more work on AttributeAdaptor, still incomplete

modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm

@@ -78,32 +78,40 @@ sub new {
 
 =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
+  Arg [1]    : Bio::EnsEMBL::MiscFeature $mf
+  Example    : @attributes = @{$attrib_adaptor->fetch_all_by_MiscFeature($mf)};
+  Description: Fetches all attributes for a given MiscFeature
+  Returntype : Bio::EnsEMBL::Attribute
+  Exceptions : throw if incorrect arguments
+               throw if provided MiscFeature does not have a dbID
+  Caller     : MiscFeature
 
 =cut
 
+sub fetch_all_by_MiscFeature {
+  my $self = shift;
+  my $mf   = shift;
+}
 
 
 =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
+  Arg [1]    : Bio::EnsEMBL::Slice $slice
+  Example    : @attributes = @{$attrib_adaptor->fetch_all_by_Slice($slice)};
+  Description: Fetches all attributes for a given sequence region (which the
+               passed in slice is on)
+  Returntype : Bio::EnsEMBL::Attribute
+  Exceptions : throw if incorrect arguments
+               throw if cannot get seq_region_id from provided Slice
+  Caller     : Slice
 
 =cut
 
+sub fetch_all_by_Slice {
+  my $self = shift;
+  my $slice = shift;
+}
+
 
 
 =head2 fetch_all_types
@@ -127,49 +135,54 @@ sub fetch_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
+  Arg [2]    : listref of Bio::EnsEMBL::Attribute objects $attribs
+  Example    : $attribute_adaptor->store_on_Slice($slice, \@attribs);
+  Description: Stores a set of attributes on a sequence region given a
+               Slice object which is on the seq_region for which attributes are
+               being stored.
+  Returntype : none
+  Exceptions : throw if $slice argument not provided
+  Caller     : general
 
 =cut
 
-
 sub store_on_Slice {
-  my $self = shift;
-  my $slice = shift;
+  my $self     = shift;
+  my $slice    = shift;
+  my $attribs = shift;
 
-  # need to access directly to prevent lazy loading
-  my $attributes = $slice->{'???????'};
+  if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
+    throw("Slice argument expected.");
+  }
 
-  if( ! defined $attributes ) {
-    return;
+  if(ref($attribs) ne 'ARRAY') {
+    throw("Reference to list of Bio::EnsEMBL::Attribute objects " .
+          "argument expected.");
   }
 
   my $seq_region_id = $slice->get_seq_region_id();
 
-  if(  ! defined $seq_region_id ) {
-    throw( );
+  if(!$seq_region_id) {
+    throw("Could not get seq_region_id for provided slice: " $slice->name());
   }
 
   my $sth = $self->prepare( "INSERT into seq_region_attrib ".
-			    "SET seq_region_id = ?, attrib_type_id = ?, ".
-			    "value = ? " );
+                            "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() );
+  foreach my $at ( @$attribs ) {
+    if(!ref($at) && $at->isa('Bio::EnsEMBL::Attribute')) {
+      throw("Reference to list of Bio::EnsEMBL::Attribute objects " .
+            "argument expected.");
+    }
+    my $atid = $self->_store_type( $at );
+    $sth->execute( $seq_region_id, $attrib_id, $attrib->value() );
   }
 
   return;
-
 }
 
 
@@ -178,40 +191,49 @@ sub store_on_Slice {
 =head2 store_on_MiscFeature
 
   Arg [1]    : Bio::EnsEMBL::MiscFeature $feature
-  Example    : $attribute_adaptor->store_on_MiscFeature( $my_misc_feature )
+  Example    : $attribute_adaptor->store_on_MiscFeature($my_misc_feature,
+                                                        $attributes)
   Description: Stores all the attributes on the misc feature. 
                Will duplicate things if called twice.
   Returntype : none
-  Exceptions : on database problems.
+  Exceptions : throw on incorrect arguments
+               throw if provided feature is not stored in this database
   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'};
+  my $self       = shift;
+  my $feature    = shift;
+  my $attributes = shift;
 
-  if( ! defined $attributes ) {
-    return;
+  if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::MiscFeature')) {
+    throw("MiscFeature argument expected");
   }
 
-  my $feature_id = $feature->dbID();
+  if(ref($attributes) ne 'ARRAY') {
+    throw("Reference to list of Bio::EnsEMBL::Attribute objects argument " .
+          "expected");
+  }
 
-  if(  ! defined $feature_id ) {
-    throw("dbID in feature is not set.".
-	  "Need to store feature before storeing attributes.\n" );
+  my $db = $self->db();
+  if(!$feature->is_stored($db)) {
+    throw("MiscFeature is not stored in this DB - cannot store attributes.");
   }
 
+  my $feature_id = $feature->dbID();
+
   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, $attrib->value() );
+    if(!ref($at) && $at->isa('Bio::EnsEMBL::Attribute')) {
+      throw("Reference to list of Bio::EnsEMBL::Attribute objects " .
+            "argument expected.");
+    }
+    my $atid = $self->_store_type( $attrib );
+    $sth->execute( $feature_id, $atid, $attrib->value() );
   }
 
   return;
@@ -225,7 +247,6 @@ sub _store_type {
   my $self = shift;
   my $attrib = shift;
 
-  
   my $sth = $self->prepare
     ("INSERT IGNORE INTO attrib_type set code = ?, name = ?, ".
      "description = ?" );
@@ -236,7 +257,7 @@ sub _store_type {
 
   $sth->finish();
 
-  if( $self->db->db_handle->{'mysql_info'} == 0 ){
+  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 " .
@@ -248,7 +269,7 @@ sub _store_type {
 
     if(!$atid) {
       throw("Could not store or fetch attrib_type code [$code]\n" .
-	    "Wrong permissions?");
+	    "Wrong database user/permissions?");
     }
   }