Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

diff --git a/doc/UnitTesting.html b/doc/UnitTesting.html
index c4d63ff..801f064 100644 (file)
--- a/doc/UnitTesting.html
+++ b/doc/UnitTesting.html
@@ -83,7 +83,7 @@ The TestNG tests for Jalview can be executed in any of the following ways:
        <ul>
             <li>Ensure that you have TestNG plugin correctly install for eclipse</li>
             <li>Ensure that your test classes are error free and properly annotated</li>
-            <li>Create a lunch configuration "Select the Run / Run... (or Run / Debug...) menu and create a new TestNG configuration"</li>
+            <li>Create a launch configuration "Select the Run / Run... (or Run / Debug...) menu and create a new TestNG configuration"</li>
            <li>Run the tests by executing the configuration target created above</li>
         </ul> 
        A more detailed guide for installing and executing TestNG in eclipse is available at <a href=http://testng.org/doc/eclipse.html>testng.org/doc/eclipse.html</a> <br>&nbsp;

diff --git a/help/html/io/export.html b/help/html/io/export.html
index 1496376..46e7fe4 100755 (executable)
--- a/help/html/io/export.html
+++ b/help/html/io/export.html
@@ -46,8 +46,7 @@
     <li>BioJS MSA - A JavaScript based multiple sequence alignment
       viewer. <br> <em>For interactive alignment data
         visualisation in a web browser.<br />Get more info about the
-        BioJS MSA viewer at a
-        href="http://msa.biojs.net/">http://msa.biojs.net/</a>
+        BioJS MSA viewer at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a>
     </em>
     </li>
 
@@ -58,12 +57,12 @@
   <p>
     In Jalview 2.9, new HTML exporting options were introduced. The
     standard HTML export option displays alignments as SVG documents
-    embedded as scollable panes. Exported pages can optionally also
+    embedded as scrollable panes. Exported pages can optionally also
     include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
     which allows Jalview to extract the original data used to create the
     page. Jalview can also generate HTML pages which embed BioJSON data
     and the BioJS MSA viewer, a pure javascript alignment viewer that
-    provides a range of interactive analysis capabiltiies.
+    provides a range of interactive analysis capabilities.
   </p>
   <p>
   <p>

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 3d59a12..efb77e7 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2860,6 +2860,15 @@ public class JalviewLite extends Applet implements
           URL localref)
   {
     String resolvedPath = "";
+    if (targetPath.startsWith("/"))
+    {
+      String codebase = localref.toString();
+      String localfile = localref.getFile();
+      resolvedPath = codebase.substring(0,
+              codebase.length() - localfile.length())
+              + targetPath;
+      return resolvedPath;
+    }
 
     /*
      * get URL path and strip off any trailing file e.g.