Fixes and STDERR prints. storing fro safe keeping (nearly therecvs up)

modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm

@@ -332,8 +332,8 @@ sub map {
   }
 
   if($fastmap) {
-    print STDERR "FAST seq region id is $seq_region_id\n";
-    return $mapper->fastmap($seq_region_id, $frm_start, $frm_end,
+    print STDERR "FAST seq region id is $seq_region_id using $frm_seq_region_name\n";
+    return $mapper->fastmap($frm_seq_region_name, $frm_start, $frm_end,
                             $frm_strand, $frm);
   }
 
@@ -486,7 +486,7 @@ sub list_seq_regions {
   }
 
   #convert them to names
-  return @{$self->adaptor()->ids_to_seq_region_names($to_cs, \@seq_regs)};
+  return @{$self->adaptor()->seq_ids_to_regions(\@seq_regs)};
 }
 
 

modules/Bio/EnsEMBL/Feature.pm

@@ -429,6 +429,10 @@ sub transform {
   }
 
   my $projection = $self->project( $cs_name, $cs_version );
+  print STDERR "projection is".$projection."\n";
+  foreach my $segment (@$projection) {
+    print STDERR "feature  project ".$segment->[2]."\t".$segment->[0]."\n";
+  }
   if( @$projection != 1 ) {
     return undef;
   } else {

modules/Bio/EnsEMBL/Mapper.pm

@@ -48,6 +48,7 @@ package Bio::EnsEMBL::Mapper;
 use strict;
 use integer;
 
+use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
 use Bio::EnsEMBL::Mapper::Pair;
 use Bio::EnsEMBL::Mapper::IndelPair;
 use Bio::EnsEMBL::Mapper::Unit;
@@ -520,6 +521,18 @@ sub add_map_coordinates{
   if( ($contig_end - $contig_start)  != ($chr_end - $chr_start) ) {
     throw("Cannot deal with mis-lengthed mappings so far");
   }
+  my $test = $contig_id;
+  $test =~ s/\d+//g;
+  if(length($test) > 0 or $contig_id < 1000){
+    print STDERR "$contig_id NOT INTEGER\n";
+    print STDERR stack_trace_dump();
+  }
+  $test = $chr_name;
+  $test =~ s/\d+//g;
+  if(length($test) > 0 or $chr_name < 1000 ){
+    print STDERR "$chr_name NOT INTEGER\n";
+    print STDERR stack_trace_dump();
+  }
 
   my $from =
     Bio::EnsEMBL::Mapper::Unit->new($contig_id, $contig_start, $contig_end);

modules/Bio/EnsEMBL/Slice.pm

@@ -734,14 +734,16 @@ sub project {
     }
 
     #construct a projection from the mapping results and return it
-    print STDERR "asm_mapper is a ".ref($asm_mapper)."\n";
-    print STDERR "#COORD id is ".$coords[0]->id."\n";
-    my $test = $coords[0]->id;
-    $test =~ s/\d+//g;
-    if(length($test) > 0 ){
-      print STDERR "NOT INTEGER\n";
-      print STDERR stack_trace_dump();
-   }
+    if($coords[0]->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
+      print STDERR "asm_mapper is a ".ref($asm_mapper)."\n";
+      print STDERR "#COORD id is ".$coords[0]->id."\n";
+      my $test = $coords[0]->id;
+      $test =~ s/\d+//g;
+      if(length($test) > 0 ){
+	print STDERR "NOT INTEGER\n";
+	print STDERR stack_trace_dump();
+      }
+    }
     foreach my $coord (@coords) {
       my $coord_start  = $coord->start();
       my $coord_end    = $coord->end();

modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm

@@ -181,11 +181,11 @@ sub map {
       my $mapper = $adaptor->fetch_by_CoordSystems($other_cs, $cs);
 
       if($fastmap) {
-        my @result = $mapper->fastmap($seq_region_id, $frm_start, $frm_end,
+        my @result = $mapper->fastmap($frm_seq_region_name, $frm_start, $frm_end,
                                       $frm_strand, $frm_cs);
         return @result if(@result);
       } else {
-        my @coords = $mapper->map($seq_region_id, $frm_start, $frm_end,
+        my @coords = $mapper->map($frm_seq_region_name, $frm_start, $frm_end,
                                   $frm_strand, $frm_cs);
 
         if(@coords > 1 || !$coords[0]->isa('Bio::EnsEMBL::Mapper::Gap')) {