From 3c0a33e1157daa5beda926886fa0af0b1fffc051 Mon Sep 17 00:00:00 2001
From: Lukas Mueller <lam87@cornell.edu>
Date: Tue, 9 Jul 2013 11:42:08 -0400
Subject: [PATCH] add option to link by marker name instead of marker id (to
 link to GBrowse etc.)

---
 lib/CXGN/Cview/Map.pm              | 22 ++++++++++++++++++++++
 lib/CXGN/Cview/Map/SGN/Genetic.pm  | 15 +++++++++++++--
 lib/CXGN/Cview/MapFactory/Cacao.pm |  3 ++-
 3 files changed, 37 insertions(+), 3 deletions(-)

diff --git a/lib/CXGN/Cview/Map.pm b/lib/CXGN/Cview/Map.pm
index 8938c75..1d8872d 100644
--- a/lib/CXGN/Cview/Map.pm
+++ b/lib/CXGN/Cview/Map.pm
@@ -1027,6 +1027,28 @@ sub set_parent2_stock_name {
   $self->{parent2_stock_name} = shift;
 }
 
+=head2 accessors get_link_by_name, set_link_by_name
+
+ Usage:
+ Desc:         set to true if the marker link should be constructed
+               using the marker name instead of the marker id 
+               (useful for linking to gbrowse etc).
+               The map subclass needs to support this.
+ Property
+ Side Effects:
+ Example:
+
+=cut
+
+sub get_link_by_name {
+  my $self = shift;
+  return $self->{link_by_name}; 
+}
+
+sub set_link_by_name {
+  my $self = shift;
+  $self->{link_by_name} = shift;
+}
 
 
 1;
diff --git a/lib/CXGN/Cview/Map/SGN/Genetic.pm b/lib/CXGN/Cview/Map/SGN/Genetic.pm
index b0d3dac..00b9244 100644
--- a/lib/CXGN/Cview/Map/SGN/Genetic.pm
+++ b/lib/CXGN/Cview/Map/SGN/Genetic.pm
@@ -261,7 +261,12 @@ sub get_chromosome {
 
 	#print STDERR "dataadapter baccount = $bac_count!\n";
 	if ($loc_type == 100) { $m -> set_frame_marker(); }
-	$m -> set_url( $self->get_marker_link($m->get_id()));
+	if ($self->get_link_by_name()) { 
+	    $m->set_url($self->get_marker_link($m->get_marker_name));
+	}
+	else { 
+	    $m -> set_url( $self->get_marker_link($m->get_id()));
+	}
 	$self->set_marker_color($m, $self->get_legend()->get_mode());
 
 	#print STDERR "CURRENT MODE IS: ".$self->get_legend()->get_mode()."\n";
@@ -406,7 +411,13 @@ sub get_chromosome_section {
 	my $seq_bac_id="";
 	if (!$plausible || $plausible == 0)  { $bac_count = 0; }
 	my $m = CXGN::Cview::Marker -> new($chromosome, $marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, , $loc_type, 0, $overgo, $bac_count);
-	$m->set_url($self->get_marker_link($m->get_id()));
+
+	if ($self->get_link_by_name()) { 
+	    $m->set_url($self->get_marker_link($m->get_marker_name()));
+	}
+	else { 
+	    $m->set_url($self->get_marker_link($m->get_id()));
+	}
 	$self->set_marker_color($m, $self->get_legend()->get_mode());
 	#print STDERR "dataadapter baccount = $bac_count!\n";
 	if ($loc_type == 100) { $m -> set_frame_marker(); }
diff --git a/lib/CXGN/Cview/MapFactory/Cacao.pm b/lib/CXGN/Cview/MapFactory/Cacao.pm
index ebfe202..8786615 100644
--- a/lib/CXGN/Cview/MapFactory/Cacao.pm
+++ b/lib/CXGN/Cview/MapFactory/Cacao.pm
@@ -136,7 +136,8 @@ sub create {
 	elsif ($map_type =~ /seq/) {
 	    print STDERR "Creating a seq map...($map_type, $id)\n";
 	    my $map = CXGN::Cview::Map::SGN::Sequence->new($self->get_dbh(), $id);
-	    $map->set_marker_link("http://gbrowse-cacao.sgn.cornell.edu/gb2/gbrowse/cacao1/?h_feat=");
+	    $map->set_marker_link("http://gbrowse-cacao.sgn.cornell.edu/gb2/gbrowse/cacao1/?q=");
+	    $map->set_link_by_name(1);
 	    return $map;
 	}
     }
-- 
2.11.4.GIT