From bee31908dc806b0dbb31f74d69b5b439e85df6c9 Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Mon, 1 Mar 2004 15:58:28 +0000
Subject: [PATCH] small changes in API related to Attributes
---
.../Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm | 60 +++++--
modules/Bio/EnsEMBL/MiscFeature.pm | 155 +++++++++++-------
modules/Bio/EnsEMBL/Slice.pm | 59 +++----
modules/t/miscFeature.t | 56 ++++---
modules/t/miscFeatureAdaptor.t | 12 +-
5 files changed, 201 insertions(+), 141 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
index f86bc9f50f..1055ca3fd2 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
@@ -49,6 +49,7 @@ package Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::MiscFeature;
+use Bio::EnsEMBL::Attribute;
use Bio::EnsEMBL::MiscSet;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@@ -214,8 +215,10 @@ sub _columns {
mf.seq_region_end
mf.seq_region_strand
ma.value
- at.code
- mfms.misc_set_id);
+ at.code
+ mfms.misc_set_id
+ at.name
+ at.description);
}
@@ -284,11 +287,13 @@ sub _objs_from_sth {
my %sr_cs_hash;
my($misc_feature_id, $seq_region_id, $seq_region_start, $seq_region_end,
- $seq_region_strand, $attrib_value, $attrib_type_code, $misc_set_id);
+ $seq_region_strand, $attrib_value, $attrib_type_code, $misc_set_id,
+ $attrib_type_name, $attrib_type_description );
$sth->bind_columns( \$misc_feature_id, \$seq_region_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand,
- \$attrib_value, \$attrib_type_code,\$misc_set_id);
+ \$attrib_value, \$attrib_type_code,\$misc_set_id,
+ \$attrib_type_name, \$attrib_type_description );
my $asm_cs;
my $cmp_cs;
@@ -334,15 +339,25 @@ sub _objs_from_sth {
if($misc_set_id) {
my $misc_set = $ms_hash{$misc_set_id} ||=
$msa->fetch_by_dbID($misc_set_id);
- #doesn't matter if it is added twice in same slot
- $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
+ if( ! exists $feat_misc_sets->{$misc_set->{'code'}} ) {
+ $feat->add_MiscSet( $misc_set );
+ $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
+ }
}
#if there is a new attribute add it to the current feature
if($attrib_value && $attrib_type_code &&
!$seen_attribs->{"$attrib_type_code:$attrib_value"}) {
- $feat_attribs->{$attrib_type_code} ||= [];
- push @{$feat_attribs->{$attrib_type_code}}, $attrib_value;
+ my $attrib = Bio::EnsEMBL::Attribute->new
+ ( -CODE => $attrib_type_code,
+ -NAME => $attrib_type_name,
+ -DESC => $attrib_type_description,
+ -VALUE => $attrib_value
+ );
+
+
+ $feat_attribs ||= [];
+ push @$feat_attribs, $attrib;
$seen_attribs->{"$attrib_type_code:$attrib_value"} = 1;
}
@@ -419,15 +434,15 @@ sub _objs_from_sth {
$slice = $dest_slice;
}
- if($misc_set_id) {
- #get the misc_set object
- my $misc_set = $ms_hash{$misc_set_id} ||=
- $msa->fetch_by_dbID($misc_set_id);
- $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
- }
if($attrib_value && $attrib_type_code) {
- $feat_attribs->{$attrib_type_code} = [$attrib_value];
+ my $attrib = Bio::EnsEMBL::Attribute->new
+ ( -CODE => $attrib_type_code,
+ -NAME => $attrib_type_name,
+ -DESC => $attrib_type_description,
+ -VALUE => $attrib_value
+ );
+ $feat_attribs = [$attrib];
$seen_attribs->{"$attrib_type_code:$attrib_value"} = 1;
}
@@ -438,9 +453,18 @@ sub _objs_from_sth {
'slice' => $slice,
'adaptor' => $self,
'dbID' => $misc_feature_id,
- 'attributes' => $feat_attribs,
- 'sets' => $feat_misc_sets});
+ 'attributes' => $feat_attribs });
push @features, $feat;
+
+ if($misc_set_id) {
+ #get the misc_set object
+ my $misc_set = $ms_hash{$misc_set_id} ||=
+ $msa->fetch_by_dbID($misc_set_id);
+ if( ! exists $feat_misc_sets->{$misc_set->{'code'}} ) {
+ $feat->add_MiscSet( $misc_set );
