Merge branch 'task/JAL-2164_mcviewforoldjalviewprojects' into develop

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3736791..15f88fb 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2831,7 +2831,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.explodeViews(this);
+    Desktop.explodeViews(this);
   }
 
   /**

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index d54e553..7811e41 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1806,7 +1806,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * 
    * @param af
    */
-  public void explodeViews(AlignFrame af)
+  public static void explodeViews(AlignFrame af)
   {
     int size = af.alignPanels.size();
     if (size < 2)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1633a5d..f12d106 100644 (file)
--- 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 d941242..915625f 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -41,8 +41,6 @@ import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
-import jalview.structure.StructureImportSettings;
-import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.io.File;
@@ -276,9 +274,6 @@ public class Jalview2xmlTests
             Boolean.TRUE.toString());
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
-     StructureImportSettings.setDefaultStructureFileFormat("PDB");
-    StructureImportSettings
-            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
     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);
@@ -369,40 +364,27 @@ public class Jalview2xmlTests
   }
 
   /**
-   * test store and recovery of expanded views - currently this is disabled
-   * since the Desktop.explodeViews method doesn't seem to result in the views
-   * being expanded to distinct align frames when executed programmatically.
+   * test store and recovery of expanded views
    * 
    * @throws Exception
    */
   @Test(groups = { "Functional" }, enabled = true)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
-    StructureImportSettings
-            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
-    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+
     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();
-    {
-      final AlignFrame xaf = af;
-      af = null;
-      new Thread(new Runnable()
-      {
-        @Override
-        public void run()
-        {
-          Desktop.instance.explodeViews(xaf);
-        }
-      }).start();
-      Thread.sleep(1000);
-    }
-    // int times = 0;
-    // while (++times < 5 && Desktop.getAlignFrames().length < )
-    // {
-    // Thread.sleep(300);
-    // }
+
+    // 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,
             Desktop.getAlignmentPanels(afid).length);
@@ -443,7 +425,6 @@ public class Jalview2xmlTests
   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
   {
     Desktop.instance.closeAll_actionPerformed(null);
-    StructureImportSettings.setDefaultStructureFileFormat("PDB");
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);