havana_gene {
sub add_DBLink{
my ($self,$value) = @_;
throw("add_DBLink is deprecated. You probably want add_DBEntry.");
throw("add_DBLink is deprecated and will be removed in e87. Please use add_DBEntry instead.");
# unless(defined $value && ref $value
# && $value->isa('Bio::Annotation::DBLink') ) {
......@@ -1553,8 +1553,7 @@ sub add_DBLink{
sub temporary_id {
my ($obj,$value) = @_;
deprecate( "I cant see what a temporary_id is good for, please use " .
"dbID or stableID or\n try without an id." );
deprecate('temporary_id is deprecated and will be removed in e87.');
if( defined $value) {
$obj->{'temporary_id'} = $value;
}
......@@ -1574,7 +1573,7 @@ sub temporary_id {
sub chr_name {
my $self = shift;
deprecate( "Use project() to obtain other coordinate systems" );
deprecate( "chr_name is deprecated and will be removed in e87. Please use project() to obtain other coordinate systems" );
my $gene_slice = $self->slice();
if( $gene_slice->coord_system()->name eq "chromosome" ) {
......@@ -1621,7 +1620,7 @@ sub fetch_coded_for_regulatory_factors {
=cut
sub type {
deprecate("Use biotype() instead");
deprecate("type is deprecated and will be removed in e87. Please use biotype() instead");
biotype(@_);
}
......@@ -1633,7 +1632,7 @@ sub type {
=cut
sub confidence {
deprecate("Use status() instead");
deprecate("confidence is deprecated and will be removed in e87. Please use status() instead");
status(@_);
}
......
modules/Bio/EnsEMBL/IdentityXref.pm
View file @ 67709b92
......@@ -452,7 +452,7 @@ sub map_feature {
=cut
sub query_identity{
deprecate("Use xref_identity instead");
deprecate("query_identity is deprecated and will be removed in e87. Please use xref_identity instead");
xref_identity(@_);
}
......@@ -465,7 +465,7 @@ sub query_identity{
=cut
sub target_identity{
deprecate("Use ensembl_identity instead");
deprecate("target_identity is deprecated and will be removed in e87. Please use ensembl_identity instead");
ensembl_identity(@_);
}
......@@ -479,7 +479,7 @@ sub target_identity{
=cut
sub translation_start {
deprecate("Use ensembl_start instead");
deprecate("translation_start is deprecated and will be removed in e87. Please use ensembl_start instead");
ensembl_start(@_);
}
......@@ -493,7 +493,7 @@ sub translation_start {
=cut
sub translation_end {
deprecate("Use ensembl_end instead");
deprecate("translation_end is deprecated and will be removed in e87. Please use ensembl_end instead");
ensembl_end(@_);
}
......@@ -507,7 +507,7 @@ sub translation_end {
=cut
sub query_start {
deprecate("Use xref_start instead");
deprecate("query_start is deprecated and will be removed in e87. Please use xref_start instead");
xref_start(@_);
}
......@@ -522,7 +522,7 @@ sub query_start {
=cut
sub query_end {
deprecate("Use xref_end instead");
deprecate("query_end is deprecated and will be removed in e87. Please use xref_end instead");
xref_end(@_);
}
......
modules/Bio/EnsEMBL/KaryotypeBand.pm
View file @ 67709b92
......@@ -230,7 +230,7 @@ sub display_id {
sub chr_name {
my $self = shift;
deprecate('Use $kary_band->slice()->seq_region_name() instead.');
deprecate('chr_name is deprecated and will be removed in e87. Please use $kary_band->slice()->seq_region_name() instead.');
if(!$self->slice) {
warning('KaryotypeBand does not have Slice - cannot get seq_region_name.');
return '';
......
modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
View file @ 67709b92
......@@ -151,7 +151,7 @@ sub fetch_all_by_Slice_and_priority {
=cut
sub fetch_all_by_RawContig_and_priority {
deprecate('Use fetch_all_by_Slice_and_priority() instead.');
deprecate('fetch_all_by_RawContig_and_priority is deprecated and will be removed in e87. Please use fetch_all_by_Slice_and_priority() instead.');
fetch_all_by_Slice_and_priority(@_);
}
......
modules/Bio/EnsEMBL/Map/DitagFeature.pm
View file @ 67709b92
......@@ -65,8 +65,9 @@ package Bio::EnsEMBL::Map::DitagFeature;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Exception qw( throw deprecate);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Feature);
......@@ -170,7 +171,7 @@ sub new {
=cut
sub fetch_ditag {
throw("Deprecated method, please use ditag() instead.\n")
deprecate("fetch_ditag is deprecated and will be removed in e87. Please use ditag() instead.")
