JAL-1213 JAL-1395 add Jmol to JalviewLite classpath - need to find a way around this...

diff --git a/examples-jbake/templates/jvl_embedded.ftl b/examples-jbake/templates/jvl_embedded.ftl
index b61c7a9..62d58b0 100644 (file)
--- a/examples-jbake/templates/jvl_embedded.ftl
+++ b/examples-jbake/templates/jvl_embedded.ftl
@@ -8,7 +8,7 @@
     <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
       Jalview Alignment Annotations File</li>
   </ul>
-  <@jvlitebutton appjar="${content.jvl}" width=756 height=560 
+  <@jvlitebutton appjar="${content.jvl},${content.jmol}" width=756 height=560 
                 params={
                 "file":"plantfdx.fa",
                 "annotations":"plantfdx.annotations",

diff --git a/examples-jbake/templates/jvl_examples.ftl b/examples-jbake/templates/jvl_examples.ftl
index f2bf8b1..ec5c684 100644 (file)
--- a/examples-jbake/templates/jvl_examples.ftl
+++ b/examples-jbake/templates/jvl_examples.ftl
@@ -12,7 +12,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
   <table width="90%">
     <tr>
       <td width="10%" valign="center">
-       <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
+       <@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
                       , "treeFile":"ferredoxin.nw"
                       , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
                       , "showFullId":"false"
@@ -24,7 +24,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
        group consensus and sequence logos are shown below the alignment.</td>
     </tr>
     <tr>
-      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions",
        "file":"uniref50.fa"
                                                     , "features":"exampleFeatures.txt"
                                                     , "showFeatureSettings":"true"
@@ -49,7 +49,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
        FER1_MAIZE</td>
     </tr>
     <tr>
-      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
                                                       , "file":"jpred_msa.fasta"
                                                       , "jnetfile":"jpred_msa.seq.concise"
                                                       , "defaultColour":"Clustal"
@@ -71,7 +71,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
   </p>
   <table width="90%">
     <tr>
-      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
                                                     , "file":"RF00031_folded.stk"
                                                     , "defaultColour":"Purine/Pyrimidine"
                                                     , "showAnnotation":"true"

diff --git a/examples-jbake/templates/jvl_formComplete.ftl b/examples-jbake/templates/jvl_formComplete.ftl
index cab6cc3..ff82339 100644 (file)
--- a/examples-jbake/templates/jvl_formComplete.ftl
+++ b/examples-jbake/templates/jvl_formComplete.ftl
@@ -5,7 +5,7 @@ instance on the page.</p>
 View the source in your browser to see how it has been done. <br/>
 <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
 <applet code="jalview.bin.JalviewLite" width="0" height="0"
-       archive="${content.jvl}" name="Jalview">
+       archive="${content.jvl},${content.jmol}" name="Jalview">
   <#if content.permissions?exists><param name="permissions" value="${content.permissions}"/></#if>
   <param name="file" value="plantfdx.fa"/>
   <param name="features" value="plantfdx.features"/>

diff --git a/examples-jbake/templates/jvl_javascriptLaunch.ftl b/examples-jbake/templates/jvl_javascriptLaunch.ftl
index 43ae6c2..a6ce80a 100644 (file)
--- a/examples-jbake/templates/jvl_javascriptLaunch.ftl
+++ b/examples-jbake/templates/jvl_javascriptLaunch.ftl
@@ -83,7 +83,7 @@ function startJalview(aligURL,title,alwvar) {
 </SCRIPT>
   <form name="Form1">
 <applet name="JalviewLite"  code="jalview.bin.JalviewLite"
-archive="${content.jvl}" width="0" height="0">
+archive="${content.jvl},${content.jmol}" width="0" height="0">
 <param name="debug" value="true"/>
 <param name="showbutton" value="false"/>
 <#if (content.permissions?exists)>

