JAL-3127 fix faulty merge

[jalview.git] / test / jalview / project / Jalview2xmlTests.java

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index d6df39a..d902fa2 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -147,12 +147,13 @@ 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");
 
@@ -818,6 +819,7 @@ 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 +932,8 @@ 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 +945,8 @@ 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");