+ $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
+ }
+ }
}
}
@@ -466,6 +490,8 @@ sub list_dbIDs {
return $self->_list_dbIDs("misc_feature");
}
+
+
1;
diff --git a/modules/Bio/EnsEMBL/MiscFeature.pm b/modules/Bio/EnsEMBL/MiscFeature.pm
index 38008c0cc6..4461fa0dc6 100644
--- a/modules/Bio/EnsEMBL/MiscFeature.pm
+++ b/modules/Bio/EnsEMBL/MiscFeature.pm
@@ -110,12 +110,29 @@ sub new_fast {
=cut
sub add_attribute {
- my ($self, $type, $value) = @_;
+ throw( "You need to make Attribute objects now, use add_Attribute" );
+}
+
+=head2 add_Attribute
+
+ Arg [1] : Bio::EnsEMBL::Attribute $attribute
+ Example : $misc_feature->add_attribute($attribute);
+ Description: Adds an attribute to this misc. feature
+ Returntype : none
+ Exceptions : throw on wrong argument type
+ Caller : general
- throw('Type argument is required') if(!$type);
+=cut
+
+sub add_Attribute {
+ my ($self, $attrib) = @_;
+
+ if( ! defined $attrib || ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
+ throw( "You have to provide a Bio::EnsEMBL::Attribute, not a [$attrib]" );
+ }
- $self->{'attributes'}->{$type} ||= [];
- push @{$self->{'attributes'}->{$type}}, $value
+ $self->{'attributes'} ||= [];
+ push @{$self->{'attributes'}}, $attrib
}
@@ -133,61 +150,42 @@ sub add_attribute {
=cut
sub add_set {
- my ($self, $set) = @_;
-
- if(!$set || !ref($set) || !$set->isa('Bio::EnsEMBL::MiscSet')) {
- throw('Set argument must be a Bio::EnsEMBL::MiscSet');
- }
-
- my $code = $set->code();
-
- throw('Set must be associated with a code to be added') if(!$code);
-
- $self->{'sets'}->{$code} = $set;
+ throw( "Use add_MiscSet instead." );
}
+=head2 add_MiscSet
-=head2 get_attribute_types
-
- Arg [1] : none
- Example : @attrib_types = $misc_feature->get_attribute_types();
- Description: returns a list of attribute types that this feature has
- Returntype : list of strings
- Exceptions : none
+ Arg [1] : Bio::EnsEMBL::MiscSet $set
+ The set to add
+ Example : $misc_feature->add_MiscSet(Bio::EnsEMBL::MiscSet->new(...));
+ Description: Associates this MiscFeature with a given Set.
+ Returntype : none
+ Exceptions : throw if the set arg is not provided,
+ throw if the set to be added does not have a code
Caller : general
=cut
-sub get_attribute_types {
- my $self = shift;
- $self->{'attributes'} ||= {};
-
- return keys %{$self->{'attributes'}};
-}
-=head2 get_set_codes
+sub add_MiscSet {
+ my $self = shift;
+ my $miscSet = shift;
- Arg [1] : none
- Example : @set_codes = $misc_feature->get_set_codes();
- Description: returns a list of codes for the sets this feature is associated
- with
- Returntype : list of strings
- Exceptions : none
- Caller : general
+ if(!$miscSet || !ref($miscSet) || !$miscSet->isa('Bio::EnsEMBL::MiscSet')) {
+ throw('Set argument must be a Bio::EnsEMBL::MiscSet');
+ }
-=cut
+ $self->{'miscSets'} ||= [];
-sub get_set_codes {
- my $self = shift;
- $self->{'sets'} ||= {};
- return keys %{$self->{'sets'}};
+ push( @{$self->{'miscSets'}}, $miscSet );
}
+
=head2 get_set
- Arg [1] : string $code
+ Arg [1] : optional string $code
The code of the set to retrieve
Example : $set = $misc_feature->get_set($code);
Description: Retrieves a set that this feature is associated with via its
@@ -200,16 +198,38 @@ sub get_set_codes {
=cut
sub get_set {
+ throw( "Use get_MiscSets()" );
+}
+
+
+=head2 get_all_MiscSets
+
+ Arg [1] : optional string $code
+ The code of the set to retrieve
+ Example : $set = $misc_feature->get_all_MiscSets($code);
+ Description: Retrieves a set that this feature is associated with via its
+ code. Can return empty lists. Usually returns about one elements lists.
