JAL-2480 cache min-max score values per sequence and feature type

[jalview.git] / test / jalview / datamodel / features / SequenceFeaturesTest.java

diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index 4cd37ee..eaf20b0 100644 (file)
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -713,4 +713,121 @@ public class SequenceFeaturesTest
     assertEquals(features.size(), 3);
     assertFalse(features.contains(sf3));
   }
+
+  @Test(groups = "Functional")
+  public void testGetTotalFeatureLength()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+    assertEquals(store.getTotalFeatureLength(), 0);
+
+    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+            Float.NaN, null);
+    assertTrue(store.add(sf1));
+    assertEquals(store.getTotalFeatureLength(), 11);
+
+    // re-add does nothing!
+    assertFalse(store.add(sf1));
+    assertEquals(store.getTotalFeatureLength(), 11);
+
+    /*
+     * add non-positional feature
+     */
+    SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 0, 0,
+            Float.NaN, null);
+    store.add(sf3);
+    assertEquals(store.getTotalFeatureLength(), 11);
+
+    /*
+     * add contact feature - counts 1 to feature length
+     */
+    SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
+            10, 20, Float.NaN, null);
+    store.add(sf4);
+    assertEquals(store.getTotalFeatureLength(), 12);
+
+    /*
+     * add another Pfam
+     */
+    SequenceFeature sf5 = new SequenceFeature("Pfam", "desc", 10, 20,
+            Float.NaN, null);
+    store.add(sf5);
+    assertEquals(store.getTotalFeatureLength(), 23);
+
+    /*
+     * delete features
+     */
+    assertTrue(store.delete(sf3)); // non-positional
+    assertEquals(store.getTotalFeatureLength(), 23); // no change
+
+    assertTrue(store.delete(sf5));
+    assertEquals(store.getTotalFeatureLength(), 12);
+
+    assertTrue(store.delete(sf4)); // contact
+    assertEquals(store.getTotalFeatureLength(), 11);
+
+    assertTrue(store.delete(sf1));
+    assertEquals(store.getTotalFeatureLength(), 0);
+  }
+
+  @Test
+  public void testGetMinimumScore_getMaximumScore()
+  {
+    SequenceFeatures sf = new SequenceFeatures();
+    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 0, 0,
+            Float.NaN, "group"); // non-positional, no score
+    sf.add(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 10, 20,
+            Float.NaN, "group"); // positional, no score
+    sf.add(sf2);
+    SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 10, 20, 1f,
+            "group");
+    sf.add(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 12, 16, 4f,
+            "group");
+    sf.add(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 0, 0, 11f,
+            "group");
+    sf.add(sf5);
+    SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, -7f,
+            "group");
+    sf.add(sf6);
+
+    assertEquals(sf.getMinimumScore("nosuchtype", true), Float.NaN);
+    assertEquals(sf.getMinimumScore("nosuchtype", false), Float.NaN);
+    assertEquals(sf.getMaximumScore("nosuchtype", true), Float.NaN);
+    assertEquals(sf.getMaximumScore("nosuchtype", false), Float.NaN);
+
+    // positional features min-max:
+    assertEquals(sf.getMinimumScore("Metal", true), 1f);
+    assertEquals(sf.getMaximumScore("Metal", true), 4f);
+    assertEquals(sf.getMinimumScore("Cath", true), Float.NaN);
+    assertEquals(sf.getMaximumScore("Cath", true), Float.NaN);
+
+    // non-positional features min-max:
+    assertEquals(sf.getMinimumScore("Cath", false), -7f);
+    assertEquals(sf.getMaximumScore("Cath", false), 11f);
+    assertEquals(sf.getMinimumScore("Metal", false), Float.NaN);
+    assertEquals(sf.getMaximumScore("Metal", false), Float.NaN);
+
+    // delete features; min-max should get recomputed
+    sf.delete(sf6);
+    assertEquals(sf.getMinimumScore("Cath", false), 11f);
+    assertEquals(sf.getMaximumScore("Cath", false), 11f);
+    sf.delete(sf4);
+    assertEquals(sf.getMinimumScore("Metal", true), 1f);
+    assertEquals(sf.getMaximumScore("Metal", true), 1f);
+    sf.delete(sf5);
+    assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
+    assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
+    sf.delete(sf3);
+    assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
+    assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
+    sf.delete(sf1);
+    sf.delete(sf2);
+    assertFalse(sf.hasFeatures());
+    assertEquals(sf.getMinimumScore("Cath", false), Float.NaN);
+    assertEquals(sf.getMaximumScore("Cath", false), Float.NaN);
+    assertEquals(sf.getMinimumScore("Metal", true), Float.NaN);
+    assertEquals(sf.getMaximumScore("Metal", true), Float.NaN);
+  }
 }