mapping fixes to use seq_region_id instead pf names

modules/Bio/EnsEMBL/AssemblyMapper.pm

@@ -213,7 +213,6 @@ sub map {
   push @tmp, $frm_seq_region_name;
   my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];
 
-  print STDERR "name = $frm_seq_region_name, id = $seq_region_id \n";
 
   #speed critical section:
   #try to do simple pointer equality comparisons of the coord system objects
@@ -241,8 +240,6 @@ sub map {
           " of this AssemblyMapper");
   }
 
-  print STDERR "seq region id is $seq_region_id\n";
-  print STDERR "mapper is of type ".ref($mapper)."\n"; 
   return $mapper->map_coordinates($seq_region_id, $frm_start, $frm_end,
                                   $frm_strand, $frm);
 }
@@ -482,6 +479,7 @@ sub list_seq_regions {
   my($self, $frm_seq_region, $frm_start, $frm_end, $frm_cs) = @_;
 
   #retrieve the seq_region names
+
   my @seq_ids =
     $self->list_ids($frm_seq_region,$frm_start,$frm_end,$frm_cs);
 
@@ -495,7 +493,7 @@ sub list_seq_regions {
   }
 
   #convert them to ids
-  return @{$self->adaptor()->seq_ids_to_regions($to_cs, \@seq_ids)};
+  return @{$self->adaptor()->seq_ids_to_regions(\@seq_ids)};
 }
 
 #sub list_ids {

modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm

@@ -303,9 +303,6 @@ sub map {
   #get a list of ranges in the requested region that have not been registered,
   #and register them at the same
 
-  #print STDERR "frm_start=$frm_start frm_end=$frm_end" .
-  #              "min_start=$min_start min_end=$min_end\n";
-
   my $ranges;
 
   if($is_insert) {
@@ -332,13 +329,10 @@ sub map {
   }
 
   if($fastmap) {
-    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,
+    return $mapper->fastmap($seq_region_id, $frm_start, $frm_end,
                             $frm_strand, $frm);
   }
 
-  print STDERR "mapper is of type ".ref($mapper)."\n";
-  print STDERR "SLOW seq region id is $seq_region_id\n";
   return $mapper->map_coordinates($seq_region_id, $frm_start, $frm_end,
                                   $frm_strand, $frm);
 }

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -195,10 +195,6 @@ sub fetch_all_by_Slice_constraint {
   # same seq_region as original slice
 
   my $sr_id = $slice->get_seq_region_id();
-  print STDERR "sr_id = $sr_id\n";
-  foreach my $pro (@proj){
-    print STDERR "projected slice -> ".$pro->to_Slice->get_seq_region_id()."\n";
-  }
 
   @proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;
 
@@ -221,8 +217,6 @@ sub fetch_all_by_Slice_constraint {
   foreach my $seg (@proj) {
     my $offset = $seg->from_start();
     my $seg_slice  = $seg->to_Slice();
-    print STDERR "MORE: ".$seg_slice->name."\n";
-    print STDERR "constraint :- $constraint\n";
     my $features = $self->_slice_fetch($seg_slice, $constraint); ## NO RESULTS
 
     # if this was a symlinked slice offset the feature coordinates as needed
@@ -230,7 +224,6 @@ sub fetch_all_by_Slice_constraint {
 
     FEATURE:
       foreach my $f (@$features) {
-	print STDERR "FEAT: ".ref($f)."\n";
         if($offset != 1) {
 
           $f->{'start'} += $offset-1;
@@ -308,7 +301,7 @@ sub _slice_fetch {
 
   my $asma = $self->db->get_AssemblyMapperAdaptor();
   my @features;
-warn "jere are $self, @feat_css\n";
+
   # fetch the features from each coordinate system they are stored in
  COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
     my $mapper;
@@ -342,16 +335,13 @@ warn "jere are $self, @feat_css\n";
           " AND ${tab_syn}.seq_region_start >= $min_start";
       }
 
-      print STDERR "#constraint $constraint\n";
       my $fs = $self->generic_fetch($constraint,undef,$slice);
 
       # features may still have to have coordinates made relative to slice
       # start
-      print STDERR"#number of features is :- ".scalar(@$fs)."\n";
       $fs = _remap($fs, $mapper, $slice);
 
       push @features, @$fs;
-      print STDERR "#number of features is :- ".scalar(@$fs)."\n";
     } else {
       $mapper = $asma->fetch_by_CoordSystems($slice_cs, $feat_cs);
 
