added function to fetch chr length from a vc via the karyotype DB adaptor

modules/Bio/EnsEMBL/DBSQL/ExternalWrapper.pm

@@ -61,7 +61,7 @@ sub new {
   bless $self,$class;
 
 
-  if( !defined $dbobj || !$dbobj->isa('Bio::EnsEMBL::DBSQL::Obj') ) {
+  if( !defined $dbobj  ) {
       $self->throw("No dbobj or not a dbobj [$dbobj]");
   }
   

modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm

@@ -55,6 +55,53 @@ use Bio::EnsEMBL::DBSQL::BaseAdaptor;
 # inherit new from BaseAdaptor
 
 
+=head2 fetch_by_chromosome_start_end
+
+ Title   : fetch_by_chromosome_start_end
+ Usage   : $band_obj = $kary_adp->fetch_by_chromosome_position('chr1',10000, 2000);
+ Function: Retrieves KaryotypeBand objects by chromosome ('chrN' notation)
+           and its absolute "golden-path" start/end on that chromosome.
+ Example :
+ Returns : A KaryotypeBand object list
+ Args    : Chromosome id (chrN notation) and start, end in absolute basepairs
+
+=cut
+
+sub fetch_by_chromosome_start_end{
+    my ($self,$chr,$start,$end) = @_;
+
+    $self->throw("Need both chromosome and start/end") unless (defined $start && defined $end);
+
+    my $sth = $self->prepare("	SELECT	chr_start,
+					chr_end,
+					band,
+					stain
+				FROM	karyotype 
+				WHERE	chr_name = '$chr'
+				AND	$start <= chr_end 
+				AND	$end > chr_start 
+			     ");
+
+    $sth->execute;
+	my @bands = ();
+	my ($chr_start,$chr_end,$band,$stain) = ();
+		
+    while (($chr_start,$chr_end,$band,$stain) = $sth->fetchrow_array()){
+    	last unless defined $band;
+    	my $band_obj = Bio::EnsEMBL::KaryotypeBand->new();
+    	$band_obj->name($band);
+    	$band_obj->chromosome($chr);
+    	$band_obj->start($chr_start);
+    	$band_obj->end($chr_end);
+    	$band_obj->stain($stain);
+		#print STDERR "Kary Get: $chr_start,$chr_end,$band,$stain\n";
+		push (@bands, $band_obj);
+	}
+
+    return @bands;
+}
+
+
 =head2 fetch_by_chromosome_position
 
  Title   : fetch_by_chromosome_position
@@ -83,8 +130,8 @@ sub fetch_by_chromosome_position{
 			     ");
 
     $sth->execute;
-    my ($chr_start,$chr_end,$band,$stain) = $sth->fetchrow_array;
-
+	
+	my ($chr_start,$chr_end,$band,$stain)  = $sth->fetchrow_array();
     return undef unless defined $band;
 
     my $band_obj = Bio::EnsEMBL::KaryotypeBand->new();
@@ -99,7 +146,6 @@ sub fetch_by_chromosome_position{
 
 
 
-
 =head2 fetch_by_chromosome_name
 
  Title   : fetch_by_chromosome_name
@@ -141,6 +187,39 @@ sub fetch_by_chromosome_name{
 }
 
 
+=head2 fetch_chromosome_length
+
+ Title   : fetch_chromosome_length
+ Usage   : 
+ Function: Returns length of a chromosome ('chrN' notation)
+ Example :
+ Returns : SV
+ Args    : Chromosome id (chrN notation) 
+
+=cut
+
+sub fetch_chromosome_length {
+    my ($self,$chr) = @_;
+
+    $self->throw("Need a chromosome") unless defined $chr;
+
+	# return a cached copy of the chromosome bands
+	if ($self->{'_karyotype_band_cache'}){
+		my @tmp = @{$self->{'_karyotype_band_cache'}};
+		return $tmp[-1]->end();
+	}
+
+    my $sth = $self->prepare("	SELECT
+											max(chr_end)
+								FROM		karyotype 
+								WHERE		chr_name = '$chr' 
+			     			");
+
+    $sth->execute;
+    my ($chr_end) = $sth->fetchrow_array();
+	return($chr_end);
+
+}
 
