JAL-2483 JAL-2481 findAllFeatures without scanning all features

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

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
new file mode 100644 (file)
index 0000000..febd306
--- /dev/null
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -0,0 +1,133 @@
+package jalview.renderer.seqfeatures;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.schemes.FeatureColour;
+
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+public class FeatureRendererTest
+{
+
+  @Test(groups = "Functional")
+  public void testFindAllFeatures()
+  {
+    String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+
+    /*
+     * with no features
+     */
+    fr.findAllFeatures(true);
+    assertTrue(fr.getRenderOrder().isEmpty());
+    assertTrue(fr.getFeatureGroups().isEmpty());
+
+    List<SequenceI> seqs = av.getAlignment().getSequences();
+
+    // add a non-positional feature - should be ignored by FeatureRenderer
+    SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
+            "Group");
+    seqs.get(0).addSequenceFeature(sf1);
+    fr.findAllFeatures(true);
+    // ? bug - types and groups added for non-positional features
+    List<String> types = fr.getRenderOrder();
+    List<String> groups = fr.getFeatureGroups();
+    assertEquals(types.size(), 0);
+    assertFalse(types.contains("Type"));
+    assertEquals(groups.size(), 0);
+    assertFalse(groups.contains("Group"));
+
+    // add some positional features
+    seqs.get(1).addSequenceFeature(
+            new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
+    seqs.get(2).addSequenceFeature(
+            new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
+    // bug in findAllFeatures - group not checked for a known feature type
+    seqs.get(2).addSequenceFeature(
+            new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
+                    "RfamGroup"));
+    seqs.get(3).addSequenceFeature(
+            new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
+    // null value for type produces NullPointerException
+    fr.findAllFeatures(true);
+    types = fr.getRenderOrder();
+    groups = fr.getFeatureGroups();
+    assertEquals(types.size(), 2);
+    assertFalse(types.contains("Type"));
+    assertTrue(types.contains("Pfam"));
+    assertTrue(types.contains("Rfam"));
+    assertEquals(groups.size(), 2);
+    assertFalse(groups.contains("Group"));
+    assertTrue(groups.contains("PfamGroup"));
+    assertTrue(groups.contains("RfamGroup"));
+    assertFalse(groups.contains(null)); // null group is ignored
+
+    /*
+     * check min-max values
+     */
+    Map<String, float[][]> minMax = fr.getMinMax();
+    assertEquals(minMax.size(), 1); // non-positional and NaN not stored
+    assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
+    assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
+
+    // increase max for Pfam, add scores for Rfam
+    seqs.get(0).addSequenceFeature(
+            new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
+    seqs.get(1).addSequenceFeature(
+            new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
+    fr.findAllFeatures(true);
+    // note minMax is not a defensive copy, shouldn't expose this
+    assertEquals(minMax.size(), 2);
+    assertEquals(minMax.get("Pfam")[0][0], 1f);
+    assertEquals(minMax.get("Pfam")[0][1], 8f);
+    assertEquals(minMax.get("Rfam")[0][0], 6f);
+    assertEquals(minMax.get("Rfam")[0][1], 6f);
+
+    /*
+     * check render order (last is on top)
+     */
+    List<String> renderOrder = fr.getRenderOrder();
+    assertEquals(renderOrder, Arrays.asList("Rfam", "Pfam"));
+
+    /*
+     * change render order (todo: an easier way)
+     * nb here last comes first in the data array
+     */
+    Object[][] data = new Object[2][];
+    FeatureColourI colour = new FeatureColour(Color.RED);
+    data[0] = new Object[] { "Rfam", colour, true };
+    data[1] = new Object[] { "Pfam", colour, false };
+    fr.setFeaturePriority(data);
+    assertEquals(fr.getRenderOrder(), Arrays.asList("Pfam", "Rfam"));
+    assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
+
+    /*
+     * add a new feature type: should go on top of render order as visible,
+     * other feature ordering and visibility should be unchanged
+     */
+    seqs.get(2).addSequenceFeature(
+            new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
+    fr.findAllFeatures(true);
+    assertEquals(fr.getRenderOrder(),
+            Arrays.asList("Pfam", "Rfam", "Metal"));
+    assertEquals(fr.getDisplayedFeatureTypes(),
+            Arrays.asList("Rfam", "Metal"));
+  }
+}