}
......
modules/Bio/EnsEMBL/Map/MapLocation.pm
View file @ 67709b92
......@@ -195,7 +195,7 @@ sub lod_score {
sub chromosome {
my $self = shift;
deprecate('use chromosome_name instead');
deprecate('chromosome is deprecated and will be removed in e87. Please use chromosome_name instead');
if(@_) {
my $chr = shift;
......
modules/Bio/EnsEMBL/OperonTranscript.pm
View file @ 67709b92
......@@ -274,7 +274,7 @@ sub add_Gene {
=cut
sub add_gene {
my ($self,$gene) = @_;
deprecate('Call is deprecated. Use $self->add_Gene()');
deprecate('add_gene is deprecated and will be removed in e87. Please use $self->add_Gene()');
return $self->add_Gene($gene);
}
=head2 add_DBEntry
......
modules/Bio/EnsEMBL/PredictionTranscript.pm
View file @ 67709b92
......@@ -574,7 +574,7 @@ sub get_all_Attributes {
sub get_exon_count {
my $self = shift;
deprecate('Use scalar(@{$transcript->get_all_Exon()s}) instead');
deprecate('get_exon_count is deprecated and will be removed in e87. Please use scalar(@{$transcript->get_all_Exon()s}) instead');
return scalar( @{$self->get_all_Exons} );
}
......@@ -586,7 +586,7 @@ sub get_exon_count {
=cut
sub set_exon_count {
deprecate('This method no longer does anything.');
deprecate('set_exon_count is deprecated and will be removed in e84.');
}
......@@ -599,7 +599,7 @@ sub set_exon_count {
sub get_cdna {
my $self = shift;
deprecate('use spliced_seq instead');
deprecate('get_cdna is deprecated and will be removed in e87. Please use spliced_seq instead');
return $self->spliced_seq();
}
......
modules/Bio/EnsEMBL/Registry.pm
View file @ 67709b92
......@@ -2649,7 +2649,7 @@ sub load_registry_from_multiple_dbs {
sub load_registry_with_web_adaptors{
my $class = shift;
deprecate('Use the load_registry_from_db instead');
deprecate('load_registry_with_web_adaptors is deprecated and will be removed in e87. Please use the load_registry_from_db instead');
my $site_eval = eval{ require SiteDefs };
if ($@ or (!defined($site_eval))){ die "Can't use SiteDefs.pm - $@\n"; }
SiteDefs->import(qw(:ALL));
......
modules/Bio/EnsEMBL/Root.pm
View file @ 67709b92
......@@ -92,11 +92,7 @@ sub new{
sub throw{
my ($self,$string) = @_;
Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
"Bio::EnsEMBL::Root::throw has been deprecated\n".
"use Bio::EnsEMBL::Utils::Exception qw(throw); \n".
"throw('message'); #instead\n".
"\n---------------------------------------------------\n");
deprecate('Root->throw has been deprecated and will be removed in e87. Please use Exception->throw instead');
Bio::EnsEMBL::Utils::Exception->throw($string);
......@@ -112,14 +108,8 @@ sub throw{
sub warn{
my ($self,$string) = @_;
deprecate('Root->warn has been deprecated and will be removed in e87. Please use Exception->warning instead');
Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
"Bio::EnsEMBL::Root::warn has been deprecated\n".
"use Bio::EnsEMBL::Utils::Exception qw(warning); \n".
"warning('message'); #instead\n".
"\n---------------------------------------------------\n");
Bio::EnsEMBL::Utils::Exception->warning($string);
}
......@@ -136,12 +126,8 @@ sub warn{
sub verbose{
my ($self,$value) = @_;
Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
"Bio::EnsEMBL::Root::verbose has been deprecated\n".
"use Bio::EnsEMBL::Utils::Exception qw(verbose); \n".
"verbose(value); #instead\n".
"\n---------------------------------------------------\n");
deprecate('Root->verbose has been deprecated and will be removed in e87. Please use Exception->verbose instead');
Bio::EnsEMBL::Utils::Exception->verbose($value);
}
......@@ -155,11 +141,7 @@ sub verbose{
sub stack_trace_dump{
my ($self) = @_;
Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
"Bio::EnsEMBL::Root::stack_trace_dump has been deprecated\n".
"use Bio::EnsEMBL::Utils::Exception qw(stack_trace_dump); \n".
"stack_trace_dump(); #instead\n".
"\n---------------------------------------------------\n");
deprecate('Root->stack_trace_dump has been deprecated and will be removed in e87. Please use Exception->stack_trace_dump instead');
Bio::EnsEMBL::Utils::Exception->stack_trace_dump();
......@@ -175,11 +157,7 @@ sub stack_trace_dump{
sub stack_trace{
my ($self) = @_;
Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
"Bio::EnsEMBL::Root::stack_trace has been deprecated\n".
"use Bio::EnsEMBL::Utils::Exception qw(stack_trace); \n".
"stack_trace(); #instead\n".
"\n---------------------------------------------------\n");
deprecate('Root->stack_trace has been deprecated and will be removed in e87. Please use Exception->stack_trace instead');
Bio::EnsEMBL::Utils::Exception->stack_trace();
......@@ -197,10 +175,7 @@ sub _rearrange {
#----------------
my($self,$order,@param) = @_;
my $mess = "use Bio::EnsEMBL::Utils::Argument qw(rearrange); \n";
$mess .= "rearrange(order, list); #instead\n";
Bio::EnsEMBL::Utils::Exception->deprecate($mess);
deprecate('Root->_rearrange is deprecated and will be removed in e84. Please use Argument->rearrange instead');
return Bio::EnsEMBL::Utils::Argument->rearrange($order,@param);
......