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raw | compact (merge: 9307d91 fe76692)
Merge branch 'Release_2_8_Branch' into WIP_fix_JAL-1423 WIP_fix_JAL-1423
authorJalview build Manager <jalview-dev@jalview.org>
Mon, 13 Jan 2014 18:15:53 +0000 (18:15 +0000)
committerJalview build Manager <jalview-dev@jalview.org>
Mon, 13 Jan 2014 18:15:53 +0000 (18:15 +0000)
Conflicts:
examples/linkedapplets_ng.html

1  2 
examples/applets.html patch | diff1 | diff2 | blob | history
examples/embedded.html patch | diff1 | diff2 | blob | history
examples/embeddedWJmol.html patch | diff1 | diff2 | blob | history
examples/linkedapplets_ng.html patch | diff1 | diff2 | blob | history

diff --combined examples/applets.html
index e228bc1,0629af0..a6d61f8
--- 1/examples/applets.html
--- 2/examples/applets.html
+++ b/examples/applets.html
@@@ -178,7 -178,7 +178,7 @@@ var _gaq = _gaq || [];_gaq.push(["_setA
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 -<param name="permissions" value="sandbox">
 +<param name="permissions" value="all-permissions">
         <param name="file" value="uniref50.fa">
          <param name="treeFile" value="ferredoxin.nw">
           <param name="userDefinedColour"
@@@ -190,9 -190,9 +190,9 @@@
            <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>
@@@ -204,7 -204,7 +204,7 @@@
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 -<param name="permissions" value="sandbox">
 +<param name="permissions" value="all-permissions">
         <param name="file" value="uniref50.fa">
          <param name="features" value="exampleFeatures.txt">
           <param name="showFeatureSettings" value="true">
@@@ -216,10 -216,10 +216,10 @@@
         <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>
@@@ -228,7 -228,7 +228,7 @@@
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 -<param name="permissions" value="sandbox">
 +<param name="permissions" value="all-permissions">
         <param name="file" value="uniref50.fa">
          <!-- <param name="debug" value="true">
                          -->
@@@ -241,9 -241,9 +241,9 @@@
         <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">
@@@ -255,7 -255,7 +255,7 @@@
        <td width="10%" valign="middle"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 -<param name="permissions" value="sandbox">
 +<param name="permissions" value="all-permissions">
         <param name="file" value="jpred_msa.fasta">
          <param name="jnetfile" value="jpred_msa.seq.concise">
           <param name="defaultColour" value="Clustal">
@@@ -269,9 -269,9 +269,9 @@@
         <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>
@@@ -288,7 -288,7 +288,7 @@@
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 -<param name="permissions" value="sandbox">
 +<param name="permissions" value="all-permissions">
         <param name="file" value="RF00031_folded.stk">
          <param name="defaultColour" value="Purine/Pyrimidine">
           <param name="showAnnotation" value="true">
diff --combined examples/embedded.html
index 58dbb2d,ce6fca5..1493ea5
--- 1/examples/embedded.html
--- 2/examples/embedded.html
+++ b/examples/embedded.html
@@@ -169,7 -169,7 +169,7 @@@ var _gaq = _gaq || [];_gaq.push(["_setA
  </ul>
  <applet code="jalview.bin.JalviewLite"
                        width="756" height="560" archive="jalviewApplet.jar">
 -                      <param name="permissions" value="sandbox">
 +                      <param name="permissions" value="all-permissions">
        <param name="file" value="plantfdx.fa">
                        <param name="annotations" value="plantfdx.annotations">
                        <param name="features" value="plantfdx.features">
@@@ -180,9 -180,9 +180,9 @@@
         <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 --combined examples/embeddedWJmol.html
index f6f8847,af15654..79cf5cb
--- 1/examples/embeddedWJmol.html
--- 2/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@@ -101,15 -101,15 +101,15 @@@ 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 : "sandbox"
 +  permissions : "all-permissions"
   };
   jmolSetCallback("hoverCallback","_jmolhover");
    jmolSetCallback("pickCallback","_jmolpick");
diff --combined examples/linkedapplets_ng.html
index fbb41ec,c36f649..6993f2f
--- 1/examples/linkedapplets_ng.html
--- 2/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>