remove partupdate mode

misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm

@@ -92,11 +92,8 @@ sub transcript_display_xref_sources {
 
   my %ignore;
 
-  if(!$fullmode){
-    $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
-  }
-  else{
-    $ignore{"EntrezGene"} =(<<'IEG');
+
+  $ignore{"EntrezGene"} =(<<'IEG');
 SELECT DISTINCT ox.object_xref_id
   FROM object_xref ox, dependent_xref dx, 
        xref xmas, xref xdep, 
@@ -118,8 +115,6 @@ SELECT object_xref_id
       AND priority_description = 'protein_evidence_gt_3'
 BIGN
 
-  }
-  
   return [\@list,\%ignore];
 
 }

misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm

@@ -29,11 +29,8 @@ sub transcript_display_xref_sources {
 		EntrezGene);
 
   my %ignore;
-  if(!$fullmode){
-    $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
-  }
-  else{
-    $ignore{"EntrezGene"} =(<<'IEG');
+
+  $ignore{"EntrezGene"} =(<<'IEG');
 SELECT DISTINCT ox.object_xref_id
   FROM object_xref ox, dependent_xref dx, 
        xref xmas, xref xdep, 
@@ -48,15 +45,13 @@ SELECT DISTINCT ox.object_xref_id
           ox.ox_status = "DUMP_OUT"
 IEG
 
-    $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+  $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
 SELECT object_xref_id
     FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
      WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' 
       AND priority_description = 'protein_evidence_gt_3'
 BIGN
 
-  }
-  
   return [\@list,\%ignore];
 }
 

misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm

@@ -16,7 +16,6 @@ use vars '@ISA';
 
 sub transcript_display_xref_sources {
   my $self     = shift;
-  my $fullmode = shift;
 
   my @list = qw(RFAM
 	      miRBase
@@ -32,12 +31,8 @@ sub transcript_display_xref_sources {
 
 
   my %ignore;
-  
-  if(!$fullmode){
-    $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
-  }
-  else{
-    $ignore{"EntrezGene"} =(<<'IEG');
+
+  $ignore{"EntrezGene"} =(<<'IEG');
 SELECT DISTINCT ox.object_xref_id
   FROM object_xref ox, dependent_xref dx, 
        xref xmas, xref xdep, 
@@ -52,15 +47,13 @@ SELECT DISTINCT ox.object_xref_id
           ox.ox_status = "DUMP_OUT"
 IEG
 
-    $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+  $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
 SELECT object_xref_id
     FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
      WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' 
       AND priority_description = 'protein_evidence_gt_3'
 BIGN
 
-  }
-  
   return [\@list,\%ignore];
   
 }

misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm

@@ -40,7 +40,6 @@ sub build_display_xrefs {
 
 sub transcript_display_xref_sources {
     my $self     = shift;
-    my $fullmode = shift;
 
     my @list = qw(
                 SGD_GENE

misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm

@@ -39,7 +39,6 @@ sub build_display_xrefs {
 
 sub transcript_display_xref_sources {
     my $self     = shift;
-    my $fullmode = shift;
 
     my @list = qw(
                 PomBase_GENE

misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm

@@ -23,17 +23,14 @@ sub transcript_display_xref_sources {
 		LocusLink);
 
   my %ignore;
-  
-  if($fullmode){
 
-    $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+  $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
 SELECT object_xref_id
     FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
      WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' 
       AND priority_description = 'protein_evidence_gt_3'
 BIGN
 
-  }
 
   return [\@list,\%ignore];
 

misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm

@@ -36,7 +36,6 @@ sub gene_description_sources {
 
 sub transcript_display_xref_sources {
   my $self     = shift;
-  my $fullmode = shift;
 
   my @list = qw(Xenopus_Jamboree
 		MGI
@@ -52,11 +51,7 @@ sub transcript_display_xref_sources {
 
   my %ignore;
 
-  if(!$fullmode){
-    $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
-  }
-  else{
-    $ignore{"EntrezGene"} =(<<'IEG');
+  $ignore{"EntrezGene"} =(<<'IEG');
 SELECT DISTINCT ox.object_xref_id
   FROM object_xref ox, dependent_xref dx, 
        xref xmas, xref xdep, 
@@ -71,14 +66,13 @@ SELECT DISTINCT ox.object_xref_id
           ox.ox_status = "DUMP_OUT"
 IEG
 
-    $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+  $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
 SELECT object_xref_id
     FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
      WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL' 
       AND priority_description = 'protein_evidence_gt_3'
 BIGN
 
-  }
 
   return [\@list,\%ignore];
 }