fix for ChainedAssemblyMapper to map using the destination slice if one is...

fix for ChainedAssemblyMapper to map using the destination slice if one is provided http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-108

modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm

@@ -404,8 +404,16 @@ sub _objs_from_sth {
 
       my $len = $seq_region_end - $seq_region_start + 1;
 
-      my @coords =
-        $mapper->map($sr_name, $seq_region_start, $seq_region_end,1, $sr_cs);
+      my @coords;
+
+      if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    
+	  @coords = $mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          1, $sr_cs, 0, $dest_slice);
+
+      } else {
+	  @coords = $mapper->map($sr_name, $seq_region_start, $seq_region_end,1, $sr_cs);
+      }
 
       #filter out gaps
       @coords = grep {!$_->isa('Bio::EnsEMBL::Mapper::Gap')} @coords;

modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm

@@ -466,11 +466,22 @@ FEATURE:
     # Remap the feature coordinates to another coord system
     # if a mapper was provided.
     if ( defined($mapper) ) {
-      ( $seq_region_id,  $seq_region_start,
-        $seq_region_end, $seq_region_strand )
-        =
-        $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+
+	if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+	} else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
                           $seq_region_strand, $sr_cs );
+	}
 
       # Skip features that map to gaps or coord system boundaries.
       if ( !defined($seq_region_id) ) { next FEATURE }

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -617,11 +617,22 @@ FEATURE: while ( $sth->fetch() ) {
     # was provided.
     #
     if ( defined($dest_mapper) ) {
-      ( $seq_region_id,  $seq_region_start,
-        $seq_region_end, $seq_region_strand )
-        = $dest_mapper->fastmap( $sr_name, $seq_region_start,
+
+      if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+      } else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		= $dest_mapper->fastmap( $sr_name, $seq_region_start,
                                  $seq_region_end, $seq_region_strand,
                                  $sr_cs );
+      }
 
       # Skip features that map to gaps or coord system boundaries.
       if ( !defined($seq_region_id) ) { next FEATURE }

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -1681,9 +1681,21 @@ sub _objs_from_sth {
     #
     if($mapper) {
 
-      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-        $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-			 $seq_region_strand, $sr_cs);
+	if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+	} else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs );
+	}
 
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));

modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm

@@ -437,9 +437,17 @@ sub _objs_from_sth {
       #
       if ($mapper) {
 
-        ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-          $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-                           $seq_region_strand, $sr_cs);
+
+	if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,$seq_region_end, $seq_region_strand ) =
+	       $mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+	} else {
+
+	    ( $seq_region_id,  $seq_region_start,$seq_region_end, $seq_region_strand ) =
+	       $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,$seq_region_strand, $sr_cs );
+	}
 
         #skip features that map to gaps or coord system boundaries
         if(!defined($seq_region_id)) {

modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm

@@ -708,10 +708,22 @@ sub _objs_from_sth {
 		#
 		if ($mapper) {
 
-			(  $seq_region_id,  $seq_region_start,
-			   $seq_region_end, $seq_region_strand )
-			  = $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
-								  $seq_region_strand, $sr_cs );
+
+		    if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+			( $seq_region_id,  $seq_region_start,
+			  $seq_region_end, $seq_region_strand )
+			    =
+			    $mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+					  $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+		    } else {
+
+			( $seq_region_id,  $seq_region_start,
+			  $seq_region_end, $seq_region_strand )
+			    =
+			    $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+					      $seq_region_strand, $sr_cs );
+		    }
 
 			#skip features that map to gaps or coord system boundaries
 			next OPERON if ( !defined($seq_region_id) );

modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm

@@ -790,11 +790,23 @@ sub _objs_from_sth {
 		#
 		if ($mapper) {
 
-			(  $seq_region_id,  $seq_region_start,
-			   $seq_region_end, $seq_region_strand )
-			  = $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
-								  $seq_region_strand, $sr_cs );
-
+		    if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+			( $seq_region_id,  $seq_region_start,
+			  $seq_region_end, $seq_region_strand )
+			    =
+			    $mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+					  $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+		    } else {
+
+			( $seq_region_id,  $seq_region_start,
+			  $seq_region_end, $seq_region_strand )
+			    =
+			    $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+					      $seq_region_strand, $sr_cs );
+		    }
+
+		
 			#skip features that map to gaps or coord system boundaries
 			next OPERON if ( !defined($seq_region_id) );
 

modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm

@@ -389,9 +389,21 @@ sub _objs_from_sth {
     #
     if($dest_mapper) {
 
-      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-        $dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-                              $seq_region_strand, $sr_cs);
+      if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+      } else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		= $dest_mapper->fastmap( $sr_name, $seq_region_start,
+                                 $seq_region_end, $seq_region_strand,
+                                 $sr_cs );
+      }
 
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));

modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm

@@ -351,9 +351,21 @@ sub _objs_from_sth {
     #
     if($mapper) {
 
-      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-        $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-			 $seq_region_strand, $sr_cs);
+      if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+      } else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs );
+      }
 
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));

modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm

@@ -255,9 +255,21 @@ sub _objs_from_sth {
     #
     if($mapper) {
 
-      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-        $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-                          $seq_region_strand, $sr_cs);
+	if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+	} else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs );
+	}
 
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));

modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm

@@ -273,9 +273,21 @@ sub _objs_from_sth {
     #
     if($mapper) {
 
-      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-        $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-                          $seq_region_strand, $sr_cs);
+      if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+      } else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs );
+      }
 
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));

modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm

@@ -260,9 +260,21 @@ sub _objs_from_sth {
     #
     if($mapper) {
 
-      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-        $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-                          $seq_region_strand, $sr_cs);
+      if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+      } else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs );
+      }
 
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));

modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm

@@ -459,11 +459,22 @@ FEATURE:
     # Remap the feature coordinates to another coord system if a mapper
     # was provided.
     if ( defined($dest_mapper) ) {
-      ( $seq_region_id,  $seq_region_start,
-        $seq_region_end, $seq_region_strand )
-        = $dest_mapper->fastmap( $sr_name, $seq_region_start,
+
+      if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+      } else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		= $dest_mapper->fastmap( $sr_name, $seq_region_start,
                                  $seq_region_end, $seq_region_strand,
                                  $sr_cs );
+      }
 
       # Skip features that map to gaps or coord system boundaries.
       if ( !defined($seq_region_id) ) { next FEATURE }

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -1539,9 +1539,21 @@ sub _objs_from_sth {
     #
     if($dest_mapper) {
 
-      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
-        $dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-                              $seq_region_strand, $sr_cs);
+      if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')  ) {
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		=
+		$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
+                          $seq_region_strand, $sr_cs, 1, $dest_slice);
+
+      } else {
+
+	    ( $seq_region_id,  $seq_region_start,
+	      $seq_region_end, $seq_region_strand )
+		= $dest_mapper->fastmap( $sr_name, $seq_region_start,
+                                 $seq_region_end, $seq_region_strand,
+                                 $sr_cs );
+      }
 
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));