LRGSlice fixes

modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm

@@ -366,13 +366,14 @@ sub _remap {
     Status:       Stable
 =cut
 
-    use Data::Dumper;
+#    use Data::Dumper;
 
 sub store{
     my $self = shift;
     my $asx = shift;
     my $asx2 = shift;
 
+
     if (! $asx->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
 	throw("$asx is not a Ensembl assemlby exception -- not stored");
     }
@@ -389,7 +390,7 @@ sub store{
     if ($asx->type !~ /PAR|HAP/){
 	throw("Only types of assembly exception features valid are PAR and HAP");
     }
-    if (! $asx->alternate_slice->isa('Bio::EnsEMBL::Slice')){
+    if ( !($asx->alternate_slice->isa('Bio::EnsEMBL::Slice') or $asx->alternate_slice->isa('Bio::EnsEMBL::LRGSlice')) ){
 	throw("Alternate slice should be a Bio::EnsEMBL::Slice");
     }
     #now check the other Assembly exception feature, the one pointing to the REF
@@ -403,8 +404,8 @@ sub store{
     if ($asx2->type !~ /HAP REF|PAR REF/){
 	throw("$asx2 should have  type of assembly exception features HAP REF or PAR REF");
     }
-    if (! $asx->alternate_slice->isa('Bio::EnsEMBL::Slice')){
-	throw("Alternate slice should be a Bio::EnsEMBL::Slice");
+    if (! ($asx2->alternate_slice->isa('Bio::EnsEMBL::Slice') or $asx2->alternate_slice->isa('Bio::EnsEMBL::LRGSlice'))){
+      throw("Alternate slice should be a Bio::EnsEMBL::Slice");
     }
     #finally check that both features are pointing to each other slice
     if ($asx->slice != $asx2->alternate_slice || $asx->alternate_slice != $asx2->slice){
@@ -487,7 +488,7 @@ sub _pre_store {
   my $slice_adaptor = $db->get_SliceAdaptor();
   my $slice = $feature->slice();
 
-  if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
+  if(!ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))  ) {
     throw('Feature must be attached to Slice to be stored.');
   }
 

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -218,7 +218,7 @@ sub fetch_all_by_Slice_constraint {
 
   my @result = ();
 
-  if(!ref($slice) || (!$slice->isa('Bio::EnsEMBL::Slice') && !$slice->isa('Bio::EnsEMBL::LRGSlice'))) {
+  if(!ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
     throw("Bio::EnsEMBL::Slice argument expected.");
   }
 
@@ -581,7 +581,7 @@ sub _pre_store {
   my $slice_adaptor = $db->get_SliceAdaptor();
   my $slice = $feature->slice();
 
-  if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
+  if(!ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))  ) {
     throw('Feature must be attached to Slice to be stored.');
   }
 
@@ -642,7 +642,7 @@ sub _pre_store_userdata {
   my $slice = $feature->slice();
   my $slice_adaptor = $slice->adaptor;
 
-  if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
+  if(!ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw('Feature must be attached to Slice to be stored.');
   }
 
@@ -927,7 +927,7 @@ sub remove {
 sub remove_by_Slice {
   my ($self, $slice) = @_;
 
-  if(!$slice || !ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
+  if(!$slice || !ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw("Slice argument is required");
   }
 

modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm

@@ -125,7 +125,7 @@ sub store{
    }
 
    my $slice = $feat->slice();
-   if(!defined($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
+   if(!defined($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
      throw("A slice must be attached to the features to be stored.");
    }
 

modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm

@@ -436,7 +436,7 @@ sub store {
     }
 
     my $slice = $rf->slice();
-    if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
+    if(!ref($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
       throw("RepeatFeature cannot be stored without an associated slice.");
     }
 

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -139,7 +139,7 @@ sub new {
 sub fetch_by_Slice_start_end_strand {
    my ( $self, $slice, $start, $end, $strand ) = @_;
 
-   if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
+   if(!ref($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
      throw("Slice argument is required.");
    }
 

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -559,7 +559,7 @@ sub get_seq_region_id {
   my $self = shift;
   my $slice = shift;
 
-  if(!$slice || !ref($slice) || (!$slice->isa('Bio::EnsEMBL::Slice') && !$slice->isa('Bio::EnsEMBL::LRGSlice'))) {
+  if(!$slice || !ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
     throw('Slice argument is required');
   }
   
@@ -1073,7 +1073,7 @@ sub fetch_by_Feature{
   }
 
   my $slice = $feature->slice();
-  if(!$slice || (!$slice->isa('Bio::EnsEMBL::Slice') && !$slice->isa('Bio::EnsEMBL::LRGSlice') )) {
+  if(!$slice || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice') )) {
     throw('Feature must be attached to a valid slice.');
   }
 
@@ -1361,7 +1361,7 @@ sub store {
   # Get all of the sanity checks out of the way before storing anything
   #
 
-  if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
+  if(!ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
     throw('Slice argument is required');
   }
 
@@ -1467,10 +1467,10 @@ sub store_assembly{
   # Get all of the sanity checks out of the way before storing anything
   #
 
-  if(!ref($asm_slice) || !$asm_slice->isa('Bio::EnsEMBL::Slice')) {
+  if(!ref($asm_slice) || !($asm_slice->isa('Bio::EnsEMBL::Slice') or $asm_slice->isa('Bio::EnsEMBL::LRGSlice'))) {
     throw('Assembled Slice argument is required');
   }
-  if(!ref($cmp_slice) || !$cmp_slice->isa('Bio::EnsEMBL::Slice')) {
+  if(!ref($cmp_slice) || !($cmp_slice->isa('Bio::EnsEMBL::Slice') or $cmp_slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw('Assembled Slice argument is required');
   }
 

modules/Bio/EnsEMBL/Exon.pm

@@ -837,7 +837,9 @@ sub transform {
   my $self = shift;
 
