From: Jalview build Manager <jalview-dev@jalview.org>
Date: Mon, 13 Jan 2014 18:15:53 +0000 (+0000)
Subject: Merge branch 'Release_2_8_Branch' into WIP_fix_JAL-1423
X-Git-Tag: Release_2_8_0b1~1^2~21
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2FWIP_fix_JAL-1423;p=jalview.git

Merge branch 'Release_2_8_Branch' into WIP_fix_JAL-1423

Conflicts:
	examples/linkedapplets_ng.html
---

1ac48a3ee02288fe52f16f9637bbaa099594fe4b
diff --cc examples/embeddedWJmol.html
index f6f8847,af15654..79cf5cb
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@@ -106,10 -106,10 +106,10 @@@ function genHref(
    ,
    linkLabel_2 : "Uniprot"
    ,
-   linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
+   linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
    APPLICATION_URL : "http://www.jalview.org/services/launchApp",
    PDBfile : "1gaq.txt FER1_MAIZE",
 -  permissions : "sandbox"
 +  permissions : "all-permissions"
   };
   jmolSetCallback("hoverCallback","_jmolhover");
    jmolSetCallback("pickCallback","_jmolpick");
diff --cc examples/linkedapplets_ng.html
index fbb41ec,c36f649..6993f2f
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@@ -200,15 -200,13 +200,13 @@@ document.onclick = mclose
      embedded : "true",
      showFullId : "false",
      RGB : "F2F2FF",
-     linkLabel_1 : "SRS",
-     linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
-  
+     linkLabel_1 : "EMBL-EBI Search",
+     linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
      ,
      linkLabel_2 : "Uniprot"
-  
      ,
-     linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
 -    permissions : 'sandbox',
+     linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
 +    permissions : 'all-permissions',
      APPLICATION_URL : "http://www.jalview.org/services/launchApp"
    };
   
@@@ -235,16 -233,14 +233,14 @@@
      embedded : "true",
      showFullId : "false",
      RGB : "F2F2FF",
-     linkLabel_1 : "SRS",
-     linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
-  
+     linkLabel_1 : "EMBL-EBI Search",
+     linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
      ,
      linkLabel_2 : "Uniprot"
-  
      ,
-     linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
 -    permissions : 'sandbox',
+     linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
 +    permissions : 'all-permissions',
-     APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+    APPLICATION_URL : "http://www.jalview.org/services/launchApp"
    };
    deployJava.runApplet(attributes, parameters, '1.6');
  </script>