JAL-1422 remove SRS and expasy links and replace with EMBL-EBI Search and Uniprot...

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 427c8b7..af1ec87 100644 (file)
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -300,7 +300,7 @@ document.onclick = mclose;
           </tr>
           <tr> 
             <td>linkLabel_1</td>
-            <td>Uniprot</td>
+            <td>EMBL-EBI Search</td>
             <td rowspan="2"><p>Right click on sequence id to see list of available 
                 links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n 
                 value. For multiple links, increment the label and url name by 
@@ -313,12 +313,12 @@ document.onclick = mclose;
               <br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
           </tr>
           <tr> 
-            <td> <p><br>
+            <td> <p>
+            <br>
                 linkUrl_1<br>
               </p></td>
             <td><p><br>
-                http://us.expasy.org/cgi-bin/<br>
-                niceprot.pl?$SEQUENCE_ID$</p>
+                http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
                                                </td>
           </tr>
           <tr> 

diff --git a/examples/applets.html b/examples/applets.html
index e3e1d3c..e88742e 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -186,9 +186,9 @@ document.onclick = mclose;
           <param name="linkLabel_1" value="Uniprot">
            <param name="linkUrl_1"
             value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-            <param name="linkLabel_2" value="Expasy">
+            <param name="linkLabel_2" value="EMBL-EBI Search">
              <param name="linkUrl_2"
-              value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+              value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
        <param name="APPLICATION_URL"
         value="http://www.jalview.org/services/launchApp">
        </applet></td>
@@ -211,10 +211,10 @@ document.onclick = mclose;
        <param name="linkLabel_1" value="Uniprot">
         <param name="linkUrl_1"
          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-         <param name="linkLabel_2" value="Expasy">
-          <param name="linkUrl_2"
-           value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
-           <param name="APPLICATION_URL"
+                     <param name="linkLabel_2" value="EMBL-EBI Search">
+             <param name="linkUrl_2"
+              value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
+        <param name="APPLICATION_URL"
             value="http://www.jalview.org/services/launchApp">
        </applet></td>
       <td valign="center">Displays a features file on the alignment</td>
@@ -235,9 +235,9 @@ document.onclick = mclose;
        <param name="linkLabel_1" value="Uniprot">
         <param name="linkUrl_1"
          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-         <param name="linkLabel_2" value="Expasy">
-          <param name="linkUrl_2"
-           value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+            <param name="linkLabel_2" value="EMBL-EBI Search">
+             <param name="linkUrl_2"
+              value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
        <param name="APPLICATION_URL"
         value="http://www.jalview.org/services/launchApp">
         <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
@@ -262,9 +262,9 @@ document.onclick = mclose;
        <param name="linkLabel_1" value="Uniprot">
         <param name="linkUrl_1"
          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-         <param name="linkLabel_2" value="Expasy">
-          <param name="linkUrl_2"
-           value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+            <param name="linkLabel_2" value="EMBL-EBI Search">
+             <param name="linkUrl_2"
+              value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
        <param name="APPLICATION_URL"
         value="http://www.jalview.org/services/launchApp">
        </applet></td>

diff --git a/examples/embedded.html b/examples/embedded.html
index 2f74116..b9d26cb 100644 (file)
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -176,9 +176,9 @@ document.onclick = mclose;
        <param name="linkLabel_1" value="Uniprot">
         <param name="linkUrl_1"
          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-         <param name="linkLabel_2" value="Expasy">
-          <param name="linkUrl_2"
-           value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+            <param name="linkLabel_2" value="EMBL-EBI Search">
+             <param name="linkUrl_2"
+              value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
                        <param name="APPLICATION_URL"
                                value="http://www.jalview.org/services/launchApp">
                </applet>

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 86dceea..a3a7c3d 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -96,12 +96,12 @@ function genHref()
   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?$SEQUENCE_ID$",
+  linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
   APPLICATION_URL : "http://www.jalview.org/services/launchApp",
   PDBfile : "1gaq.txt FER1_MAIZE"
  };

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 4296146..3418068 100644 (file)
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -196,14 +196,12 @@ 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?$SEQUENCE_ID$",
+    linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
     APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
  
@@ -230,15 +228,13 @@ 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?$SEQUENCE_ID$",
-    APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+    linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+   APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
   deployJava.runApplet(attributes, parameters, '1.6');
 </script>