X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRendererTest.java;h=745eec337a3f73f29023057162597751e6d7bb18;hb=9e926ac4305fd9dff38b6e079e55b4f50664d544;hp=dc86605ea6219b389045b6ade5a04793911a2472;hpb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;p=jalview.git

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index dc86605..745eec3 100644
--- 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;
@@ -12,10 +13,15 @@ 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;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -252,6 +258,37 @@ public class FeatureRendererTest
     features = fr.findFeaturesAtColumn(seq, 5);
     assertEquals(features.size(), 1);
     assertTrue(features.contains(sf8));
+    
+    /*
+     * give "Type3" features a graduated colour scheme
+     * - first with no threshold
+     */
+    FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f,
+            10f);
+    fr.getFeatureColours().put("Type3", gc);
+    features = fr.findFeaturesAtColumn(seq, 8);
+    assertTrue(features.contains(sf4));
+    // now with threshold > 2f - feature score of 1f is excluded
+    gc.setAboveThreshold(true);
+    gc.setThreshold(2f);
+    features = fr.findFeaturesAtColumn(seq, 8);
+    assertFalse(features.contains(sf4));
+
+    /*
+     * make "Type3" graduated colour by attribute "AF"
+     * - first with no attribute held - feature should be excluded
+     */
+    gc.setAttributeName("AF");
+    features = fr.findFeaturesAtColumn(seq, 8);
+    assertFalse(features.contains(sf4));
+    // now with the attribute above threshold - should be included
+    sf4.setValue("AF", "2.4");
+    features = fr.findFeaturesAtColumn(seq, 8);
+    assertTrue(features.contains(sf4));
+    // now with the attribute below threshold - should be excluded
+    sf4.setValue("AF", "1.4");
+    features = fr.findFeaturesAtColumn(seq, 8);
+    assertFalse(features.contains(sf4));
   }
 
   @Test(groups = "Functional")
@@ -264,7 +301,7 @@ public class FeatureRendererTest
     FeatureRenderer fr = new FeatureRenderer(av);
 
     List<SequenceFeature> features = new ArrayList<>();
-    fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
+    fr.filterFeaturesForDisplay(features); // empty list, does nothing
 
     SequenceI seq = av.getAlignment().getSequenceAt(0);
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
@@ -297,7 +334,7 @@ public class FeatureRendererTest
      * filter out duplicate (co-located) features
      * note: which gets removed is not guaranteed
      */
-    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    fr.filterFeaturesForDisplay(features);
     assertEquals(features.size(), 3);
     assertTrue(features.contains(sf1) || features.contains(sf4));
     assertFalse(features.contains(sf1) && features.contains(sf4));
@@ -306,58 +343,165 @@ public class FeatureRendererTest
     assertTrue(features.contains(sf5));
 
     /*
-     * hide group 3 - sf3 is removed, sf2 is retained
+     * hide groups 2 and 3 makes no difference to this method
      */
+    fr.setGroupVisibility("group2", false);
     fr.setGroupVisibility("group3", false);
     features = seq.getSequenceFeatures();
-    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    fr.filterFeaturesForDisplay(features);
     assertEquals(features.size(), 3);
     assertTrue(features.contains(sf1) || features.contains(sf4));
     assertFalse(features.contains(sf1) && features.contains(sf4));
-    assertTrue(features.contains(sf2));
-    assertFalse(features.contains(sf3));
+    assertTrue(features.contains(sf2) || features.contains(sf3));
+    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);
 
     /*
-     * hide group 2, show group 3 - sf2 is removed, sf3 is retained
+     * simple colour, feature type and group displayed
      */
-    fr.setGroupVisibility("group2", false);
-    fr.setGroupVisibility("group3", true);
-    features = seq.getSequenceFeatures();
-    fr.filterFeaturesForDisplay(features, null);
-    assertEquals(features.size(), 3);
-    assertTrue(features.contains(sf1) || features.contains(sf4));
-    assertFalse(features.contains(sf1) && features.contains(sf4));
-    assertFalse(features.contains(sf2));
-    assertTrue(features.contains(sf3));
-    assertTrue(features.contains(sf5));
+    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);
 
     /*
-     * no filtering of co-located features with graduated colour scheme
-     * filterFeaturesForDisplay does _not_ check colour threshold
-     * sf2 is removed as its group is hidden
+     * hide feature type, then unhide
      */
-    features = seq.getSequenceFeatures();
-    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.black,
-            Color.white, 0f, 1f));
-    assertEquals(features.size(), 4);
-    assertTrue(features.contains(sf1));
-    assertTrue(features.contains(sf3));
-    assertTrue(features.contains(sf4));
-    assertTrue(features.contains(sf5));
+    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);
 
     /*
-     * filtering of co-located features with colour by label
+     * hide feature group, then unhide
      */
-    features = seq.getSequenceFeatures();
-    FeatureColour fc = new FeatureColour(Color.black);
-    fc.setColourByLabel(true);
-    fr.filterFeaturesForDisplay(features, fc);
-    assertEquals(features.size(), 3);
-    assertTrue(features.contains(sf1) || features.contains(sf4));
-    assertFalse(features.contains(sf1) && features.contains(sf4));
-    assertFalse(features.contains(sf2));
-    assertTrue(features.contains(sf3));
-    assertTrue(features.contains(sf5));
+    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)
+    Color expected = new Color(255, 128, 0);
+    assertEquals(fr.getColour(sf2), expected);
+    
+    /*
+     * above threshold, score is above threshold - no change
+     */
+    gc.setAboveThreshold(true);
+    gc.setThreshold(5f);
+    assertEquals(fr.getColour(sf2), expected);
+
+    /*
+     * 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), expected);
+
+    // 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), expected);
+    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), expected);
+
+    // with filter on CSQ.Feature contains "ENST01234"
+    filter = new KeyedMatcherSet();
+    filter.and(new KeyedMatcher(Condition.Matches, "ENST01234", "CSQ",
+            "Feature"));
+    fr.setFeatureFilter("Cath", filter);
+    // if feature has no CSQ data, no colour
+    assertNull(fr.getColour(sf2));
+    // if CSQ data does not include Feature, no colour
+    Map<String, String> csqData = new HashMap<>();
+    csqData.put("BIOTYPE", "Transcript");
+    sf2.setValue("CSQ", csqData);
+    assertNull(fr.getColour(sf2));
+    // if attribute does not match filter, no colour
+    csqData.put("Feature", "ENST9876");
+    assertNull(fr.getColour(sf2));
+    // attribute matches filter
+    csqData.put("Feature", "ENST01234");
+    assertEquals(fr.getColour(sf2), expected);
   }
 }