diff --git a/examples-jbake/templates/jvl_linkedapplets_ng.ftl b/examples-jbake/templates/jvl_linkedapplets_ng.ftl
index 1de2e58..6c0e6d5 100644 (file)
--- a/examples-jbake/templates/jvl_linkedapplets_ng.ftl
+++ b/examples-jbake/templates/jvl_linkedapplets_ng.ftl
@@ -24,7 +24,7 @@
        <script> 
   var attributes = {
     code : 'jalview.bin.JalviewLite',
-    archive : '${content.jvl}',
+    archive : '${content.jvl},${content.jmol}',
     width : 800,
     height : 300,
     mayscript : 'True', scriptable: 'True',
@@ -57,7 +57,7 @@
 <script> 
   var attributes = {
     code : 'jalview.bin.JalviewLite',
-    archive : '${content.jvl}',
+    archive : '${content.jvl},${content.jmol}',
     width : 800,
     height : 300,
     mayscript : 'True', scriptable: 'True',

diff --git a/examples/applets.html b/examples/applets.html
index cc85e86..6fcc8df 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -189,7 +189,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td width="10%" valign="center">
        <applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="uniref50.fa"/>
 <param name="treeFile" value="ferredoxin.nw"/>
@@ -215,7 +215,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="uniref50.fa"/>
 <param name="features" value="exampleFeatures.txt"/>
@@ -266,7 +266,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="jpred_msa.fasta"/>
 <param name="jnetfile" value="jpred_msa.seq.concise"/>
@@ -297,7 +297,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="RF00031_folded.stk"/>
 <param name="showFullId" value="false"/>

diff --git a/examples/embedded.html b/examples/embedded.html
index a14dd75..63d0fe0 100644 (file)
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -185,7 +185,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
   </ul>
   <applet
    code="jalview.bin.JalviewLite" width="756" height="560"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="plantfdx.fa"/>
 <param name="features" value="plantfdx.features"/>

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index f482ebe..e60f8b2 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -138,7 +138,7 @@ function genHref()
  var _jvA=new Object();
  _jvA.attributes = {
   code : 'jalview.bin.JalviewLite',
-  archive : 'jalviewApplet.jar',
+  archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
   width : '500',
   height : '350',
   mayscript : 'True',

diff --git a/examples/formComplete.html b/examples/formComplete.html
index b37c65e..86b294b 100644 (file)
--- a/examples/formComplete.html
+++ b/examples/formComplete.html
@@ -180,7 +180,7 @@ instance on the page.</p>
 View the source in your browser to see how it has been done. <br/>
 <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
 <applet code="jalview.bin.JalviewLite" width="0" height="0"
-       archive="jalviewApplet.jar" name="Jalview">
+       archive="jalviewApplet.jar,JmolApplet-12.2.4.jar" name="Jalview">
   
   <param name="file" value="plantfdx.fa"/>
   <param name="features" value="plantfdx.features"/>

diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index 4a9abfe..fd47cd5 100644 (file)
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -258,7 +258,7 @@ function startJalview(aligURL,title,alwvar) {
 </SCRIPT>
   <form name="Form1">
 <applet name="JalviewLite"  code="jalview.bin.JalviewLite"
-archive="jalviewApplet.jar" width="0" height="0">
+archive="jalviewApplet.jar,JmolApplet-12.2.4.jar" width="0" height="0">
 <param name="debug" value="true"/>
 <param name="showbutton" value="false"/>
 </applet>

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 9c88710..71f1540 100644 (file)
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -201,7 +201,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
        <script> 
   var attributes = {
     code : 'jalview.bin.JalviewLite',
-    archive : 'jalviewApplet.jar',
+    archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
     width : 800,
     height : 300,
     mayscript : 'True', scriptable: 'True',
@@ -234,7 +234,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
 <script> 
   var attributes = {
     code : 'jalview.bin.JalviewLite',
-    archive : 'jalviewApplet.jar',
+    archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
     width : 800,
     height : 300,
     mayscript : 'True', scriptable: 'True',