+ Returntype : listref of Bio::EnsEMBL::MiscSet
+ Exceptions : throw if the code arg is not provided
+ Caller : general
+
+=cut
+
+
+sub get_all_MiscSets {
my $self = shift;
my $code = shift;
- throw('Code arg is required.') if (!$code);
-
- return $self->{'sets'}->{$code};
+ $self->{'miscSets'} ||= [];
+ if( defined $code ) {
+ my @results = grep { uc($_->code())eq uc( $code ) } @{$self->{'miscSets'}};
+ return \@results;
+ } else {
+ return $self->{'miscSets'};
+ }
}
-
=head2 get_attribute
Arg [1] : string $type
@@ -223,20 +243,39 @@ sub get_set {
=cut
sub get_attribute {
+ throw( "Use get_Attributes now" );
+}
+
+
+=head2 get_all_Attributes
+
+ Arg [1] : optional string $code
+ The code of the Attribute objects to retrieve
+ Example : @attributes = $misc_feature->get_all_Attributes('name');
+ Description: Retrieves a list of Attribute objects for given code or all
+ of the associated Attributes.
+ Returntype : listref of Bio::EnsEMBL::Attribute
+ Exceptions :
+ Caller : general
+
+=cut
+
+sub get_all_Attributes {
my $self = shift;
- my $type = shift;
+ my $code = shift;
- throw('Type arg is required.') if(!$type);
+ my @results;
+ my $result;
- if(exists $self->{'attributes'}->{$type}) {
- return wantarray() ? @{$self->{'attributes'}->{$type}} : $self->{'attributes'}->{$type}->[0];
+ if( defined $code ) {
+ @results = grep { uc( $_->code() ) eq uc( $code )} @{$self->{'attributes'}};
+ return \@results;
+ } else {
+ return $self->{'attributes'};
}
-
- return ();
}
-
=head2 display_id
Arg [1] : none
@@ -252,9 +291,13 @@ sub get_attribute {
sub display_id {
my $self = shift;
- my ($attrib) = $self->get_attribute('name');
- ($attrib) = $self->get_attribute('synonym') if(!$attrib);
- return $attrib || '';
+ my ($attrib) = @{$self->get_all_Attributes('name')};
+ ($attrib) = @{$self->get_all_Attributes('synonym')} if(!$attrib);
+ if( defined $attrib ) {
+ return $attrib->value();
+ } else {
+ return '';
+ }
}
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 1286e5c6bf..d975be2edb 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -795,59 +795,44 @@ sub get_seq_region_id {
}
-=head2 get_all_attribute_types
-
- Arg [1] : none
- Example : my @attribute_types = $slice->get_attribute_types();
- Description: Gets a list of the types of attributes associated with the
- seq_region this slice is on.
- Returntype : list of strings
- Exceptions : warning if slice does not have attached adaptor
- Caller : general
-
-=cut
-
-sub get_attribute_types {
- my $self = shift;
-
- if(!$self->adaptor()) {
- warning('Cannot get attributes without an adaptor.');
- return ();
- }
- my %attrib_hash = %{$self->adaptor->get_seq_region_attribs($self)};
- return keys %attrib_hash;
-}
+=head2 get_all_Attributes
-=head2 get_attribute
-
- Arg [1] : string $attrib_type
+ Arg [1] : optional string $attrib_code
The code of the attribute type to retrieve values for.
- Example : ($htg_phase) = $slice->get_attribute('htg_phase');
- @synonyms = $slice->get_attribute('synonyms');
- Description: Gets a list of values for a given attribute of this
- slice''s seq_region.
- Returntype : list of strings
- Exceptions : warning is slice does not have attached adaptor
- throw if argument is not provided
+ Example : ($htg_phase) = @{$slice->get_all_Attributes('htg_phase')};
+ @slice_attributes = @{$slice->get_all_Attributes()};
+ Description: Gets a list of Attributes of this slice''s seq_region.
+ Optionally just get Attrubutes for given code.