 
 =head2 fetch_all_by_chromosome
@@ -159,6 +238,11 @@ sub fetch_all_by_chromosome{
 
     $self->throw("Need a chromosome") unless defined $chr;
 
+	# return a cached copy of the chromosome bands
+	if ($self->{'_karyotype_band_cache'}){
+		return(@{$self->{'_karyotype_band_cache'}});
+	}
+
     my $sth = $self->prepare("	SELECT	chr_start,
 					chr_end,
 					band,
@@ -185,6 +269,9 @@ sub fetch_all_by_chromosome{
 	push @bands,$band_obj;
     }
 
+	# save a copy in the local cache
+	$self->{'_karyotype_band_cache'} = \@bands;
+
     return @bands;
 }
 

modules/Bio/EnsEMBL/DBSQL/Obj.pm

@@ -202,7 +202,8 @@ sub new {
           -ENSDB  => $db,
           };
     }
-
+	#$self->store_mapdb_handle();
+	
   # What source of contigoverlaps should we use?
   $self->contig_overlap_source($contig_overlap_source) if $contig_overlap_source;
   
@@ -242,6 +243,22 @@ sub dbname {
   $self->{_dbname};
 }
 
+ # make the cunningly stored map DB handle available to everybody
+ # who wants to play with it...
+ 
+sub store_mapdb_handle {
+	my ($self, $arg ) = @_;
+	my $dsn = "DBI:"       . $self->{'_mapdb'}->{'-DRIVER'}
+			. ":database=" . $self->{'_mapdb'}->{'-DBNAME'}
+			. ";host="     . $self->{'_mapdb'}->{'-HOST'}
+			. ";port="     . $self->{'_mapdb'}->{'-PORT'}
+		;
+	$self->warn("Using mapdb DSN $dsn");
+	my $mapdbh = DBI->connect("$dsn",$self->{'_mapdb'}->{'-USER'},$self->{'_mapdb'}->{'-PASS'}, {RaiseError => 1});
+	$mapdbh || $self->throw("Could not connect to maps database!");
+	$self->_mapdb_handle($mapdbh);
+}
+
 sub username {
   my ($self, $arg ) = @_;
   ( defined $arg ) &&

modules/Bio/EnsEMBL/Virtual/StaticContig.pm

@@ -511,7 +511,10 @@ sub get_all_PredictionFeatures {
 #   my $id     = $self->internal_id();
    my $length = $self->length();
 
-
+	
+   if( exists $self->{'_genscan_cache'} ) {
+       return @{$self->{'_genscan_cache'}};
+   }
 
 
   my $glob_start=$self->_global_start;
@@ -640,6 +643,9 @@ sub get_all_PredictionFeatures {
        $previous = $hid;
   }
  
+
+   $self->{'_genscan_cache'} = \@array;
+
    return @array;
 }
 
@@ -1128,7 +1134,10 @@ sub get_all_Genes_exononly{
    unless ($idlist){
        return ();
    }
-   
+
+   if( exists $self->{'_all_Genes_exononly'} ) {
+       return @{$self->{'_all_Genes_exononly'}};
+   }
 
    my $query = "SELECT e.id,e.sticky_rank,et.rank,et.transcript,t.gene, 
                         IF     (sgp.raw_ori=1,(e.seq_start+sgp.chr_start-sgp.raw_start-$glob_start),
@@ -1181,9 +1190,9 @@ sub get_all_Genes_exononly{
 	   $current_gene->add_Transcript($current_transcript);
 	   push(@trans,$current_transcript);
 	   if( $rank == 1 ) {
-	       $current_transcript->is_start_exon_in_context(1);
+	       $current_transcript->is_start_exon_in_context('dummy',1);
 	   } else {
-	       $current_transcript->is_start_exon_in_context(0);
+	       $current_transcript->is_start_exon_in_context('dummy',0);
 	   }
 