   # catch for old style transform calls
-  if( !@_  || ( ref $_[0] && $_[0]->isa( "Bio::EnsEMBL::Slice" ))) {
+  if( !@_  || ( ref $_[0] && 
+	       ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" ))
+	      )) {
     deprecate('Calling transform without a coord system name is deprecated.');
     return $self->_deprecated_transform(@_);
   }

modules/Bio/EnsEMBL/FeaturePair.pm

@@ -302,7 +302,7 @@ sub hslice {
 
   if(@_) {
     my $sl = shift;
-    if(defined($sl) && (!ref($sl) || !$sl->isa('Bio::EnsEMBL::Slice'))) {
+    if(defined($sl) && (!ref($sl) || !($sl->isa('Bio::EnsEMBL::Slice') or $sl->isa('Bio::EnsEMBL::Slice')) )) {
       throw('slice argument must be a Bio::EnsEMBL::Slice');
     }
 

modules/Bio/EnsEMBL/Gene.pm

@@ -925,7 +925,7 @@ sub transform {
   my $self = shift;
 
   # catch for old style transform calls
-  if( !@_  || ( ref $_[0] && $_[0]->isa( "Bio::EnsEMBL::Slice" ))) {
+  if( !@_  || ( ref $_[0] && ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" )) )) {
     deprecate('Calling transform without a coord system name is deprecated.');
     return $self->_deprecated_transform(@_);
   }

modules/Bio/EnsEMBL/MappedSlice.pm

@@ -211,7 +211,7 @@ sub add_Slice_Mapper_pair {
   my $mapper = shift;
 
   # argument check
-  unless ($slice and ref($slice) and $slice->isa('Bio::EnsEMBL::Slice')) {
+  unless ($slice and ref($slice) and ($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw("You must provide a slice.");
   }
 

modules/Bio/EnsEMBL/MappedSliceContainer.pm

@@ -154,7 +154,7 @@ sub new {
 
   # argument check
   unless ($ref_slice and ref($ref_slice) and
-          $ref_slice->isa('Bio::EnsEMBL::Slice')) {
+          ($ref_slice->isa('Bio::EnsEMBL::Slice') or $ref_slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw("You must provide a reference slice.");
   }
 
@@ -184,7 +184,7 @@ sub _create_container_slice {
 
   # argument check
   unless ($ref_slice and ref($ref_slice) and
-          $ref_slice->isa('Bio::EnsEMBL::Slice')) {
+          ($ref_slice->isa('Bio::EnsEMBL::Slice') or $ref_slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw("You must provide a reference slice.");
   }
 
@@ -483,7 +483,7 @@ sub ref_slice {
   if (@_) {
     my $slice = shift;
     
-    unless (ref($slice) and $slice->isa('Bio::EnsEMBL::Slice')) {
+    unless (ref($slice) and ($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
       throw("Need a Bio::EnsEMBL::Slice.");
     }
     
@@ -517,7 +517,7 @@ sub container_slice {
   if (@_) {
     my $slice = shift;
     
-    unless (ref($slice) and $slice->isa('Bio::EnsEMBL::Slice')) {
+    unless (ref($slice) and ($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
       throw("Need a Bio::EnsEMBL::Slice.");
     }
     

modules/Bio/EnsEMBL/PredictionExon.pm

@@ -185,7 +185,7 @@ sub transform {
   my $self = shift;
 
   # catch for old style transform calls
-  if( !@_ || ( ref $_[0] && $_[0]->isa( "Bio::EnsEMBL::Slice" ))) {
+  if( !@_ || ( ref $_[0] && ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" )))) {
     throw( "transform needs coordinate systems details now," .
            "please use transfer" );
   }

modules/Bio/EnsEMBL/PredictionTranscript.pm

@@ -409,7 +409,7 @@ sub transform {
   my $self = shift;
 
   # catch for old style transform calls
-  if( ref $_[0] && $_[0]->isa( "Bio::EnsEMBL::Slice" )) {
+  if( ref $_[0] && ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" ))) {
     throw("transform needs coordinate systems details now," .
           "please use transfer");
   }

modules/Bio/EnsEMBL/SeqFeature.pm

@@ -999,7 +999,7 @@ sub transform {
       # transform to slice coords from raw contig coords
       return $self->_transform_to_Slice($slice);
     }
-    elsif ($self->contig->isa( "Bio::EnsEMBL::Slice" )) {
+    elsif ($self->contig->isa( "Bio::EnsEMBL::Slice" ) or $self->contig->isa( "Bio::EnsEMBL::LRGSlice" )) {
 
       # transform to slice coords from other slice coords
       return $self->_transform_between_Slices($slice);
@@ -1088,7 +1088,7 @@ sub _transform_between_Slices {
   my $from_slice = $self->contig;
 
   $self->throw("New contig [$to_slice] is not a Bio::EnsEMBL::Slice")
-   unless $to_slice->isa("Bio::EnsEMBL::Slice");
+   unless ($to_slice->isa("Bio::EnsEMBL::Slice") or $to_slice->isa("Bio::EnsEMBL::LRGSlice") );
 
   if ((my $c1 = $from_slice->chr_name) ne (my $c2 = $to_slice->chr_name)) {
     $self->warn("Can't transform between chromosomes: $c1 and $c2");