X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=e9221e0506121df61962bebb34ce6362ca4c99aa;hb=89bee60470f83e553493a40460f1f135a02d0696;hp=d6df39a07e9ee6b3605beba9eff203ec41dea068;hpb=6db15a0553c0323a33121baad6d23ac9d8d4250b;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index d6df39a..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;
@@ -147,16 +148,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
-    assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+    AlignViewport viewport = af.getViewport();
+    assertSame(viewport.getGlobalColourScheme().getClass(),
             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
     assertNotNull(
-            ColourSchemeProperty.getColourScheme(
-                    af.getViewport().getAlignment(),
-                    af.getViewport().getGlobalColourScheme()
+            ColourSchemeProperty.getColourScheme(viewport,
+                    viewport.getAlignment(),
+                    viewport.getGlobalColourScheme()
                             .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;
@@ -202,7 +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;
@@ -818,6 +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);
@@ -930,8 +935,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     fr.setColour("type2", byLabel);
 
     // type3: by score above threshold
-    FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
-            10);
+    FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+            Color.BLUE, null, 1, 10);
     byScore.setAboveThreshold(true);
     byScore.setThreshold(2f);
     fr.setColour("type3", byScore);
@@ -943,8 +948,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     fr.setColour("type4", byAF);
 
     // type5: by attribute CSQ:PolyPhen below threshold
-    FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
-            1, 10);
+    FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+            Color.BLUE, null, 1, 10);
     byPolyPhen.setBelowThreshold(true);
     byPolyPhen.setThreshold(3f);
     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
@@ -979,7 +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.");
 
     /*