From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 1 Aug 2016 07:49:54 +0000 (+0100)
Subject: JAL-1772 make sure we actually return reference to AlignFrame that is visible after... 
X-Git-Tag: Release_2_10_0~127^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=74d1897e700018c3a1eb01b6d6ed94f26b171824;p=jalview.git

JAL-1772 make sure we actually return reference to AlignFrame that is visible after views are gathered
---

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1633a5d..f12d106 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2276,12 +2276,20 @@ public class Jalview2XML
           if (true) // !skipViewport(object))
           {
             _af = loadFromObject(object, file, true, jprovider);
-            if (object.getJalviewModelSequence().getViewportCount() > 0)
+            if (_af != null
+                    && object.getJalviewModelSequence().getViewportCount() > 0)
             {
-              af = _af;
-              if (af.viewport.isGatherViewsHere())
+              if (af == null)
               {
-                gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+                // store a reference to the first view
+                af = _af;
+              }
+              if (_af.viewport.isGatherViewsHere())
+              {
+                // if this is a gathered view, keep its reference since
+                // after gathering views, only this frame will remain
+                af = _af;
+                gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
               }
             }
           }
diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 26fba58..915625f 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -371,12 +371,19 @@ public class Jalview2xmlTests
   @Test(groups = { "Functional" }, enabled = true)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
+
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);
     String afid = af.getViewport().getSequenceSetId();
 
-    Desktop.explodeViews(Desktop.getAlignFrameFor(af.getViewport()));
+    // check FileLoader returned a reference to the one alignFrame that is
+    // actually on the Desktop
+    assertTrue(
+            "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
+            af == Desktop.getAlignFrameFor(af.getViewport()));
+
+    Desktop.explodeViews(af);
 
     int oldviews = Desktop.getAlignFrames().length;
     Assert.assertEquals(Desktop.getAlignFrames().length,