Merge branch 'Release_2_8_Branch' into WIP_fix_JAL-1423

Conflicts:
	examples/linkedapplets_ng.html

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 4779046..5f7305d 100644 (file)
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -308,7 +308,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
           </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 
@@ -321,12 +321,12 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
               <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 e228bc1..a6d61f8 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -190,9 +190,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
           <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>
@@ -216,10 +216,10 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
        <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>
@@ -241,9 +241,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
        <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">
@@ -269,9 +269,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
        <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 58dbb2d..1493ea5 100644 (file)
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -180,9 +180,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
        <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 f6f8847..79cf5cb 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -101,12 +101,12 @@ 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",
   permissions : "all-permissions"

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index fbb41ec..6993f2f 100644 (file)
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -200,14 +200,12 @@ 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/$SEQUENCE_ID$",
     permissions : 'all-permissions',
     APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
@@ -235,16 +233,14 @@ 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/$SEQUENCE_ID$",
     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>

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 3adaa14..070004f 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -73,10 +73,21 @@ public class IdPanel extends Panel implements MouseListener,
 
       }
     }
+    {
+      // upgrade old SRS link
+      int srsPos = links
+              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      if (srsPos > -1)
+      {
+        links.setElementAt(
+                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+                srsPos);
+      }
+    }
     if (links.size() < 1)
     {
       links = new java.util.Vector();
-      links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
     }
   }
 

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index a0fa216..0f23ecd 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -58,7 +58,7 @@ public class Preferences extends GPreferences
     String string = Cache
             .getDefault(
                     "SEQUENCE_LINKS",
-                    "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
     sequenceURLLinks = new Vector();
 
     try
@@ -80,6 +80,18 @@ public class Preferences extends GPreferences
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
+    {
+      // upgrade old SRS link
+      int srsPos = sequenceURLLinks
+              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      if (srsPos > -1)
+      {
+        sequenceURLLinks.setElementAt(
+                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+                srsPos);
+      }
+    }
+
     /**
      * TODO: reformulate groupURL encoding so two or more can be stored in the
      * .properties file as '|' separated strings