Skip to content

GitLab

Commit 9f32ff54 authored by Graham McVicker's avatar Graham McVicker
Browse files

renamed many fetch_by_YYYYY methods to fetch_all_by_XXXX

parent 47b8c369
Hide whitespace changes
Inline Side-by-side
Showing with 859 additions and 204 deletions
modules/Bio/EnsEMBL/Clone.pm
View file @ 9f32ff54
......@@ -153,7 +153,7 @@ sub get_all_Contigs {
#from the database
unless ($c_list = $self->{'_contig_list'}) {
my $ra = $self->adaptor->db->get_RawContigAdaptor;
$c_list = $ra->fetch_by_Clone($self);
$c_list = $ra->fetch_all_by_Clone($self);
$self->{'_contig_list'} = $c_list;
}
......
modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
View file @ 9f32ff54
......@@ -54,7 +54,7 @@ use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
=head2 fetch_by_Contig_and_pid
=head2 fetch_all_by_RawContig_and_pid
Arg [1] : Bio::EnsEMBL::RawContig
the contig to obtain align features from
......@@ -62,18 +62,18 @@ use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
a lower bound for the percentage identifier of feats to obtain
Arg [3] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @feats = $adaptor->fetch_by_Contig_and_pid($contig, 50.0);
Description: Returns a list of features created from the database which are
are on the contig defined by $cid and with a percentage id
Example : $fts = $adaptor->fetch_all_by_RawContig_and_pid($contig, 50.0);
Description: Returns a listref of features created from the database which
are on the contig defined by $contig and with a percentage id
greater than $pid. If logic name is defined, only features
with an analysis of type $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::*AlignFeature in contig coordinates
Returntype : listref of Bio::EnsEMBL::BaseAlignFeature in contig coordinates
Exceptions : thrown if $pid is not defined
Caller : general
=cut
sub fetch_by_Contig_and_pid {
sub fetch_all_by_Contig_and_pid {
my($self, $contig, $pid, $logic_name) = @_;
my $constraint;
......@@ -82,11 +82,14 @@ sub fetch_by_Contig_and_pid {
$constraint = "perc_ident > $pid";
}
return $self->fetch_by_Contig_constraint($contig, $constraint, $logic_name);
return $self->fetch_all_by_Contig_constraint($contig,
$constraint, $logic_name);
}
=head2 fetch_by_Slice_and_pid
=head2 fetch_all_by_Slice_and_pid
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice from which to obtain align features.
......@@ -94,8 +97,8 @@ sub fetch_by_Contig_and_pid {
a lower bound for the percentage identifier of feats to obtain
Arg [3] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @feats = $adaptor->fetch_by_Slice_and_pid($slice, 50.0);
Description: Returns a list of features created from the database which are
Example : @feats = $adaptor->fetch_all_by_Slice_and_pid($slice, 50.0);
Description: Returns a listref of features created from the database which
are on the Slice $slice and with a percentage id
greater than $pid. If logic name is defined, only features
with an analysis of type $logic_name will be returned.
......@@ -105,7 +108,7 @@ sub fetch_by_Contig_and_pid {
=cut
sub fetch_by_Slice_and_pid {
sub fetch_all_by_Slice_and_pid {
my ($self,$slice,$pid, $logic_name) = @_;
my $constraint;
......@@ -113,7 +116,8 @@ sub fetch_by_Slice_and_pid {
$constraint = "perc_ident > $pid";
}
return $self->fetch_by_Slice_constraint($slice, $constraint, $logic_name);
return $self->fetch_all_by_Slice_constraint($slice, $constraint,
$logic_name);
}
......@@ -125,6 +129,47 @@ sub fetch_by_Slice_and_pid {
# _obj_from_hashref
=head2 fetch_by_Contig_and_pid
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_and_pid instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Contig_and_pid {
my ($self, @args) = @_;
$self->warn("fetch_by_Contig_and_pid has been renamed fetch_all_by_RawContig_and_pid\n" . caller);
return $self->fetch_all_by_RawContig_and_pid(@args);
}
=head2 fetch_by_Slice_and_pid
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice_and_pid instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Slice_and_pid {
my ($self, @args) = @_;
$self->warn("fetch_by_Slice_and_pid has been renamed fetch_all_by_Slice_and_pid\n" . caller);
return $self->fetch_all_by_Slice_and_pid(@args);
}
1;
modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
View file @ 9f32ff54
......@@ -86,10 +86,10 @@ sub new {
An SQL query constraint (i.e. part of the WHERE clause)
Arg [2] : (optional) string $logic_name
the logic_name of the analysis of the features to obtain
Example : @fts = $a->generic_fetch('contig_id in (1234, 1235)', 'swall');
Example : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
Description: Performs a database fetch and returns feature objects in
contig coordinates.
