Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 427c8b7..3b10c14 100644 (file)
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -80,7 +80,11 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script> 
 </head>
 
 
@@ -88,10 +92,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -100,39 +104,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -546,7 +549,7 @@ document.onclick = mclose;
           </li>
           <li>Note parameter &quot;PDBSeq&quot; is no longer required.<br>
           </li>
-          <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li> 
+          <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li> 
             <p>&nbsp;</p>
           </li>
         </ul>
@@ -599,18 +602,5 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </div>
 </div>
-
-<script type="text/javascript">
-    var gaJsHost = (("https:" == document.location.protocol) ?
- "https://ssl." : "http://www.");
-    document.write(unescape("%3Cscript src=\'" + gaJsHost +
- "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-    var pageTracker = _gat._getTracker("'UA-9060947-1'");
-    pageTracker._trackPageview();
-} catch(err) {}
-</script>
 </body>
 </html>

diff --git a/examples/applets.html b/examples/applets.html
index e3e1d3c..c53cc7a 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -79,7 +79,11 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script>
 </head>
 
 
@@ -87,10 +91,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -99,39 +103,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -319,4 +322,4 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </body>
 </html>
-          
\ No newline at end of file
+          

diff --git a/examples/embedded.html b/examples/embedded.html
index 2f74116..2384737 100644 (file)
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -79,7 +79,11 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script>
 </head>
 
 
@@ -87,10 +91,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -99,39 +103,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 86dceea..5a65953 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -19,6 +19,11 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
 <head>
 <TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script>
 <script src="javascript/deployJava.js"></script>
 <script src="jmol/Jmol.js"></script>
 <script src="javascript/jquery-1.4.4.min.js"></script>
@@ -177,10 +182,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -189,39 +194,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -269,18 +273,5 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </div>
 </div>
-
-<script type="text/javascript">
-    var gaJsHost = (("https:" == document.location.protocol) ?
- "https://ssl." : "http://www.");
-    document.write(unescape("%3Cscript src=\'" + gaJsHost +
- "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-    var pageTracker = _gat._getTracker("'UA-9060947-1'");
-    pageTracker._trackPageview();
-} catch(err) {}
-</script>
 </body>
 </html>

diff --git a/examples/formComplete.html b/examples/formComplete.html
index 71a904a..91b0670 100644 (file)
--- a/examples/formComplete.html
+++ b/examples/formComplete.html
@@ -79,7 +79,11 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script>
 </head>
 
 
@@ -87,10 +91,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -99,39 +103,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -218,18 +221,6 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </div>
 </div>
-
-<script type="text/javascript">
-    var gaJsHost = (("https:" == document.location.protocol) ?
- "https://ssl." : "http://www.");
-    document.write(unescape("%3Cscript src=\'" + gaJsHost +
- "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-    var pageTracker = _gat._getTracker("'UA-9060947-1'");
-    pageTracker._trackPageview();
-} catch(err) {}
-</script></body>
+</body>
 </html>
-  
\ No newline at end of file
+  

diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html
index 5d0af5d..0e8b78a 100644 (file)
--- a/examples/jalviewLiteJs.html
+++ b/examples/jalviewLiteJs.html
@@ -80,7 +80,9 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
 </head>
 
 
@@ -88,10 +90,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -100,39 +102,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
-       <li><a href="#">Home</a></li>
-       <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
-               <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-               <a href="#">Documentation</a>
-               <a href="#">Publications</a>
-               <a href="#">Credits</a>
-               <a href="#">Screenshots</a>
-               </div>
-       </li>
-       <li><a href="#">FAQ</a></li>
-       <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
-               <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-               <a href="#">News Mailing List</a>
-               <a href="#">Discussion Mailing List</a>
-               <a href="#">Links</a>
-               <a href="#">Community News</a>
-               </div>
-       </li>
-       <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
-               <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-               <a href="#">Release History</a>
-               <a href="#">Jalview Bug Tracker</a>
-               <a href="#">Jalview Git Web</a>
-               <a href="#">Development News</a>
-               </div>
-       </li>
-       <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
-               <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-               <a href="#">Training Courses</a>
-               <a href="#">Training News</a>
-               </div>
-       </li>
-       <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+  <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
+  </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+  <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
+  </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+  <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
+  </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+  <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
+  </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -422,17 +423,5 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </div>
 </div>
-
-<script type="text/javascript">
-    var gaJsHost = (("https:" == document.location.protocol) ?
- "https://ssl." : "http://www.");
-    document.write(unescape("%3Cscript src=\'" + gaJsHost +
- "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-    var pageTracker = _gat._getTracker("'UA-9060947-1'");
-    pageTracker._trackPageview();
-} catch(err) {}
-</script></body>
+</body>
 </html>

diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index 7dbf8e0..f555265 100644 (file)
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -79,7 +79,9 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
 </head>
 
