X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRendererTest.java;h=723f3b8c9dcf3cc7e8404cc1d0bf0908bfda2801;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=7c9927f86c8e550c12989ec19b1add2f18be90e2;hpb=356260e6aa37640091849355ed97cd4103cc4c6c;p=jalview.git

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index 7c9927f..723f3b8 100644
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -285,8 +285,8 @@ public class FeatureRendererTest
      * give "Type3" features a graduated colour scheme
      * - first with no threshold
      */
-    FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f,
-            10f);
+    FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
+            Color.red, null, 0f, 10f);
     fr.getFeatureColours().put("Type3", gc);
     features = fr.findFeaturesAtColumn(seq, 8);
     assertTrue(features.contains(sf4));
@@ -328,18 +328,18 @@ public class FeatureRendererTest
     SequenceI seq = av.getAlignment().getSequenceAt(0);
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
             "group1");
-    seq.addSequenceFeature(sf1);
     SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
             "group2");
-    seq.addSequenceFeature(sf2);
     SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
             "group3");
-    seq.addSequenceFeature(sf3);
     SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
             "group4");
-    seq.addSequenceFeature(sf4);
     SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
             "group4");
+    seq.addSequenceFeature(sf1);
+    seq.addSequenceFeature(sf2);
+    seq.addSequenceFeature(sf3);
+    seq.addSequenceFeature(sf4);
     seq.addSequenceFeature(sf5);
 
     fr.findAllFeatures(true);
@@ -365,17 +365,17 @@ public class FeatureRendererTest
     assertTrue(features.contains(sf5));
 
     /*
-     * hide groups 2 and 3 makes no difference to this method
+     * features in hidden groups are removed
      */
     fr.setGroupVisibility("group2", false);
     fr.setGroupVisibility("group3", false);
     features = seq.getSequenceFeatures();
     fr.filterFeaturesForDisplay(features);
-    assertEquals(features.size(), 3);
+    assertEquals(features.size(), 2);
     assertTrue(features.contains(sf1) || features.contains(sf4));
     assertFalse(features.contains(sf1) && features.contains(sf4));
-    assertTrue(features.contains(sf2) || features.contains(sf3));
-    assertFalse(features.contains(sf2) && features.contains(sf3));
+    assertFalse(features.contains(sf2));
+    assertFalse(features.contains(sf3));
     assertTrue(features.contains(sf5));
 
     /*
@@ -428,8 +428,8 @@ public class FeatureRendererTest
      * graduated colour by score, no threshold, no score
      * 
      */
-    FeatureColourI gc = new FeatureColour(Color.yellow, Color.red,
-            Color.green, 1f, 11f);
+    FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
+            Color.red, Color.green, 1f, 11f);
     fr.getFeatureColours().put("Cath", gc);
     assertEquals(fr.getColour(sf1), Color.green);
 
@@ -453,7 +453,8 @@ public class FeatureRendererTest
      * threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
      * or from yellow(255, 255, 0) to red(255, 0, 0)
      */
-    gc = new FeatureColour(Color.yellow, Color.red, Color.green, 5f, 11f);
+    gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+            5f, 11f);
     fr.getFeatureColours().put("Cath", gc);
     gc.setAutoScaled(false); // this does little other than save a checkbox setting!
     assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
@@ -476,7 +477,8 @@ public class FeatureRendererTest
      * colour by feature attribute value
      * first with no value held
      */
-    gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f);
+    gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+            1f, 11f);
     fr.getFeatureColours().put("Cath", gc);
     gc.setAttributeName("AF");
     assertEquals(fr.getColour(sf2), Color.green);
@@ -574,7 +576,7 @@ public class FeatureRendererTest
     /*
      * feature score outwith colour threshold (score > 2)
      */
-    FeatureColourI fc = new FeatureColour(Color.white, Color.black,
+    FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
             Color.white, 0, 10);
     fc.setAboveThreshold(true);
     fc.setThreshold(2f);