Merge branch 'releases/Release_2_10_Branch' into develop

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index caaa7f9..31ad2f5 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -46,7 +46,11 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 
-lib/htsjdk-1.120-SNAPSHOT.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+
+lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
+
+lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
 
 
 Additional dependencies
@@ -55,6 +59,3 @@ examples/javascript/deployJava.js : http://java.com/js/deployJava.js
 examples/javascript/jquery*.js : BSD license
 examples/javascript/jshashtable-2.1.js : Apache License
 
-Tools not bundled with Jalview source
-jbake (http://jbake.org MIT license) was used to build the JalviewLite examples pages found in the examples directory.
-

diff --git a/help/html/releases.html b/help/html/releases.html
index c88d13d..c547ffb 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,12 +47,15 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
         </div>
       </td>
       <td><em>General</em>
         <ul>
           <li>
+          <!-- JAL-2124 -->Updated Spanish translations.
+          </li> 
+          <li>
             <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
             for importing structure data to Jalview. Enables mmCIF and
             better PDB parsing.
@@ -208,7 +211,11 @@
             Ref Fetcher fails to match, or otherwise updates sequence
             data from external database records.
           </li>
-
+          <li>
+            <!-- JAL-2154 -->Revised Jalview Project format for
+            efficient recovery of sequence coding and alignment
+            annotation relationships.
+          </li>
         </ul> <!-- <em>Applet</em>
         <ul>
           <li>
@@ -421,7 +428,7 @@
             </li>
             <li>
               <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
-              after fetching cross-references
+              after fetching cross-references, and restoring from project
             </li>
             <li>
               <!-- JAL-2032 -->Mouseover of a copy of a sequence is not

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d24daa1..9a8e5f6 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2544,6 +2544,8 @@ public class Jalview2XML
           SplitFrame sf = createSplitFrame(dnaFrame, af);
           addedToSplitFrames.add(dnaFrame);
           addedToSplitFrames.add(af);
+          dnaFrame.setMenusForViewport();
+          af.setMenusForViewport();
           if (af.viewport.isGatherViewsHere())
           {
             gatherTo.add(sf);
@@ -2565,6 +2567,7 @@ public class Jalview2XML
         Viewport view = candidate.getKey();
         Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
                 view.getHeight());
+        af.setMenusForViewport();
         System.err.println("Failed to restore view " + view.getTitle()
                 + " to split frame");
       }