@@ -381,14 +371,11 @@ warn "jere are $self, @feat_css\n";
         $constraint .= " AND " if($constraint);
         $constraint .= "${tab_syn}.seq_region_id IN ($id_str)";
 
-	print STDERR ".con: $constraint\n";
         my $fs = $self->generic_fetch($constraint, $mapper, $slice);
 
-	print STDERR ".number of features is :- ".scalar(@$fs)."\n";
         $fs = _remap($fs, $mapper, $slice);
 
         push @features, @$fs;
-	print STDERR ".number of features is :- ".scalar(@features)."\n";
 
       } else {
         # do multiple split queries using start / end constraints
@@ -411,12 +398,9 @@ warn "jere are $self, @feat_css\n";
               " AND ${tab_syn}.seq_region_start >= $min_start";
           }
 
-	print STDERR "~con: $constraint\n";
           my $fs = $self->generic_fetch($constraint,$mapper,$slice);
 
-	  print STDERR "~number of features is :- ".scalar(@$fs)."\n";
           $fs = _remap($fs, $mapper, $slice);
-	  print STDERR "~number after _remap features is :- ".scalar(@$fs)."\n";
 
           push @features, @$fs;
         }

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -180,11 +180,8 @@ sub fetch_all_by_Transcript {
                    " AND e.exon_id = et.exon_id";
 
   # fetch all of the exons
-  print STDERR "\n".$slice."\n\t".$slice->name."\n";
-  print STDERR "$constraint\n";
   my $exons = $self->fetch_all_by_Slice_constraint($slice,$constraint);
 
-  print STDERR "ther are ".scalar(@$exons)." exons\n";
   #un-override the table definition
   $self->{'tables'} = undef;
   $self->{'final_clause'} = undef;
@@ -193,7 +190,6 @@ sub fetch_all_by_Transcript {
   if($slice->name() ne $tslice->name()) {
     my @out;
     foreach my $ex (@$exons) {
-      print STDERR "$ex being transfered\n";
       push @out, $ex->transfer($tslice);
     }
     $exons = \@out;

modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm

@@ -251,7 +251,6 @@ sub _objs_from_sth {
         $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
                           $seq_region_strand, $sr_cs);
 
-      print STDERR "SR_NAME".$seq_region_id."\n";
       #skip features that map to gaps or coord system boundaries
       next FEATURE if(!defined($seq_region_id));
       
@@ -302,7 +301,6 @@ sub _objs_from_sth {
        'display_label' => $display_label,
        'score'    => $score});
     }
-  print STDERR "FEATURE COUNT $count\n";
 
   return \@features;
 }

modules/Bio/EnsEMBL/DBSQL/StatementHandle.pm

@@ -84,56 +84,56 @@ sub sql {
 ## call   Bio::EnsEMBL::DBSQL::StatementHandle->dump(0); to end log
 ## and set $dump to 0 
 ## leave $dump = 1 for continuous log
-#my @bind_args=();
-#my $dump = 1;
-#my $total_time = 0;
+my @bind_args=();
+my $dump = 0;
+my $total_time = 0;
+
+sub dump {
+  $dump = shift;
+  if($total_time){
+    print STDERR "###################Time taken was $total_time\n";
+  }
+  $total_time = 0;
+}
 
-#sub dump {
-#  $dump = shift;
-#  if($total_time){
-#    print "Time taken was $total_time\n";
-#  }
-#  $total_time = 0;
-#}
+sub bind_param{ 
+  my ($self,@args) = @_;
 
-#sub bind_param{ 
-#  my ($self,@args) = @_;
+  $bind_args[$args[0]-1] = $args[1];
+  $self->SUPER::bind_param(@args);
+} 
 
-#  $bind_args[$args[0]-1] = $args[1];
-#  $self->SUPER::bind_param(@args);
-#} 
+sub execute {
+  my ($self,@args) = @_;
   
-#sub execute {
-#  my ($self,@args) = @_;
+  if(!$dump){ # skip dumping
+    return $self->SUPER::execute(@args);
+  }
+  my $sql = $self->sql();
   
-#  if(!$dump){ # skip dumping
-#    return $self->SUPER::execute(@args);
-#  }
-#  my $sql = $self->sql();
   
+  my @chrs = split(//, $sql);
   
-#  my @chrs = split(//, $sql);
+  my $j = 0;
+  for(my $i =0; $i < @chrs; $i++) {
+    $chrs[$i] = $bind_args[$j++] if($chrs[$i] eq '?' && defined($bind_args[$j]));
+  }
   
