From 3bdff434d35a6713ebbdc94c9e1fedab7aee1b81 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 28 Jan 2014 11:41:12 +0000
Subject: [PATCH] JAL-957 permissions property for example pages (jbake
 generated)

---
 examples/applets.html  |   44 +++++++++++++++++++++++++++++++++++++++-----
 examples/embedded.html |    7 ++++++-
 2 files changed, 45 insertions(+), 6 deletions(-)

diff --git a/examples/applets.html b/examples/applets.html
index fcbcb9a..a83270c 100755
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -185,7 +185,14 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
 	<applet
    code="jalview.bin.JalviewLite" width="140" height="35"
    archive="jalviewApplet.jar">
-<param name="file" value="uniref50.fa"/><param name="treeFile" value="ferredoxin.nw"/><param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/><param name="sortByTree" value="True"/><param name="showSequenceLogo" value="true"/><param name="showGroupConsensus" value="true"/><param name="showFullId" value="false"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="treeFile" value="ferredoxin.nw"/>
+<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+<param name="sortByTree" value="True"/>
+<param name="showSequenceLogo" value="true"/>
+<param name="showGroupConsensus" value="true"/>
+<param name="showFullId" value="false"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -204,7 +211,15 @@ 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">
-<param name="file" value="uniref50.fa"/><param name="features" value="exampleFeatures.txt"/><param name="showFullId" value="false"/><param name="windowHeight" value="500"/><param name="windowWidth" value="650"/><param name="showFeatureSettings" value="true"/><param name="wrap" value="true"/><param name="showAnnotation" value="false"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="features" value="exampleFeatures.txt"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="showFeatureSettings" value="true"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -221,7 +236,14 @@ 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,JmolApplet-12.2.4.jar">
-<param name="file" value="uniref50.fa"/><param name="showFullId" value="false"/><param name="windowHeight" value="500"/><param name="windowWidth" value="650"/><param name="wrap" value="true"/><param name="showAnnotation" value="false"/><param name="defaultColour" value="Strand Propensity"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
+<param name="defaultColour" value="Strand Propensity"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -239,7 +261,13 @@ 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">
-<param name="file" value="jpred_msa.fasta"/><param name="showFullId" value="false"/><param name="windowHeight" value="515"/><param name="windowWidth" value="650"/><param name="showAnnotation" value="true"/><param name="defaultColour" value="Clustal"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="jpred_msa.fasta"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Clustal"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
@@ -263,7 +291,13 @@ 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">
-<param name="file" value="RF00031_folded.stk"/><param name="showFullId" value="false"/><param name="windowHeight" value="515"/><param name="windowWidth" value="650"/><param name="showAnnotation" value="true"/><param name="defaultColour" value="Purine/Pyrimidine"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="RF00031_folded.stk"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
    <param name="APPLICATION_URL"
      value="http://www.jalview.org/services/launchApp"/>
 </applet>
diff --git a/examples/embedded.html b/examples/embedded.html
index 3be159e..e1029e0 100644
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -181,7 +181,12 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
   <applet
    code="jalview.bin.JalviewLite" width="756" height="560"
    archive="jalviewApplet.jar">
-<param name="file" value="plantfdx.fa"/><param name="features" value="plantfdx.features"/><param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/><param name="showFullId" value="false"/><param name="embedded" value="true"/>
+<param name="permissions" value="sandbox"/>
+<param name="file" value="plantfdx.fa"/>
+<param name="features" value="plantfdx.features"/>
+<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+<param name="showFullId" value="false"/>
+<param name="embedded" value="true"/>
    <param name="linkLabel_1" value="Uniprot"/>
    <param name="linkUrl_1"
      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
-- 
1.7.10.2