initial AttributeAdaptor. Used by Slice and SliceAdaptor to store Attribute...

initial AttributeAdaptor. Used by Slice and SliceAdaptor to store Attribute objects. Used by MiscFeature and MiscFeatureAdaptor as well

modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm

+#
+# Ensembl module for Bio::EnsEMBL::DBSQL::AttributeAdaptor
+#
+# Copyright (c) 2003 EnsEMBL
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::AttributeAdaptor - Provides database interaction for
+Bio::EnsEMBL::Attribute objects.
+
+
+=head1 SYNOPSIS
+
+  #$db is a Bio::EnsEMBL::DBSQL::DBAdaptor object:
+  $attribute_adaptor = $db->get_AttributeAdaptor();
+
+  $attributes = $attribute_adaptor->fetch_all_by_MiscFeature( $feature );
+
+  $attributes = $attribute_adaptor->fetch_all_by_Slice( $slice );
+
+  $attribute_types = $attribute_adaptor->fetch_all_types();
+
+  $attribute_adaptor->store_on_Slice( $slice, $attributes );
+
+  $attribute_adaptor->store_on_MiscFeature( $misc_feature, $attributes )
+
+
+=head1 DESCRIPTION
+
+
+=head1 CONTACT
+
+This modules is part of the Ensembl project http://www.ensembl.org
+
+Questions can be posted to the ensembl-dev mailing list:
+ensembl-dev@ebi.ac.uk
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::DBSQL::AttributeAdaptor;
+
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::Attribute;
+
+use vars qw(@ISA);
+
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+
+
+=head2 new
+
+  Arg [...]  : Superclass args.  See Bio::EnsEMBL::DBSQL::BaseAdaptor
+  Description: Instantiates a Bio::EnsEMBL::DBSQL::AttributeAdaptor
+  Returntype : Bio::EnsEMBL::AttributeAdaptor
+  Exceptions : none
+  Caller     : DBAdaptor
+
+=cut
+
+
+sub new {
+  my $class = shift;
+
+  my $self = $class->SUPER::new(@_);
+
+  # cache creation could go here
+  return $self;
+}
+
+
+
+=head2 fetch_all_by_MiscFeature
+
+  Arg [1]    : none, string, int, Bio::EnsEMBL::Example $formal_parameter_name
+    Additional description lines
+    list, listref, hashref
+  Example    :  ( optional )
+  Description: testable description
+  Returntype : none, txt, int, float, Bio::EnsEMBL::Example
+  Exceptions : none
+  Caller     : object::methodname or just methodname
+
+=cut
+
+
+
+=head2 fetch_all_by_Slice
+
+  Arg [1]    : none, string, int, Bio::EnsEMBL::Example $formal_parameter_name
+    Additional description lines
+    list, listref, hashref
+  Example    :  ( optional )
+  Description: testable description
+  Returntype : none, txt, int, float, Bio::EnsEMBL::Example
+  Exceptions : none
+  Caller     : object::methodname or just methodname
+
+=cut
+
+
+
+=head2 fetch_all_types
+
+  Arg [1]    : none, string, int, Bio::EnsEMBL::Example $formal_parameter_name
+    Additional description lines
+    list, listref, hashref
+  Example    :  ( optional )
+  Description: testable description
+  Returntype : none, txt, int, float, Bio::EnsEMBL::Example
+  Exceptions : none
+  Caller     : object::methodname or just methodname
+
+=cut
+
+sub fetch_all_types {
+  my $self = shift;
+
+  return $all_types;
+}
+
+
+
+
+
+
+=head2 store_on_Slice
+
+  Arg [1]    : Bio::EnsEMBL::Slice $slice
+  Example    :  ( optional )
+  Description: testable description
+  Returntype : none, txt, int, float, Bio::EnsEMBL::Example
+  Exceptions : none
+  Caller     : object::methodname or just methodname
+
+=cut
+
+
+sub store_on_Slice {
+  my $self = shift;
+  my $slice = shift;
+
+  # need to access directly to prevent lazy loading
+  my $attributes = $slice->{'???????'};
+
+  if( ! defined $attributes ) {
+    return;
+  }
+
+  my $seq_region_id = $slice->get_seq_region_id();
+
+  if(  ! defined $seq_region_id ) {
+    throw( );
+  }
+
+  my $sth = $self->prepare( "INSERT into seq_region_attrib ".
+			    "SET seq_region_id = ?, attrib_type_id = ?, ".
+			    "value = ? " );
+
+  for my $attrib ( @$attributes ) {
+    my $attrib_id = $self->_store_type( $attrib );
+    $sth->excute( $seq_region_id, $attrib_id, $attrib->value() );
+  }
+
+  return;
+
+}
+
+
+
+
+=head2 store_on_MiscFeature
+
+  Arg [1]    : Bio::EnsEMBL::MiscFeature $feature
+  Example    : $attribute_adaptor->store_on_MiscFeature( $my_misc_feature )
+  Description: Stores all the attributes on the misc feature. 
+               Will duplicate things if called twice.
+  Returntype : none
+  Exceptions : on database problems.
+  Caller     : general, MiscFeatureAdaptor
+
+=cut
+
+sub store_on_MiscFeature {
+  my $self = shift;
+  my $feature = shift;
+
+  # need to access directly to prevent lazy loading
+  my $attributes = $feature->{'attributes'};
+
+  if( ! defined $attributes ) {
+    return;
+  }
+
+  my $feature_id = $feature->dbID();
+
+  if(  ! defined $feature_id ) {
+    throw("dbID in feature is not set.".
+	  "Need to store feature before storeing attributes.\n" );
+  }
+
+  my $sth = $self->prepare( "INSERT into misc_attrib ".
+			    "SET misc_feature_id = ?, attrib_type_id = ?, ".
+			    "value = ? " );
+
+  for my $attrib ( @$attributes ) {
+    my $attrib_id = $self->_store_type( $attrib );
+    $sth->excute( $feature_id, $attrib_id, $attrib->value() );
+  }
+
+  return;
+}
+
+
+
+# _store_type 
+
+sub _store_type {
+  my $self = shift;
+  my $attrib = shift;
+
+  
+  my $sth = $self->prepare
+    ("INSERT IGNORE INTO attrib_type set code = ?, name = ?, ".
+     "description = ?" );
+
+  $sth->execute($attrib->code(), $attrib->name(), $attrib->description() );
+
+  my $atid = $sth->{'mysql_insertid'};
+
+  $sth->finish();
+
+  if( $self->db->db_handle->{'mysql_info'} == 0 ){
+    # the insert failed because the code is already stored
+    $sth = $self->prepare
+      ("SELECT attrib_type_id FROM attrib_type " .
+       "WHERE code = ?");
+    $sth->execute($code);
+    ($atid) = $sth->fetchrow_array();
+
+    $sth->finish();
+
+    if(!$atid) {
+      throw("Could not store or fetch attrib_type code [$code]\n" .
+	    "Wrong permissions?");
+    }
+  }
+
+  return $atid;
+}
+
+
+sub _obj_from_sth {
+  my $self = shift;
+  my $sth = shift;
+
+  return $results;
+}
+
+
+
+
+#
+# Called during db destruction to clean up internal cache structures
+# that result in circular references
+#
+sub deleteObj {
+  my $self = shift;
+
+  #break circular db <-> adaptor references
+  $self->SUPER::deleteObj();
+
+  #break circular object <-> adaptor references
+
+}
+
+
+1;