Returntype : list of Bio::EnsEMBL::*Feature in contig coordinates
Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
Exceptions : none
Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
......@@ -103,7 +103,8 @@ sub generic_fetch {
if($logic_name) {
#determine the analysis id via the logic_name
my $analysis = $self->db->get_AnalysisAdaptor()->fetch_by_logic_name($logic_name);
my $analysis =
$self->db->get_AnalysisAdaptor()->fetch_by_logic_name($logic_name);
unless(defined $analysis && $analysis->dbID() ) {
$self->warn("No analysis for logic name $logic_name exists\n");
return [];
......@@ -118,7 +119,8 @@ sub generic_fetch {
}
}
my $sql = "SELECT $columns FROM $tablename ".($constraint ? " where $constraint " : '' );
my $sql = "SELECT $columns FROM $tablename " .
($constraint ? " where $constraint " : '' );
my $sth = $self->prepare($sql);
$sth->execute;
return $self->_objs_from_sth($sth, $mapper, $slice);
......@@ -132,7 +134,7 @@ sub generic_fetch {
Example : $feat = $adaptor->fetch_by_dbID(1234);
Description: Returns the feature created from the database defined by the
the id $id.
Returntype : Bio::EnsEMBL::*Feature
Returntype : Bio::EnsEMBL::SeqFeature
Exceptions : thrown if $id is not defined
Caller : general
......@@ -154,7 +156,7 @@ sub fetch_by_dbID{
}
=head2 fetch_by_Contig_constraint
=head2 fetch_all_by_Contig_constraint
Arg [1] : Bio::EnsEMBL::RawContig $contig
The contig object from which features are to be obtained
......@@ -162,18 +164,18 @@ sub fetch_by_dbID{
An SQL query constraint (i.e. part of the WHERE clause)
Arg [3] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @fts = $a->fetch_by_Contig_constraint($contig, 'perc_ident>5.0');
Description: Returns a list of features created from the database which are
Example : $fs = $a->fetch_all_by_Contig_constraint($ctg,'perc_ident>5.0');
Description: Returns a listref of features created from the database which
are on the contig defined by $cid and fulfill the SQL constraint
defined by $constraint. If logic name is defined, only features
with an analysis of type $logic_name will be returned.
Returntype : list of Bio::EnsEMBL::*Feature in contig coordinates
Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
Exceptions : thrown if $cid is not defined
Caller : general
=cut
sub fetch_by_Contig_constraint {
sub fetch_all_by_Contig_constraint {
my ($self, $contig, $constraint, $logic_name) = @_;
unless( defined $contig ) {
......@@ -196,32 +198,32 @@ sub fetch_by_Contig_constraint {
}
=head2 fetch_by_Contig
=head2 fetch_all_by_Contig
Arg [1] : Bio::EnsEMBL::RawContig $contig
the contig from which features should be obtained
Arg [2] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @fts = $a->fetch_by_Contig($contig, 'swall');
Example : @fts = $a->fetch_all_by_Contig($contig, 'wall');
Description: Returns a list of features created from the database which are
are on the contig defined by $cid If logic name is defined,
only features with an analysis of type $logic_name will be
returned.
Returntype : list of Bio::EnsEMBL::*Feature in contig coordinates
Returntype : listref of Bio::EnsEMBL::*Feature in contig coordinates
Exceptions : none
Caller : general
=cut
sub fetch_by_Contig{
sub fetch_all_by_Contig{
my ($self, $contig, $logic_name) = @_;
#fetch by contig id constraint with empty constraint
return $self->fetch_by_Contig_constraint($contig, '',$logic_name);
return $self->fetch_all_by_Contig_constraint($contig, '',$logic_name);
}
=head2 fetch_by_Contig_and_score
=head2 fetch_all_by_Contig_and_score
Arg [1] : Bio::EnsEMBL::RawContig $contig
the contig from which features should be obtained
......@@ -229,18 +231,18 @@ sub fetch_by_Contig{
the lower bound of the score of the features to obtain
Arg [3] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @fts = $a->fetch_by_Contig_and_score(1, 50.0, 'swall');
Example : @fts = $a->fetch_by_Contig_and_score(1, 50.0, 'Swall');
Description: Returns a list of features created from the database which are
are on the contig defined by $cid and which have score greater
than score. If logic name is defined, only features with an
analysis of type $logic_name will be returned.