+ Returntype : listref Bio::EnsEMBL::Attribute
+ Exceptions : warning if slice does not have attached adaptor
Caller : general
=cut
-sub get_attribute {
+sub get_all_Attributes {
my $self = shift;
my $attrib_code = shift;
- throw('Attrib code argument is required.') if(!$attrib_code);
+ my $result;
+ my @results;
if(!$self->adaptor()) {
warning('Cannot get attributes without an adaptor.');
- return ();
+ return [];
}
- my %attribs = %{$self->adaptor->get_seq_region_attribs($self)};
+ my $attribute_adaptor = $self->db->get_AttributeAdaptor();
- return @{$attribs{uc($attrib_code)} || []};
+ if( defined $attrib_code ) {
+ @results = grep { uc($_->code()) eq uc($attrib_code) }
+ @{$attribute_adaptor->fetch_all_by_Slice( $self )};
+ $result = \@results;
+ } else {
+ $result = $attribute_adaptor->fetch_all_by_Slice( $self );
+ }
+
+ return $result;
}
diff --git a/modules/t/miscFeature.t b/modules/t/miscFeature.t
index 5d29c0a4d9..62d020a119 100644
--- a/modules/t/miscFeature.t
+++ b/modules/t/miscFeature.t
@@ -3,10 +3,11 @@ use strict;
BEGIN { $| = 1;
use Test ;
- plan tests => 11
+ plan tests => 8
}
use MultiTestDB;
+use Bio::EnsEMBL::Attribute;
use Bio::EnsEMBL::MiscFeature;
use Bio::EnsEMBL::MiscSet;
use TestUtils qw(debug test_getter_setter);
@@ -39,43 +40,47 @@ my $ms2 = Bio::EnsEMBL::MiscSet->new(4, undef,
-$mf->add_set($ms1);
-$mf->add_set($ms2);
+$mf->add_MiscSet($ms1);
+$mf->add_MiscSet($ms2);
-ok($mf->get_set($ms1->code) == $ms1);
-ok($mf->get_set($ms2->code) == $ms2);
+my $ms3 = $mf->get_all_MiscSets($ms1->code)->[0];
+my $ms4 = $mf->get_all_MiscSets($ms2->code)->[0];
-my @codes = $mf->get_set_codes;
+ok( $ms3 == $ms1);
+ok( $ms4 == $ms2);
-ok(@codes == 2);
-
-@codes = grep {($_ eq $ms1->code()) || ($_ eq $ms2->code())} @codes;
-
-ok(@codes == 2);
#
# Test add_attribute, get_attribute_types, get_attribute
#
-my $name1 = 'test name';
-my $name2 = 'AL4231124.1';
+my $name1 = Bio::EnsEMBL::Attribute->new
+ ( -CODE => 'name',
+ -VALUE => 'test name'
+ );
+
+my $name2 = Bio::EnsEMBL::Attribute->new
+ ( -CODE => 'name',
+ -VALUE => 'AL4231124.1'
+ );
-$mf->add_attribute('name', $name1);
-ok($mf->display_id eq $name1);
+$mf->add_Attribute( $name1 );
-$mf->add_attribute('name', $name2);
-$mf->add_attribute('version', '4');
+ok($mf->display_id eq "test name");
-my @types = $mf->get_attribute_types();
-ok(@types == 2);
+$mf->add_Attribute( $name2 );
-@types = grep {$_ eq 'name' || $_ eq 'version'} @types;
+my $vers1 = Bio::EnsEMBL::Attribute->new
+ ( -CODE => 'version',
+ -VALUE => 4
+ );
-ok(@types == 2);
+$mf->add_Attribute( $vers1 );
-my @attribs = $mf->get_attribute('name');
+
+my @attribs = @{$mf->get_all_Attributes('name')};
ok(@attribs == 2);
@@ -83,5 +88,8 @@ ok(@attribs == 2);
ok(@attribs == 2);
-@attribs = $mf->get_attribute('version');
-ok(@attribs == 1 && $attribs[0] eq '4');
+@attribs = @{$mf->get_all_Attributes('version')};
+ok(@attribs == 1 && $attribs[0]->value() eq '4');
+
+@attribs = @{$mf->get_all_Attributes()};
+ok( @attribs == 3 );
diff --git a/modules/t/miscFeatureAdaptor.t b/modules/t/miscFeatureAdaptor.t
index 9868abaa0a..ec7a9f1ece 100644
--- a/modules/t/miscFeatureAdaptor.t
+++ b/modules/t/miscFeatureAdaptor.t
@@ -87,14 +87,12 @@ sub print_features {
my $features = shift;
foreach my $f (@$features) {
if(defined($f)) {
- my @attrib_types = $f->get_attribute_types;
- my @attrib_vals = map {"$_ => " . join(',',$f->get_attribute($_))} @attrib_types;
+ my @attribs = @{$f->get_all_Attributes() };
+ my @sets = @{$f->get_all_MiscSets()};
- my @set_codes = $f->get_set_codes;
- my @set_names = map {"$_ => " . $f->get_set($_)->name()} @set_codes;
-
- my $attrib_string = join(":", @attrib_vals);
- my $set_string = join(":", @set_names);
+
+ my $attrib_string = join(":", map { $_->code()." => ".$_->value() } @attribs );;
+ my $set_string = join(":", map { $_->code() } @sets );
my $seqname = $f->slice->seq_region_name();
debug($seqname . ' ' . $f->start().'-'.$f->end().'('.$f->strand().
--
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