diff variant_effect_predictor/Bio/EnsEMBL/DB/ExternalFeatureFactoryI.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/EnsEMBL/DB/ExternalFeatureFactoryI.pm	Thu Apr 11 02:01:53 2013 -0400
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+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DB::ExternalFeatureFactoryI -
+Legacy Abstract interface for External Feature
+Factories. Bio::EnsEMBL::External::ExternalFeatureAdaptor should be used
+instead if possible.
+
+=head1 SYNOPSIS
+
+  $external_ff = new ImplementingExternalFeatureFactoryClass;
+
+  $database_adaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+    -host   => 'blah',
+    -dbname => 'other',
+    -pass   => 'pass'
+  );
+
+  # alternatively, you can add external databases to an obj once made
+  $database_adaptor->add_ExternalFeatureFactory($external_ff);
+
+  # now the ExternalFeatureFactory has been added, Ensembl RawContigs
+  # and Slices will now have ExternalFeatures on them
+  $contig =
+    $db_adaptor->get_RawContigAdaptor->fetch_by_name('AC00056.00001');
+  @external = @{ $contig->get_all_ExternalFeatures() };
+
+  # this works on Slices as well
+  $slice =
+    $db_adaptor->get_SliceAdaptor->fetch_by_chr_start_end( '12', 10000,
+    30000 );
+  @external = @{ $slice->get_all_ExternalFeatures() };
+
+=head1 DESCRIPTION
+
+This is a legacy class.  It is included only for backwards
+compatibility with ExternalFeatureFactories which are presumably
+still used to place data into ensembl.  It is recommended that if
+you wish to create EnsEMBL features externally that you use the
+Bio::EnsEMBL::External::ExternalFeatureAdaptor instead.
+
+This object defines the abstract interface for External Database access
+inside Ensembl. The aim is that one can attach an External Database
+which will generate Sequence Features and these Sequence Features will
+be accessible along side all the internal Ensembl sequence features, for
+drawing, EMBL dumping etc. In particular, the external database does not
+have to worry about the transformation of the Sequence Feature objects
+into VirtualContigs.
+
+Sequence Features have to be defined in one of two coordinate systems:
+Original EMBL/GenBank coordinates of a particular sequnence version or
+the Ensembl contig coordinates. This means you have to calculate your
+sequence features in one these two coordinate systems
+
+The methods that have to be implemented are:
+
+  get_External_SeqFeatures_contig( $ensembl_contig_identifier,
+    $sequence_version, $start, $end );
+
+  get_External_SeqFeatures_clone( $embl_accession_number,
+    $sequence_version, $start, $end );
+
+The semantics of this method is as follows:
+
+  $ensembl_contig_identifier - the ensembl contig id (external id).
+  $sequence_version - embl/genbank sequence version
+  $embl_accession_number - the embl/genbank accession number
+
+The $start/$end can be ignored, but methods can take advantage of it.
+This is so that ensembl can ask for features only on a region of DNA,
+and if desired, the external database can respond with features only in
+this region, rather than the entire sequence.
+
+The hope is that the second method could potentially have a very complex
+set of mappings of other embl_accession numbers to one embl_accession
+number and provide the complex mapping.
+
+The methods should return Sequence Features with the following spec:
+
+  a) must implement the Bio::SeqFeatureI interface.
+
+  b) must accept "set" calls on 
+
+  start,end,strand
+
+  to provide coordinate transformation of the feature.
+
+  c) must be unique in-memory objects, ie, the implementation is not
+  allowed to cache the sequence feature in its entirity. Two separate
+  calls to get_External_SeqFeatures_contig must be able to separately
+  set start,end,strand information without clobbering each other. The
+  other information, if so wished, can be cached by each SeqFeature
+  holding onto another object, but this is left to the implementor to
+  decide on the correct strategy.
+
+  d) must return an unique identifier when called with method id.
+
+You must implement both functions. In most cases, one function will
+always return an empty list, whereas the other function will actually
+query the external database.