Returntype : list of Bio::EnsEMBL::*Feature in contig coordinates
Returntype : listref of Bio::EnsEMBL::*Feature in contig coordinates
Exceptions : thrown if $score is not defined
Caller : general
=cut
sub fetch_by_Contig_and_score{
sub fetch_all_by_Contig_and_score{
my($self, $contig, $score, $logic_name) = @_;
my $constraint;
......@@ -249,36 +251,37 @@ sub fetch_by_Contig_and_score{
$constraint = "score > $score";
}
return $self->fetch_by_Contig_constraint($contig, $constraint, $logic_name);
return $self->fetch_all_by_Contig_constraint($contig, $constraint,
$logic_name);
}
=head2 fetch_by_Slice
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
the slice from which to obtain features
Arg [2] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @fts = $a->fetch_by_Slice($slice, 'swall');
Description: Returns a list of features created from the database which are
are on the Slice defined by $slice.If $logic_name is defined,
only features with an analysis of type $logic_name will be
returned.
Returntype : list of Bio::EnsEMBL::*Feature in Slice coordinates
Example : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
Description: Returns a listref of features created from the database
which are on the Slice defined by $slice. If $logic_name is
defined only features with an analysis of type $logic_name
will be returned.
Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
Exceptions : none
Caller : Bio::EnsEMBL::Slice
=cut
sub fetch_by_Slice {
sub fetch_all_by_Slice {
my ($self, $slice, $logic_name) = @_;
#fetch by constraint with empty constraint
return $self->fetch_by_Slice_constraint($slice, '', $logic_name);
return $self->fetch_all_by_Slice_constraint($slice, '', $logic_name);
}
=head2 fetch_by_Slice_and_score
=head2 fetch_all_by_Slice_and_score
Arg [1] : Bio::EnsEMBL::Slice $slice
the slice from which to obtain features
......@@ -286,19 +289,19 @@ sub fetch_by_Slice {
lower bound of the the score of the features retrieved
Arg [3] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @fts = $a->fetch_by_Slice($slice, 'swall');
Example : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
Description: Returns a list of features created from the database which are
are on the Slice defined by $slice and which have a score
greated than $score. If $logic_name is defined,
only features with an analysis of type $logic_name will be
returned.
Returntype : list of Bio::EnsEMBL::*Feature in Slice coordinates
Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
Exceptions : none
Caller : Bio::EnsEMBL::Slice
=cut
sub fetch_by_Slice_and_score {
sub fetch_all_by_Slice_and_score {
my ($self, $slice, $score, $logic_name) = @_;
my $constraint;
......@@ -306,12 +309,12 @@ sub fetch_by_Slice_and_score {
$constraint = "score > $score";
}
return $self->fetch_by_Slice_constraint($slice, $constraint, $logic_name);
#&eprof_end('transform');
return $self->fetch_all_by_Slice_constraint($slice, $constraint,
$logic_name);
}
=head2 fetch_by_Slice_constraint
=head2 fetch_all_by_Slice_constraint
Arg [1] : Bio::EnsEMBL::Slice $slice
the slice from which to obtain features
......@@ -319,19 +322,19 @@ sub fetch_by_Slice_and_score {
An SQL query constraint (i.e. part of the WHERE clause)
Arg [3] : (optional) string $logic_name
the logic name of the type of features to obtain
Example : @fts = $a->fetch_by_Slice_constraint($slice, 'perc_ident > 5');
Description: Returns a list of features created from the database which are
Example : $fs = $a->fetch_all_by_Slice_constraint($slc, 'perc_ident > 5');
Description: Returns a listref of features created from the database which
are on the Slice defined by $slice and fulfill the SQL
constraint defined by $constraint. If logic name is defined,
only features with an analysis of type $logic_name will be
returned.
Returntype : list of Bio::EnsEMBL::*Feature in Slice coordinates
Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
Exceptions : thrown if $slice is not defined
Caller : Bio::EnsEMBL::Slice
=cut
sub fetch_by_Slice_constraint {
sub fetch_all_by_Slice_constraint {
my($self, $slice, $constraint, $logic_name) = @_;
unless(defined $slice && ref $slice && $slice->isa("Bio::EnsEMBL::Slice")) {
......@@ -342,15 +345,18 @@ sub fetch_by_Slice_constraint {
$logic_name = '' unless defined $logic_name;
my $key = join($slice->name, $constraint, $logic_name);
return $self->{'_slice_feature_cache'}{$key} if $self->{'_slice_feature_cache'}{$key};
return $self->{'_slice_feature_cache'}{$key}
if $self->{'_slice_feature_cache'}{$key};
my $chr_start = $slice->chr_start();
my $chr_end = $slice->chr_end();
my $mapper = $self->db->get_AssemblyMapperAdaptor->fetch_by_type($slice->assembly_type);
my $mapper =
$self->db->get_AssemblyMapperAdaptor->fetch_by_type($slice->assembly_type);
