Merge branch 'develop' into Release_2_9_0b1_Branch

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

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 9bdc2b5..e0b050f 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -33,8 +33,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ZappoColourScheme;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -124,9 +124,11 @@ public class JSONFileTest
     grpSeqs.add(seqs[2]);
     grpSeqs.add(seqs[3]);
     grpSeqs.add(seqs[4]);
-    ColourSchemeI scheme = JSONFile.getJalviewColorScheme("zappo");
     SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
-            scheme, true, true, false, 21, 29);
+            null, true, true, false, 21, 29);
+    ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+            "zappo", seqGrp);
+    seqGrp.cs = scheme;
     seqGrp.setShowNonconserved(false);
     seqGrp.setDescription(null);
 
@@ -232,7 +234,10 @@ public class JSONFileTest
               jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
               AlignFrame.DEFAULT_HEIGHT);
       af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
-      af.changeColour(jf.getColourScheme());
+      String colourSchemeName = jf.getGlobalColourScheme();
+      ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+              colourSchemeName, alignment);
+      af.changeColour(cs);
       af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
 
       formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
@@ -315,11 +320,13 @@ public class JSONFileTest
   @Test(groups = { "Functional" })
   public void colorSchemeTest()
   {
-    Assert.assertNotNull(testJsonFile.getColourScheme(),
+    Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
             "Colourscheme is null, parsing failed!");
-    Assert.assertTrue(
-            testJsonFile.getColourScheme() instanceof ZappoColourScheme,
+    Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
             "Zappo colour scheme expected!");
+    // Assert.assertTrue(
+    // testJsonFile.getGlobalColourScheme() instanceof ZappoColourScheme,
+    // "Zappo colour scheme expected!");
   }
 
   @Test(groups = { "Functional" })
@@ -419,13 +426,14 @@ public class JSONFileTest
             + actualGrp.getStartRes());
     System.out.println(expectedGrp.getEndRes() + " | "
             + actualGrp.getEndRes());
+    System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
 
     if (expectedGrp.getName().equals(actualGrp.getName())
             && expectedGrp.getColourText() == actualGrp.getColourText()
             && expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
             && expectedGrp.getIgnoreGapsConsensus() == actualGrp
                     .getIgnoreGapsConsensus()
-            && expectedGrp.cs.equals(actualGrp.cs)
+            && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
             && expectedGrp.getSequences().size() == actualGrp
                     .getSequences().size()
             && expectedGrp.getStartRes() == actualGrp.getStartRes()