JAL-2816 tests for findFeaturesAtColumn

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index fb20dd4..821c3b7 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -2,6 +2,7 @@ package jalview.renderer.seqfeatures;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
 import jalview.api.AlignViewportI;
@@ -12,6 +13,10 @@ import jalview.gui.AlignFrame;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
+import jalview.util.matcher.Condition;
+import jalview.util.matcher.KeyedMatcher;
+import jalview.util.matcher.KeyedMatcherSet;
+import jalview.util.matcher.KeyedMatcherSetI;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -350,4 +355,132 @@ public class FeatureRendererTest
     assertFalse(features.contains(sf2) && features.contains(sf3));
     assertTrue(features.contains(sf5));
   }
+
+  @Test(groups = "Functional")
+  public void testGetColour()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(">s1\nABCD\n",
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+
+    /*
+     * simple colour, feature type and group displayed
+     */
+    FeatureColourI fc = new FeatureColour(Color.red);
+    fr.getFeatureColours().put("Cath", fc);
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
+            "group1");
+    assertEquals(fr.getColour(sf1), Color.red);
+
+    /*
+     * hide feature type, then unhide
+     */
+    Object[][] data = new Object[1][];
+    data[0] = new Object[] { "Cath", fc, false };
+    fr.setFeaturePriority(data);
+    assertNull(fr.getColour(sf1));
+    data[0] = new Object[] { "Cath", fc, true };
+    fr.setFeaturePriority(data);
+    assertEquals(fr.getColour(sf1), Color.red);
+
+    /*
+     * hide feature group, then unhide
+     */
+    fr.setGroupVisibility("group1", false);
+    assertNull(fr.getColour(sf1));
+    fr.setGroupVisibility("group1", true);
+    assertEquals(fr.getColour(sf1), Color.red);
+
+    /*
+     * graduated colour by score, no threshold, no score
+     * 
+     */
+    FeatureColourI gc = new FeatureColour(Color.yellow, Color.red,
+            Color.green, 1f, 11f);
+    fr.getFeatureColours().put("Cath", gc);
+    assertEquals(fr.getColour(sf1), Color.green);
+
+    /*
+     * graduated colour by score, no threshold, with score value
+     */
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f,
+            "group1");
+    // score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0)
+    assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+    
+    /*
+     * above threshold, score is above threshold - no change
+     */
+    gc.setAboveThreshold(true);
+    gc.setThreshold(5f);
+    assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+
+    /*
+     * 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);
+    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));
+
+    /*
+     * feature score is below threshold - no colour
+     */
+    gc.setAboveThreshold(true);
+    gc.setThreshold(7f);
+    assertNull(fr.getColour(sf2));
+
+    /*
+     * feature score is above threshold - no colour
+     */
+    gc.setBelowThreshold(true);
+    gc.setThreshold(3f);
+    assertNull(fr.getColour(sf2));
+
+    /*
+     * colour by feature attribute value
+     * first with no value held
+     */
+    gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f);
+    fr.getFeatureColours().put("Cath", gc);
+    gc.setAttributeName("AF");
+    assertEquals(fr.getColour(sf2), Color.green);
+
+    // with non-numeric attribute value
+    sf2.setValue("AF", "Five");
+    assertEquals(fr.getColour(sf2), Color.green);
+
+    // with numeric attribute value
+    sf2.setValue("AF", "6");
+    assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+
+    // with numeric value outwith threshold
+    gc.setAboveThreshold(true);
+    gc.setThreshold(10f);
+    assertNull(fr.getColour(sf2));
+
+    // with filter on AF < 4
+    gc.setAboveThreshold(false);
+    assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+    KeyedMatcherSetI filter = new KeyedMatcherSet();
+    filter.and(new KeyedMatcher(Condition.LT, 4f, "AF"));
+    fr.setFeatureFilter("Cath", filter);
+    assertNull(fr.getColour(sf2));
+
+    // with filter on 'Consequence contains missense'
+    filter = new KeyedMatcherSet();
+    filter.and(new KeyedMatcher(Condition.Contains, "missense",
+            "Consequence"));
+    fr.setFeatureFilter("Cath", filter);
+    // if feature has no Consequence attribute, no colour
+    assertNull(fr.getColour(sf2));
+    // if attribute does not match filter, no colour
+    sf2.setValue("Consequence", "Synonymous");
+    assertNull(fr.getColour(sf2));
+    // attribute matches filter
+    sf2.setValue("Consequence", "Missense variant");
+    assertEquals(fr.getColour(sf2), new Color(255, 128, 0));
+  }
 }