-#  my $j = 0;
-#  for(my $i =0; $i < @chrs; $i++) {
-#    $chrs[$i] = $bind_args[$j++] if($chrs[$i] eq '?' && defined($bind_args[$j]));
-#  }
+  my $str = join('', @chrs);
   
-#  my $str = join('', @chrs);
+  print STDERR "\nSQL:\n$str\n\n";
   
-#  print "\nSQL:\n$str\n\n";
+  my $time = time;
+  my $res = $self->SUPER::execute(@args);
+  $time = time - $time;
 
-#  my $time = time;
-#  my $res = $self->SUPER::execute(@args);
-#  $time = time - $time;
+  $total_time += $time;
+  print "DONE ($time)\n";
+  return $res;
+}
 
-#  $total_time += $time;
-#  print "DONE ($time)\n";
-#  return $res;
-#}
-#
 # End uncomment
-#
+
 
 sub DESTROY {
   my ($obj) = @_;

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -1196,7 +1196,6 @@ sub _objs_from_sth {
     #
     if($dest_mapper) {
 
-      print STDERR "NAME: $sr_name\n";
       ($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);
@@ -1206,13 +1205,9 @@ sub _objs_from_sth {
 
       #get a slice in the coord system we just mapped to
       if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
-	print STDERR "---$cmp_cs_name, $seq_region_id,undef, undef, undef,
-                               $cmp_cs_vers\n";
         $slice = $slice_hash{"ID:".$seq_region_id} ||=
           $sa->fetch_by_seq_region_id($seq_region_id);
       } else {
-	print STDERR "----$asm_cs_name, $seq_region_id, undef, undef, undef,
-                               $asm_cs_vers\n";
         $slice = $slice_hash{"ID:".$seq_region_id} ||=
           $sa->fetch_by_seq_region_id($seq_region_id);
       }

modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm

@@ -110,7 +110,6 @@ sub fetch_by_Transcript {
   # but I guess thats ok ....
 
   foreach my $exon (@{$transcript->get_all_Exons()}) {
-    print STDERR "exon id $exon";
     if($exon->dbID() == $start_exon_id ) {
       $start_exon = $exon;
     }

modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm

@@ -266,6 +266,7 @@ sub fetch_all_by_Slice {
   my $slice_end    = $slice->end;
   my $slice_strand = $slice->strand;
   my $slice_seq_region  = $slice->seq_region_name;
+  my $slice_seq_region_id  = $slice->get_seq_region_id;
   my $coord_system = $slice->coord_system;
 
   if($self->_supported('SLICE')) {
@@ -309,8 +310,8 @@ sub fetch_all_by_Slice {
     foreach my $segment (@{$slice->project($from_coord_system->name,
                                            $from_coord_system->version)}) {
       my ($start,$end,$pslice) = @$segment;
-      $features{$pslice->seq_region_name} ||= [];
-      push @{$features{$pslice->seq_region_name}},
+      $features{$pslice->seq_region_name } ||= [];
+      push @{$features{$pslice->seq_region_name }},
            @{&$fetch_method($self, $pslice->seq_region_name,
                             $pslice->start(),
                             $pslice->end())};
@@ -334,17 +335,17 @@ sub fetch_all_by_Slice {
       $slice_setter = _guess_slice_setter($feats) if(!$slice_setter);
 
       foreach my $f (@$feats) {
-        my($sr_name, $start, $end, $strand) = 
+        my($sr_id, $start, $end, $strand) = 
           $mapper->fastmap($fseq_region,$f->start,$f->end,$f->strand,
                            $from_coord_system);
         
         #maps to gap
-        next if(!defined($sr_name));
+        next if(!defined($sr_id));
 
         #maps to unexpected seq region, probably error in the externally
-        if($sr_name ne $slice_seq_region) {
-          warning("Externally created Feature mapped to [$sr_name] " .
-                  "which is not on requested seq_region [$slice_seq_region]");
+        if($sr_id ne $slice_seq_region_id) {
+          warning("Externally created Feature mapped to [$sr_id] " .
+                  "which is not on requested seq_region_id [$slice_seq_region_id]");
           next;
         }
 

modules/Bio/EnsEMBL/Feature.pm

@@ -429,10 +429,7 @@ 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/Map/DBSQL/MarkerFeatureAdaptor.pm

@@ -172,7 +172,7 @@ sub _objs_from_sth {
 
   my %marker_cache;
   my %slice_hash;
-  my %sr_name_hash;
+#  my %sr_name_hash;
   my %sr_cs_hash;
   my %analysis_cache;
   my $marker_adp = $self->db->get_MarkerAdaptor;
@@ -225,12 +225,12 @@ sub _objs_from_sth {
     }
 