 	   $current_transcript_id = $transcriptid;
@@ -1207,6 +1216,7 @@ sub get_all_Genes_exononly{
        $exon->end($end);
        $exon->strand($strand);
        $exon->id($exonid);
+       $exon->seqname($self->id);
        $previous_exon = $exon;
        $current_transcript->add_Exon($exon);
        $current_transcript->end_exon_rank($rank);
@@ -1223,10 +1233,11 @@ sub get_all_Genes_exononly{
        $sth2->execute;
        my ($rank) = $sth2->fetchrow_array();
        if( $rank == $trans->end_exon_rank) {
-	   $trans->is_end_exon_in_context(1);
+	   $trans->is_end_exon_in_context('dummy',1);
        } else {
-	   $trans->is_end_exon_in_context(0);
+	   $trans->is_end_exon_in_context('dummy',0);
        }
+                                                              
    }
 
 
@@ -1242,6 +1253,7 @@ sub get_all_Genes_exononly{
        $gene_obj->_get_description($g);
    }
 
+   $self->{'_all_Genes_exononly'} = \@out;
 
    return @out;
 
@@ -1579,7 +1591,70 @@ sub get_all_Genes{
    return @newgenes;
 }
 
+=head2 fetch_chromosome_length
+
+ Title   : fetch_chromosome_length
+ Usage   : $length_in_bp = $self->fetch_chromosome_length
+ Function:
+ Example :
+ Returns : SV 
+ Args    :
+
+
+=cut
+
+sub fetch_chromosome_length {
+   my ($self,$chr) = @_;
+
+   unless (defined $chr){
+      $chr = $self->_chr_name();
+   }
+   my $kba = $self->dbobj->get_KaryotypeBandAdaptor();
+   my $len = $kba->fetch_chromosome_length($chr);
+	return($len);
+}
+
+
+=head2 fetch_karyotype_adaptor
+
+ Title   : fetch_karyotype_adaptor
+ Usage   : $band_obj = $self->fetch_karyotype_adaptor
+ Function:
+ Example :
+ Returns : karyotype band adaptor 
+ Args    :
+
+
+=cut
+
+sub fetch_karyotype_adaptor {
+   my ($self,@args) = @_;
+
+   return ($self->dbobj->get_KaryotypeBandAdaptor());
+
+}
+
+
+=head2 fetch_karyotype_band_byname
 
+ Title   : fetch_karyotype_band_byname
+ Usage   : $band_obj = $self->fetch_karyotype_band_byname
+ Function:
+ Example :
+ Returns : karyotype band object 
+ Args    :
+
+
+=cut
+
+sub fetch_karyotype_band_by_name {
+   my ($self,$chr, $band) = @_;
+
+   my $kadp = $self->dbobj->get_KaryotypeBandAdaptor();
+   my $band = $kadp->fetch_by_chromosome_name($chr, $band);
+
+   return $band; 
+}
 
 
 

modules/Bio/EnsEMBL/WebTranscript.pm

@@ -88,7 +88,7 @@ use Bio::EnsEMBL::Transcript;
 =cut
 
 sub is_start_exon_in_context{
-   my ($obj,$value) = @_;
+   my ($obj,$dummy,$value) = @_;
    if( defined $value) {
       $obj->{'is_start_exon_in_context'} = $value;
     }
@@ -96,7 +96,7 @@ sub is_start_exon_in_context{
 
 }
 
-
+       
 =head2 is_end_exon_in_context
 
  Title   : is_end_exon_in_context
@@ -110,7 +110,7 @@ sub is_start_exon_in_context{
 =cut
 
 sub is_end_exon_in_context{
-   my ($obj,$value) = @_;
+   my ($obj,$dummy,$value) = @_;
    if( defined $value) {
       $obj->{'is_end_exon_in_context'} = $value;
     }