From f952b675e48b983d9774253c5ec08b72402b3a92 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Tue, 7 Aug 2012 10:31:02 +0000
Subject: [PATCH] added gene_display_xref_sources

---
 .../xref_mapping/XrefMapper/aedes_aegypti.pm  | 13 +++++++++-
 .../XrefMapper/anopheles_gambiae.pm           | 14 +++++++++++
 .../XrefMapper/culex_quinquefasciatus.pm      | 13 ++++++++++
 .../XrefMapper/ixodes_scapularis.pm           | 25 ++++++++++++++-----
 .../XrefMapper/neurospora_crassa.pm           | 13 +++++++++-
 .../XrefMapper/schizosaccharomyces_pombe.pm   | 14 ++++++++++-
 6 files changed, 83 insertions(+), 9 deletions(-)

diff --git a/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm b/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm
index 86eee2381d..6a54d7d378 100644
--- a/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm
@@ -28,6 +28,18 @@ sub gene_description_sources {
 	  );
 }
 
+sub gene_display_xref_sources {
+  my @list = qw(
+		Uniprot/SWISSPROT
+		VB_Community_Annotation
+                );
+
+  my %ignore;
+
+  return [\@list,\%ignore];
+
+}
+
 sub transcript_display_xref_sources {
   my @list = qw(
 		Uniprot/SWISSPROT
@@ -35,7 +47,6 @@ sub transcript_display_xref_sources {
                 );
 
   my %ignore;
-  #$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
 
   return [\@list,\%ignore];
 
diff --git a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm b/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
index 8a5157985d..c2a78c3c73 100644
--- a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
@@ -37,6 +37,20 @@ sub gene_description_sources {
           );
 }
 
+sub gene_display_xref_sources {
+
+  my @list = qw(RFAM
+		miRBase
+		VB_Community_Annotation
+		Uniprot/SWISSPROT
+		VB_RNA_Description
+	       );
+
+  my %ignore;
+  return [\@list,\%ignore];
+
+}
+
 sub transcript_display_xref_sources {
 
   my @list = qw(RFAM
diff --git a/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm b/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm
index 9193f32fc6..f96f667ecc 100644
--- a/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm
@@ -33,6 +33,19 @@ sub gene_description_sources {
           );
 }
 
+sub gene_display_xref_sources {
+
+  my @list = qw(RFAM
+		miRBase
+		Uniprot/SWISSPROT
+		VB_Community_Annotation
+             );
+
+  my %ignore;
+  return [\@list,\%ignore];
+
+}
+
 sub transcript_display_xref_sources {
 
   my @list = qw(RFAM
diff --git a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm b/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
index 303efe90d5..b48d640874 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
@@ -15,20 +15,33 @@ sub set_methods{
   return $default_method, \%override_method_for_source;
 }
 
-#Reverse order: second one has higher priority!
+
 sub gene_description_sources {
-  return ("Uniprot/SWISSPROT",
-	  "Ixodes_ManualAnnotation",
+  return ("Ixodes_ManualAnnotation",
+	  "Uniprot/SWISSPROT",	  
   ) ;
 }
 
-#Reverse order: second one has higher priority!
+sub gene_display_xref_sources {
+  my $self     = shift;
+  my $fullmode = shift;
+
+  my @list = qw(Ixodes_ManualAnnotation
+                Uniprot/SWISSPROT		
+                );
+
+  my %ignore;
+
+  return [\@list,\%ignore];
+
+}
+
 sub transcript_display_xref_sources {
   my $self     = shift;
   my $fullmode = shift;
 
-  my @list = qw(Uniprot/SWISSPROT
-		Ixodes_ManualAnnotation
+  my @list = qw(Ixodes_ManualAnnotation
+                Uniprot/SWISSPROT		
                 );
 
   my %ignore;
diff --git a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
index 7b7ac28ddb..1515e2fe85 100644
--- a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
@@ -7,9 +7,20 @@ use vars qw(@ISA);
 @ISA = qw(XrefMapper::BasicMapper);
 
 
+sub gene_display_xref_sources {
+    my $self     = shift;
+
+    my @list = qw(
+                 Uniprot_genename
+               );
+    
+    my %ignore;
+    
+    return [\@list,\%ignore];
+}
+
 sub transcript_display_xref_sources {
     my $self     = shift;
-    my $fullmode = shift;
 
     my @list = qw(
                  Uniprot_genename
diff --git a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
index 03307399c0..361ad0eaef 100644
--- a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
@@ -41,11 +41,23 @@ sub build_display_xrefs {
 }
 
 
-sub transcript_display_xref_sources {
+sub gene_display_xref_sources {
     my $self     = shift;
 
     my @list = qw(
                 PomBase_GENE
+               );
+    
+    my %ignore;
+    
+    return [\@list,\%ignore];
+}
+
+
+sub transcript_display_xref_sources {
+    my $self     = shift;
+
+    my @list = qw(
                 PomBase_TRANSCRIPT
                );
     
-- 
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