Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 434619e..5b99fa1 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -45,6 +45,8 @@ import jalview.gui.JvOptionPane;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.viewmodel.AlignmentViewport;
@@ -83,10 +85,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue("Didn't read input file " + inFile, af != null);
     int olddsann = countDsAnn(af.getViewport());
     assertTrue("Didn't find any dataset annotations", olddsann > 0);
-    af.rnahelicesColour_actionPerformed();
-    assertTrue(
-            "Couldn't apply RNA helices colourscheme",
-            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+    af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
+            .toString());
+    assertTrue("Couldn't apply RNA helices colourscheme", af.getViewport()
+            .getGlobalColourScheme() instanceof RNAHelicesColour);
     assertTrue("Failed to store as a project.",
             af.saveAlignment(tfile, FileFormat.Jalview));
     af.closeMenuItem_actionPerformed(true);
@@ -103,7 +105,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
                     + olddsann + ")");
     assertTrue(
             "RNA helices colourscheme was not applied on import.",
-            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+            af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour);
   }
 
   @Test(groups = { "Functional" })
@@ -119,7 +121,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertSame("Didn't set T-coffee colourscheme", af.getViewport()
             .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
     assertNotNull("Recognise T-Coffee score from string",
-            ColourSchemeProperty.getColour(af.getViewport()
+            ColourSchemeProperty.getColourScheme(af.getViewport()
                     .getAlignment(), af.getViewport()
                     .getGlobalColourScheme().getSchemeName()));
 
@@ -161,7 +163,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     SequenceGroup sg = new SequenceGroup();
     sg.setStartRes(57);
     sg.setEndRes(92);
-    sg.cs = gcs;
+    sg.cs.setColourScheme(gcs);
     af.getViewport().getAlignment().addGroup(sg);
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
@@ -177,7 +179,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
-            .get(0).cs;
+            .get(0).getColourScheme();
     assertNotNull("Didn't recover global colourscheme", _rcs);
     assertTrue("Didn't recover annotation colour global scheme",
             _rcs instanceof AnnotationColourGradient);
@@ -190,8 +192,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
             && (!diffseqcols || !diffgseqcols); p++)
     {
-      if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
-              .findColour(sqs[5].getCharAt(p), p, sqs[5]))
+      if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
+              .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
       {
         diffseqcols = true;
       }
@@ -210,8 +212,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
             && (!diffseqcols || !diffgseqcols); p++)
     {
-      if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
-              .findColour(sqs[2].getCharAt(p), p, sqs[2]))
+      if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
+              .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
       {
         diffgseqcols = true;
       }
@@ -379,8 +381,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
     Assert.assertEquals(
-            oldviews,
-            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
+            oldviews);
   }
 
   /**