     #get the slice object
-    my $slice = $slice_hash{"ID:".$seq_region_id};
+    my $slice = $slice_hash{$seq_region_id};
 
     if(!$slice) {
       $slice = $sa->fetch_by_seq_region_id($seq_region_id);
-      $slice_hash{"ID:".$seq_region_id} = $slice;
-      $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
+      $slice_hash{$seq_region_id} = $slice;
+#      $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
       $sr_cs_hash{$seq_region_id} = $slice->coord_system();
     }
 
@@ -246,26 +246,18 @@ sub _objs_from_sth {
     # if a mapper was provided
     #
     if($mapper) {
-      my $sr_name = $sr_name_hash{$seq_region_id};
+#      my $sr_name = $sr_name_hash{$seq_region_id};
       my $sr_cs   = $sr_cs_hash{$seq_region_id};
 
-      ($sr_name,$seq_region_start,$seq_region_end) =
-        $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
-                         0, $sr_cs);
+     ($seq_region_id,$seq_region_start,$seq_region_end) =
+        $mapper->fastmap($slice->seq_region_name(), $seq_region_start, $seq_region_end, 0, $sr_cs);
 
       #skip features that map to gaps or coord system boundaries
-      next FEATURE if(!defined($sr_name));
+      next FEATURE if(!defined($seq_region_id));
 
       #get a slice in the coord system we just mapped to
-      if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
-        $slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
-          $sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
-                               $cmp_cs_vers);
-      } else {
-        $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
-          $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
-                               $asm_cs_vers);
-      }
+      $slice = $slice_hash{"$seq_region_id"} ||=
+	$sa->fetch_by_seq_region_id($seq_region_id);
     }
 
     #

modules/Bio/EnsEMBL/Mapper.pm

@@ -523,16 +523,9 @@ sub add_map_coordinates{
   }
   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

@@ -706,7 +706,6 @@ sub project {
   my $normal_slice_proj =
     $slice_adaptor->fetch_normalized_slice_projection($self);
   foreach my $segment (@$normal_slice_proj) {
-    print STDERR "slice project ".$segment->[2]->name."\t".$segment->[2]->coord_system->name."\n";
     my $normal_slice = $segment->[2];
 
     $slice_cs = $normal_slice->coord_system();
@@ -718,11 +717,11 @@ sub project {
     my @coords;
 
     if( defined $asm_mapper ) {
-      print STDERR "HI ".$normal_slice->seq_region_name()."\n";
-      print STDERR "\t".$normal_slice->start(),
-	"\t".$normal_slice->end(),
-	  "\t",$normal_slice->strand(),
-	    "\t",$slice_cs->name." -> ".$cs->name."\n";
+#      print STDERR "HI ".$normal_slice->seq_region_name()."\n";
+#      print STDERR "\t".$normal_slice->start(),
+#	"\t".$normal_slice->end(),
+#	  "\t",$normal_slice->strand`(),
+#	    "\t",$slice_cs->name." -> ".$cs->name."\n";
      @coords = $asm_mapper->map($normal_slice->seq_region_name(),
 				 $normal_slice->start(),
 				 $normal_slice->end(),
@@ -734,16 +733,6 @@ sub project {
     }
 
     #construct a projection from the mapping results and return it
-    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();
@@ -764,7 +753,7 @@ sub project {
         }
 
         #create slices for the mapped-to coord system
-	print STDERR "COORD id is ".$coord->id."\n";
+#	print STDERR "COORD id is ".$coord->id."\n";
 #        my $slice = $slice_adaptor->fetch_by_region($coord_cs->name(),
 #                                                    $coord->id(),
 #                                                    $coord_start,
@@ -776,8 +765,8 @@ sub project {
                                                     $coord->id(),
                                                     $coord_start,
                                                     $coord_end,
-                                                    $coord->strand(),);
-	print STDERR "slice poject ".$slice."\n";
+                                                    $coord->strand());
+
 	my $current_end = $current_start + $length - 1;
 	
         push @projection, bless([$current_start, $current_end, $slice],

modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm

@@ -328,10 +328,10 @@ sub _list {
       my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];
 
       if($seq_regions) {
-        @result = $mapper->list_seq_regions($seq_region_id, $frm_start,
+        @result = $mapper->list_seq_regions($frm_seq_region_name, $frm_start,
                                             $frm_end, $frm_cs);
       } else {
-        @result = $mapper->list_ids($seq_region_id, $frm_start,
+        @result = $mapper->list_ids($frm_seq_region_name, $frm_start,
                                     $frm_end, $frm_cs);
       }