JAL-2480 SequenceFeaturesI encapsulates features api

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

diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java
index 8aabc56..b04f810 100644 (file)
--- a/test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreTest.java
@@ -365,12 +365,16 @@ public class FeatureStoreTest
             Float.NaN, null);
 
     assertTrue(fs.addFeature(sf1));
+    assertEquals(fs.size(true), 1); // positional
+    assertEquals(fs.size(false), 0); // non-positional
 
     /*
      * re-adding the same or an identical feature should fail
      */
     assertFalse(fs.addFeature(sf1));
+    assertEquals(fs.size(true), 1);
     assertFalse(fs.addFeature(sf2));
+    assertEquals(fs.size(true), 1);
   }
 
   @Test(groups = "Functional")
@@ -378,6 +382,7 @@ public class FeatureStoreTest
   {
     FeatureStore fs = new FeatureStore();
     assertTrue(fs.isEmpty());
+    assertEquals(fs.size(true), 0);
 
     /*
      * non-nested feature
@@ -386,8 +391,10 @@ public class FeatureStoreTest
             Float.NaN, null);
     fs.addFeature(sf1);
     assertFalse(fs.isEmpty());
+    assertEquals(fs.size(true), 1);
     fs.delete(sf1);
     assertTrue(fs.isEmpty());
+    assertEquals(fs.size(true), 0);
 
     /*
      * non-positional feature
@@ -395,8 +402,11 @@ public class FeatureStoreTest
     sf1 = new SequenceFeature("Cath", "", 0, 0, Float.NaN, null);
     fs.addFeature(sf1);
     assertFalse(fs.isEmpty());
+    assertEquals(fs.size(false), 1); // non-positional
+    assertEquals(fs.size(true), 0); // positional
     fs.delete(sf1);
     assertTrue(fs.isEmpty());
+    assertEquals(fs.size(false), 0);
 
     /*
      * contact feature
@@ -404,8 +414,10 @@ public class FeatureStoreTest
     sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN, null);
     fs.addFeature(sf1);
     assertFalse(fs.isEmpty());
+    assertEquals(fs.size(true), 1);
     fs.delete(sf1);
     assertTrue(fs.isEmpty());
+    assertEquals(fs.size(true), 0);
 
     /*
      * sf2, sf3 added as nested features
@@ -418,14 +430,18 @@ public class FeatureStoreTest
     fs.addFeature(sf1);
     fs.addFeature(sf2);
     fs.addFeature(sf3);
+    assertEquals(fs.size(true), 3);
     assertTrue(fs.delete(sf1));
+    assertEquals(fs.size(true), 2);
     // FeatureStore should now only contain features in the NCList
     assertTrue(fs.nonNestedFeatures.isEmpty());
     assertEquals(fs.nestedFeatures.size(), 2);
     assertFalse(fs.isEmpty());
     assertTrue(fs.delete(sf2));
+    assertEquals(fs.size(true), 1);
     assertFalse(fs.isEmpty());
     assertTrue(fs.delete(sf3));
+    assertEquals(fs.size(true), 0);
     assertTrue(fs.isEmpty()); // all gone
   }
 
@@ -481,4 +497,29 @@ public class FeatureStoreTest
     groups = fs.getFeatureGroups(true);
     assertTrue(groups.isEmpty());
   }
+
+  @Test(groups = "Functional")
+  public void testGetAverageFeatureLength()
+  {
+    FeatureStore fs = new FeatureStore();
+    assertEquals(fs.getAverageFeatureLength(), 0f);
+
+    addFeature(fs, 10, 20); // 11
+    assertEquals(fs.getAverageFeatureLength(), 11f);
+    addFeature(fs, 17, 37); // 21
+    addFeature(fs, 14, 74); // 61
+    assertEquals(fs.getAverageFeatureLength(), 31f);
+
+    // non-positional features don't count
+    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 0, 0, 1f,
+            "group1");
+    fs.addFeature(sf1);
+    assertEquals(fs.getAverageFeatureLength(), 31f);
+
+    // contact features count 1
+    SequenceFeature sf2 = new SequenceFeature("disulphide bond", "desc",
+            15, 35, 1f, "group1");
+    fs.addFeature(sf2);
+    assertEquals(fs.getAverageFeatureLength(), 94f / 4f);
+  }
 }