Merge branch 'Release_2_8_Branch' into WIP_fix_JAL-1423

Conflicts:
	examples/linkedapplets_ng.html

diff --git a/build.xml b/build.xml
index c29f2c1..e7f05bc 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -97,7 +97,7 @@
 
     <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
     <property name="application.codebase" value="*.jalview.org"/>
-    <property name="applet.codebase" value="*.jalview.org"/>
+    <property name="applet.codebase" value="*"/>
     <property name="applet.caller-codebase" value="${applet.codebase}"/>
 
                <!-- build directory configuration -->
@@ -424,7 +424,6 @@
                        <manifest>
                                <attribute name="Main-Class" value="jalview.bin.Jalview" />
         <attribute name="Permissions" value="all-permissions" />
-        <!--<attribute name="Trusted-Lib" value="true" /> -->
         <attribute name="Application-Name" value="Jalview Desktop"/>
         <attribute name="Codebase" value="${application.codebase}"/>
                        </manifest>
@@ -475,11 +474,9 @@
                <jar destfile="in.jar" index="true">
                        <manifest>
                                <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
-                               <attribute name="Application-Name" value="JalviewLite Applet"/>
-                               <!--            <attribute name="Permissions" value="sandbox" /> -->
-                               <!--<attribute name="Trusted-Lib" value="true" /> -->
+                               <attribute name="Application-Name" value="JalviewLite"/>
+                               <attribute name="Permissions" value="all-permissions" />
                                <attribute name="Codebase" value="${applet.codebase}"/>
-                               <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
                        </manifest>
                        <fileset dir="${outputDir}">
                                <include name="com/**" />
@@ -596,22 +593,48 @@
       <include name="jmol/*"/>
          </fileset>
                <fileset dir=".">
-               <include name="jalviewApplet.jar"/>
+               <include name="${jalviewLiteJar}"/>
                        </fileset>
                <fileset dir="appletlib">
                      <include name="**/*"/>
                        </fileset>
          </copy>
-           <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
-           <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+         <presetdef name="applet.jar">
+           <jar update="true" index="true">
                <manifest>
-               <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
-               <!--          <attribute name="Permissions" value="sandbox" /> -->
-               <!--<attribute name="Trusted-Lib" value="true" /> -->
-               <attribute name="Codebase" value="${applet.codebase}"/>
-               <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
-                 </manifest>
-               </jar>
+               <attribute name="Application-Name" value="JalviewLite"/>
+               <attribute name="Permissions" value="all-permissions"/>
+               <attribute name="Codebase" value="${applet.codebase}"/>
+               <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+               <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}"/>
+               <!--
+               <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}"/>
+               -->
+<!--           <attribute name="Trusted-Only" value="true"/>
+-->
+<!--           <attribute name="Trusted-Library" value="true"/>
+-->
+               </manifest>
+         </jar>
+         </presetdef>
+         <presetdef name="applet_tl.jar">
+           <jar update="true" index="true" jarfile="@{jarfile}">
+               <manifest>
+               <attribute name="Application-Name" value="JalviewLite"/>
+               <attribute name="Permissions" value="all-permissions" />
+               <attribute name="Codebase" value="${applet.codebase}"/>
+               <attribute name="Trusted-Only" value="true"/>
+               <attribute name="Trusted-Library" value="true"/>
+               </manifest>
+         </jar>
+
+         </presetdef>
+         <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
+         <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}"/>
+         <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+         <applet_tl.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
+         <applet.jar jarfile="${packageDir}/examples/${jmolJar}"/>
+         <applet_tl.jar jarfile="${packageDir}/examples/tl_${jmolJar}"/>
     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 
       <fileset dir="${packageDir}/examples">

diff --git a/examples/applets.html b/examples/applets.html
index 0629af0..a6d61f8 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -178,7 +178,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
       <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"
@@ -204,7 +204,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
       <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">
@@ -228,7 +228,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
       <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">
                         -->
@@ -255,7 +255,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
       <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">
@@ -288,7 +288,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
       <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 --git a/examples/embedded.html b/examples/embedded.html
index ce6fca5..1493ea5 100644 (file)
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -169,7 +169,7 @@ 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">
-                       <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">

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index af15654..79cf5cb 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -109,7 +109,7 @@ function genHref()
   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 --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index d565ed2..9020e2b 100644 (file)
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -242,7 +242,7 @@ function startJalview(aligURL,title,alwvar) {
 archive="jalviewApplet.jar" width="0" height="0">
 <param name="debug" value="true"/>
 <param name="showbutton" value="false"/>
-<param name="permissions" value="sandbox"/>
+<param name="permissions" value="all-permissions"/>
 </applet>
 
 

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index c36f649..6993f2f 100644 (file)
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -205,8 +205,8 @@ document.onclick = mclose;
     ,
     linkLabel_2 : "Uniprot"
     ,
-    permissions : 'sandbox',
     linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+    permissions : 'all-permissions',
     APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
  
@@ -238,8 +238,8 @@ document.onclick = mclose;
     ,
     linkLabel_2 : "Uniprot"
     ,
-    permissions : 'sandbox',
     linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+    permissions : 'all-permissions',
    APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
   deployJava.runApplet(attributes, parameters, '1.6');