+
+The second way of accessing the External Database from Ensembl is using
+unique internal identifiers in that database. The method is:
+
+  get_SeqFeature_by_id($id);
+
+It should return exactly one Sequence Feature object of the same type as
+above.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::DB::ExternalFeatureFactoryI;
+use Bio::EnsEMBL::External::ExternalFeatureAdaptor;
+use vars qw(@ISA);
+
+@ISA = ( 'Bio::EnsEMBL::External::ExternalFeatureAdaptor' );
+
+
+=head2 coordinate_systems
+
+  Arg [1]    : none
+  Example    : none
+  Description: This method is present to make the ExternalFeatureFactory 
+               interface behave as an ExternalFeatureAdaptor. It is for
+               backwards compatibility.
+  Returntype : none
+  Exceptions : none
+  Caller     : internal
+
+=cut
+
+sub coordinate_systems {
+  my $self = shift;
+  return qw(CONTIG);
+}
+
+
+=head2 fetch_all_by_contig_name
+
+  Arg [1]    : none
+  Example    : none
+  Description: This method is present to make the ExternalFeatureFactory 
+               interface behave as an ExternalFeatureAdaptor. It is for
+               backwards compatibility.
+  Returntype : none
+  Exceptions : none
+  Caller     : internal
+
+=cut
+
+sub fetch_all_by_contig_name {
+   my ($self, $contig_name) = @_;
+
+   unless($self->db) {
+     $self->throw('DB attribute not set.  This value must be set for the ' .
+		  'ExternalFeatureFactory to function correctly');
+   }
+
+   my @features = ();
+
+   my $ctg = $self->db->get_RawContigAdaptor->fetch_by_name($contig_name);
+   my $clone = $ctg->clone;
+   my $version = $clone->version;
+   my $ctg_length = $ctg->length;
+   
+   #get contig features
+   push @features, $self->get_Ensembl_SeqFeatures_contig($ctg->name, 
+							 $version, 
+							 1,
+							 $ctg_length);
+
+   #get clone features
+   my $clone_start = $ctg->embl_offset;
+   my $clone_end   = $clone_start + $ctg_length - 1;
+   my @clone_features = $self->get_Ensembl_SeqFeatures_clone($clone->id,
+							     $version,
+							     $clone_start,
+							     $clone_end);
+
+   #change clone coordinates to contig coordinates
+   my ($start, $end); 
+   foreach my $f (@clone_features) {
+     $start = $f->start - $clone_start + 1;
+     $end   = $f->end   - $clone_start + 1;
+
+     #skip features outside the contig
+     next if($end < 1 || $start > $ctg_length);
+
+     $f->start($start);
+     $f->end($end);
+
+     push @features, $f;
+   }
+
+   return \@features;
+}
+
+=head2 get_Ensembl_SeqFeatures_contig
+
+ Title   : get_Ensembl_SeqFeatures_contig (Abstract)
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub get_Ensembl_SeqFeatures_contig{
+   my ($self) = @_;
+
+   $self->warn("Abstract method get_External_SeqFeatures_contig " .
+	    "encountered in base class. Implementation failed to complete it");
+
+}
+
+=head2 get_Ensembl_SeqFeatures_clone
+
+ Title   : get_Ensembl_SeqFeatures_clone (Abstract)
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub get_Ensembl_SeqFeatures_clone{
+   my ($self) = @_;
+   
+   $self->warn("Abstract method get_Ensembl_SeqFeatures_clone " .
+	    "encountered in base class. Implementation failed to complete it");
+
+}
+
+=head2 get_Ensembl_Genes_clone
+
+ Title   : get_Ensembl_Genes_clone
+ Function: returns Gene objects in clone coordinates from a gene id
+ Returns : An array of Gene objects
+ Args    : clone id
+
+=cut
+
+sub get_Ensembl_Genes_clone {
+    my $self = @_;
+
+    return;
+}
+
+=head2 get_SeqFeature_by_id
+
+ Title   : get_SeqFeature_by_id (Abstract)
+ Usage   : 
+ Function: Return SeqFeature object for any valid unique id  
+ Example :
+ Returns : 
+ Args    : id as determined by the External Database
+
+
+=cut
+
+       
+sub get_SeqFeature_by_id {
+   my ($self) = @_;
+   $self->warn("Abstract method get_SeqFeature_by_id  encountered " .
+	       "in base class. Implementation failed to complete it");
+}
+
+
+1;
+
+
+
+
+
+
+