#get the list of contigs this slice is on
my @cids = $mapper->list_contig_ids( $slice->chr_name, $chr_start ,$chr_end );
my @cids =
$mapper->list_contig_ids( $slice->chr_name, $chr_start ,$chr_end );
return [] unless scalar(@cids);
......@@ -363,14 +369,15 @@ sub fetch_by_Slice_constraint {
$constraint = "contig_id IN ($cid_list)";
}
my $features = $self->generic_fetch($constraint, $logic_name, $mapper, $slice);
my $features =
$self->generic_fetch($constraint, $logic_name, $mapper, $slice);
if(@$features && $features->[0]->contig == $slice) {
#features have been converted to slice coords already, cache and return
return $self->{'_slice_feature_cache'}{$key} = $features;
}
my @out;
my @out = ();
#convert the features to slice coordinates from raw contig coordinates
......@@ -379,10 +386,13 @@ sub fetch_by_Slice_constraint {
my $contig_id = $f->contig->dbID();
my ($chr_name, $start, $end, $strand) =
$mapper->fast_to_assembly($contig_id, $f->start(), $f->end(),$f->strand(),"rawcontig");
$mapper->fast_to_assembly($contig_id, $f->start(),
$f->end(),$f->strand(),"rawcontig");
next unless defined $start; # not defined start means gap
next if ($start > $chr_end) || ($end <= $chr_start); # maps to region outside desired area
# not defined start means gap
next unless defined $start;
# maps to region outside desired area
next if ($start > $chr_end) || ($end <= $chr_start);
#shift the feature start, end and strand in one call
$f->move( $start - $chr_start, $end - $chr_start, $strand );
......@@ -398,7 +408,7 @@ sub fetch_by_Slice_constraint {
=head2 store
Arg [1] : list of Bio::EnsEMBL::*Feature
Arg [1] : list of Bio::EnsEMBL::SeqFeature
Example : $adaptor->store(@feats);
Description: ABSTRACT Subclasses are responsible for implementing this
method. It should take a list of features and store them in
......@@ -543,6 +553,133 @@ sub deleteObj {
%{$self->{'_slice_feature_cache'}} = ();
}
=head2 fetch_by_Contig_constraint
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Contig_constraint {
my ($self, @args) = @_;
$self->warn("fetch_by_Contig_constraint has been renamed fetch_all_by_RawContig_constraint\n" . caller);
return $self->fetch_all_by_RawContig_constraint(@args);
}
=head2 fetch_by_Contig
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Contig {
my ($self, @args) = @_;
$self->warn("fetch_by_Contig has been renamed fetch_all_by_RawContig\n" . caller);
return $self->fetch_all_by_RawContig(@args);
}
=head2 fetch_by_Contig_and_score
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_RawContig_and_score instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Contig_and_score {
my ($self, @args) = @_;
$self->warn("fetch_by_Contig_and_score has been renamed fetch_all_by_RawContig_and_score\n" . caller);
return $self->fetch_all_by_RawContig_and_score(@args);
}
=head2 fetch_by_Slice_and_score
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice_and_score instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Slice_and_score {
my ($self, @args) = @_;
$self->warn("fetch_by_Slice_and_score has been renamed fetch_all_by_Slice_and_score\n" . caller);
return $self->fetch_all_by_Slice_and_score(@args);
}
=head2 fetch_by_Slice_constraint
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice_constraint instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Slice_constraint {
my ($self, @args) = @_;
$self->warn("fetch_by_Slice_constraint has been renamed fetch_all_by_Slice_constraint\n" . caller);
return $self->fetch_all_by_Slice_constraint(@args);
}
=head2 fetch_by_Slice
Arg [1] : none
Example : none
Description: DEPRECATED use fetch_all_by_Slice instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub fetch_by_Slice {
my ($self, @args) = @_;
$self->warn("fetch_by_Slice has been renamed fetch_all_by_Slice\n" . caller);
return $self->fetch_all_by_Slice(@args);
}
1;
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
View file @ 9f32ff54
......@@ -303,7 +303,7 @@ sub store {
=head2 fetch_by_Gene
=head2 fetch_all_by_Gene
Arg [1] : Bio::EnsEMBL::Gene $gene
The gene to retrienve DBEntries for
......@@ -315,7 +315,7 @@ sub store {
=cut
sub fetch_by_Gene {
sub fetch_all_by_Gene {
my ( $self, $gene ) = @_;
my $query1 = "SELECT t.translation_id
......@@ -343,7 +343,7 @@ sub fetch_by_Gene {
=head2 fetch_by_RawContig
=head2 fetch_all_by_RawContig
Arg [1] : Bio::EnsEMBL::RawContig $contig
Example : @db_entries = @{$db_entry_adaptor->fetch_by_RawContig($contig)}
......@@ -354,13 +354,13 @@ sub fetch_by_Gene {
=cut
sub fetch_by_RawContig {
sub fetch_all_by_RawContig {
my ( $self, $contig ) = @_;
return $self->_fetch_by_object_type($contig->dbID, 'RawContig' );
}
=head2 fetch_by_Transcript
=head2 fetch_all_by_Transcript