Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch

[jalview.git] / test / jalview / renderer / seqfeatures / FeatureRendererTest.java

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index 31348c6..6bb611c 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.renderer.seqfeatures;
 
 import static org.testng.Assert.assertEquals;
@@ -14,6 +34,7 @@ import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
 
 import java.awt.Color;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
@@ -252,4 +273,117 @@ public class FeatureRendererTest
     assertEquals(features.size(), 1);
     assertTrue(features.contains(sf8));
   }
+
+  @Test(groups = "Functional")
+  public void testFilterFeaturesForDisplay()
+  {
+    String seqData = ">s1\nabcdef\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+
+    List<SequenceFeature> features = new ArrayList<>();
+    fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
+
+    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(sf5);
+
+    fr.findAllFeatures(true);
+
+    features = seq.getSequenceFeatures();
+    assertEquals(features.size(), 5);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * filter out duplicate (co-located) features
+     * note: which gets removed is not guaranteed
+     */
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    assertEquals(features.size(), 3);
+    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));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * hide group 3 - sf3 is removed, sf2 is retained
+     */
+    fr.setGroupVisibility("group3", false);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    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(sf5));
+
+    /*
+     * hide group 2, show group 3 - sf2 is removed, sf3 is retained
+     */
+    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));
+
+    /*
+     * no filtering of co-located features with graduated colour scheme
+     * filterFeaturesForDisplay does _not_ check colour threshold
+     * sf2 is removed as its group is hidden
+     */
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.black,
+            Color.white, 0f, 1f));
+    assertEquals(features.size(), 4);
+    assertFalse(features.contains(sf2));
+
+    /*
+     * co-located features with colour by label
+     * should not get filtered
+     */
+    features = seq.getSequenceFeatures();
+    FeatureColour fc = new FeatureColour(Color.black);
+    fc.setColourByLabel(true);
+    fr.filterFeaturesForDisplay(features, fc);
+    assertEquals(features.size(), 4);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * no filtering if transparency is applied
+     */
+    fr.setTransparency(0.5f);
+    features = seq.getSequenceFeatures();
+    fr.setGroupVisibility("group2", true);
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.RED));
+    assertEquals(features.size(), 5);
+  }
 }