 
@@ -87,10 +89,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -99,39 +101,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -267,19 +268,6 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </div>
 </div>
-
-<script type="text/javascript">
-    var gaJsHost = (("https:" == document.location.protocol) ?
- "https://ssl." : "http://www.");
-    document.write(unescape("%3Cscript src=\'" + gaJsHost +
- "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-    var pageTracker = _gat._getTracker("'UA-9060947-1'");
-    pageTracker._trackPageview();
-} catch(err) {}
-</script>
 </body>
 </head>
-</html>
\ No newline at end of file
+</html>

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 4296146..86f4bc0 100644 (file)
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -23,6 +23,11 @@
   
  <link href="css/reset.css" rel="stylesheet" type="text/css" />
  <link href="css/style.css" rel="stylesheet" type="text/css" />
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script>
 <script src="http://www.java.com/js/deployJava.js"></script>
 <script src="javascript/jalview.js" language="javascript"></script>
 <script>  //deployJava.debug="true";
@@ -106,10 +111,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -118,39 +123,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -267,18 +271,5 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </div>
 </div>
-
-<script type="text/javascript">
-    var gaJsHost = (("https:" == document.location.protocol) ?
- "https://ssl." : "http://www.");
-    document.write(unescape("%3Cscript src=\'" + gaJsHost +
- "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
-</script>
-<script type="text/javascript">
-try{
-    var pageTracker = _gat._getTracker("'UA-9060947-1'");
-    pageTracker._trackPageview();
-} catch(err) {}
-</script>
 </body>
 </html>

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index c85de33..3d54ae1 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -762,7 +762,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               dragEvent.getY());
     }
 
-    if ((aa == null) || (aa.length < 1))
+    if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
     {
       g.setColor(Color.black);
       g.drawString("Right click", 2, 8);

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 1577477..dd6f190 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -960,7 +960,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               dragEvent.getY() - scrollOffset);
     }
 
-    if ((aa == null) || (aa.length < 1))
+    if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
     {
       g.drawString("Right click", 2, 8);
       g.drawString("to add annotation", 2, 18);

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 7ab7fda..ab27d8a 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -257,7 +257,10 @@ public class AnnotationRenderer
     updateFromAwtRenderPanel(annotPanel, av);
     fm = g.getFontMetrics();
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-
+    if (aa==null)
+    {
+      return false;
+    }
     int x = 0, y = 0;
     int column = 0;
     char lastSS;

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 78f2477..0940f40 100644 (file)
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -83,4 +83,10 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
     return "EMBL (CDS)";
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+
 }

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 4495be1..c7be59a 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -114,4 +114,10 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
   {
     return "EMBL"; // getDbSource();
   }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 125a295..81c8ea3 100644 (file)
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -118,4 +118,9 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
   {
     return "GeneDB"; // getDbSource();
   }
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index b432dff..b96a65c 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -209,4 +209,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return "PDB"; // getDbSource();
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 75d4559..077b929 100644 (file)
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -65,4 +65,9 @@ public class PfamFull extends Pfam implements DbSourceProxy
     return null;
   }
 
+   @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index cab4999..cb00a1d 100644 (file)
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -62,4 +62,9 @@ public class PfamSeed extends Pfam implements DbSourceProxy
     return "PF03760";
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java
index 3703e41..e20527a 100644 (file)
--- a/src/jalview/ws/dbsources/RfamFull.java
+++ b/src/jalview/ws/dbsources/RfamFull.java
@@ -70,4 +70,9 @@ public class RfamFull extends Rfam implements DbSourceProxy
     return null;
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
index eb3c2c3..75fa62b 100644 (file)
--- a/src/jalview/ws/dbsources/RfamSeed.java
+++ b/src/jalview/ws/dbsources/RfamSeed.java
@@ -69,4 +69,9 @@ public class RfamSeed extends Rfam implements DbSourceProxy
     return null;
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 48f8649..1b967c4 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -294,4 +294,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   {
     return "Uniprot"; // getDbSource();
   }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
index 1511e6b..308bc21 100644 (file)
--- a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
+++ b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
@@ -74,4 +74,10 @@ public interface jalviewSourceI
    */
   boolean isNewerThan(jalviewSourceI jalviewSourceI);
 
