X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=e9221e0506121df61962bebb34ce6362ca4c99aa;hb=89bee60470f83e553493a40460f1f135a02d0696;hp=e0f0db3fd4ad9ef3ad4c0db28f5c613a3986da64;hpb=16d109024847af92482237e43f99b82fd997451a;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index e0f0db3..e9221e0 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -115,7 +115,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             af.getViewport()
                     .getGlobalColourScheme() instanceof RNAHelicesColour,
             "Couldn't apply RNA helices colourscheme");
-    assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+    af.saveAlignment(tfile, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
     af = null;
@@ -157,14 +158,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase
                             .getSchemeName()),
             "Recognise T-Coffee score from string");
 
-    assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+    af.saveAlignment(tfile, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
     af = null;
     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
             DataSourceType.FILE);
     assertNotNull(af, "Failed to import new project");
-    assertSame(viewport.getGlobalColourScheme().getClass(),
+    assertSame(af.getViewport().getGlobalColourScheme().getClass(),
             TCoffeeColourScheme.class,
             "Didn't set T-coffee colourscheme for imported project.");
     System.out.println(
@@ -203,7 +205,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
     af.alignPanel.alignmentChanged();
-    assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+    af.saveAlignment(tfile, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
     af = null;
@@ -819,6 +822,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     /*
      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
      */
+    av.setColourAppliesToAllGroups(false);
     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
     af.abovePIDThreshold_actionPerformed(true);
@@ -980,7 +984,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     File tfile = File.createTempFile("JalviewTest", ".jvp");
     tfile.deleteOnExit();
     String filePath = tfile.getAbsolutePath();
-    assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+    af.saveAlignment(filePath, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
 
     /*