+  /**
+   * test if the source is a reference source for the authority
+   * @return
+   */
+  boolean isReferenceSource();
+
 }

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 95ff7d0..9650b8c 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -70,6 +70,11 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   protected MultipleConnectionPropertyProviderI connprops = null;
 
   /**
+   * DAS sources are tier 1 - if we have a direct DB connection then we should prefer it
+   */
+  private int tier=1;
+
+  /**
    * create a new DbSource proxy for a DAS 1 source
    * 
    * @param dbnbame
@@ -94,6 +99,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
       throw new Exception("Source " + source.getTitle()
               + " does not support the sequence command.");
     }
+    this.tier = 1+((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
     this.source = source;
     this.dbname = dbname;
     this.dbrefname = dbrefname.toUpperCase();
@@ -334,4 +340,10 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   {
     return coordsys;
   }
+
+  @Override
+  public int getTier()
+  {
+    return tier;
+  }
 }

diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index eb9d807..f68a005 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -366,4 +366,11 @@ public class JalviewSource implements jalviewSourceI
     return isLaterThan(getVersion().getCreated(), other.getVersion()
             .getCreated());
   }
+
+  @Override
+  public boolean isReferenceSource()
+  {
+    // TODO check source object for indication that we are the primary for a DAS coordinate system
+    return false;
+  }
 }

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 1a21fea..8ad14e0 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -23,6 +23,7 @@ import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.ws.WSMenuEntryProviderI;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ParamDatastoreI;
 
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -250,7 +251,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
     services.add(service);
     // retrieve the presets and parameter set and cache now
-    service.getParamStore().getPresets();
+    ParamDatastoreI pds = service.getParamStore();
+    if (pds != null)
+    {
+      pds.getPresets();
+    }
     service.hasParameters();
     if (validServiceUrls == null)
     {

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 09f4a48..aa42ff7 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -173,6 +173,8 @@ public class Jws2Instance
                         : null));
       } catch (Exception ex)
       {
+        System.err.println("Unexpected exception creating JabaParamStore.");
+        ex.printStackTrace();
       }
 
     }

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 45b866e..e475915 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -272,9 +272,10 @@ public class ASequenceFetcher
       DbSourceProxy[] l = dblist.values().toArray(new DbSourceProxy[0]);
       int i = 0;
       String[] nm = new String[l.length];
+      // make sure standard dbs appear first, followed by reference das sources, followed by anything else.
       for (DbSourceProxy s : l)
       {
-        nm[i++] = s.getDbName().toLowerCase();
+        nm[i++] = ""+s.getTier()+s.getDbName().toLowerCase();
       }
       jalview.util.QuickSort.sort(nm, l);
       dbs = new ArrayList<DbSourceProxy>();

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index cc9997f..e4b76b9 100644 (file)
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -134,4 +134,11 @@ public interface DbSourceProxy
    * @return true if the source has this property
    */
   public boolean isA(Object dbsourceproperty);
+
+  /**
+   * Tier for this data source
+   *  
+   * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
+   */
+  public int getTier();
 }

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
new file mode 100644 (file)
index 0000000..2f826b3
--- /dev/null
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -0,0 +1,78 @@
+/**
+ * 
+ */
+package jalview.ws.seqfetcher;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import jalview.datamodel.DBRefSource;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.SequenceFetcher;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+/**
+ * @author jimp
+ *
+ */
+public class DbRefFetcherTest
+{
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @BeforeClass
+  public static void setUpBeforeClass() throws Exception
+  {
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception
+  {
+  }
+
+  @Test
+  public void testStandardProtDbs()
+  {
+    String[] defdb = DBRefSource.PROTEINDBS;
+  List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+  for (String ddb : defdb)
+  {
+    SequenceFetcher sfetcher= new SequenceFetcher();
+    List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+    
+    if (srcesfordb != null)
+    {
+      srces.addAll(srcesfordb);
+    }
+  }
+  DbSourceProxy uniprot=null;
+  int i=0;
+  // append the selected sequence sources to the default dbs
+  for (DbSourceProxy s:srces)
+  {
+    if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+    {
+      i++;
+    }
+    
+    if (s instanceof jalview.ws.dbsources.Uniprot)
+    {
+      uniprot = s;
+      break;
+    }
+  }
+          
+  assertTrue("Failed to find Uniprot source as first source amongst "+srces.size()+" sources (source was at position "+i+")", uniprot!=null && i<2);
+  }
+
+}