X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesTest.java;h=39d6dce4e9f68618d4b94b3f6de59416a4546ffc;hb=9a8ce9061282f9a9ff237947322d571a7c3d203b;hp=f4ec05be311be1fe15f043bac6825b55432b22e3;hpb=b44349fe3a5f2d70b74a1b110018a753a1036aca;p=jalview.git

diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index f4ec05b..39d6dce 100644
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -10,13 +10,47 @@ import jalview.datamodel.SequenceFeature;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
+import junit.extensions.PA;
+
 import org.testng.annotations.Test;
 
 public class SequenceFeaturesTest
 {
   @Test(groups = "Functional")
+  public void testConstructor()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+    assertFalse(store.hasFeatures());
+
+    store = new SequenceFeatures((List<SequenceFeature>) null);
+    assertFalse(store.hasFeatures());
+
+    List<SequenceFeature> features = new ArrayList<>();
+    store = new SequenceFeatures(features);
+    assertFalse(store.hasFeatures());
+
+    SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+            Float.NaN, null);
+    features.add(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Metal", "desc", 15, 18,
+            Float.NaN, null);
+    features.add(sf2); // nested
+    SequenceFeature sf3 = new SequenceFeature("Pfam", "desc2", 0, 0,
+            Float.NaN, null); // non-positional
+    features.add(sf3);
+    store = new SequenceFeatures(features);
+    assertTrue(store.hasFeatures());
+    assertEquals(2, store.getFeatureCount(true)); // positional
+    assertEquals(1, store.getFeatureCount(false)); // non-positional
+    assertFalse(store.add(sf1)); // already contained
+    assertFalse(store.add(sf2)); // already contained
+    assertFalse(store.add(sf3)); // already contained
+  }
+
+  @Test(groups = "Functional")
   public void testGetPositionalFeatures()
   {
     SequenceFeaturesI store = new SequenceFeatures();
@@ -334,6 +368,11 @@ public class SequenceFeaturesTest
     groups = sf.getFeatureGroups(false); // for non-positional
     assertEquals(groups.size(), 1);
     assertTrue(groups.contains("AGroup"));
+    groups = sf.getFeatureGroups(false, "AType");
+    assertEquals(groups.size(), 1);
+    assertTrue(groups.contains("AGroup"));
+    groups = sf.getFeatureGroups(true, "AnotherType");
+    assertTrue(groups.isEmpty());
 
     /*
      * add, then delete, more non-positional features of different types
@@ -730,6 +769,8 @@ public class SequenceFeaturesTest
             Float.NaN, null);
     assertTrue(store.add(sf1));
     assertEquals(store.getTotalFeatureLength(), 11);
+    assertEquals(store.getTotalFeatureLength("Metal"), 11);
+    assertEquals(store.getTotalFeatureLength("Plastic"), 0);
 
     // re-add does nothing!
     assertFalse(store.add(sf1));
@@ -848,12 +889,15 @@ public class SequenceFeaturesTest
      * no type specified - get all types stored
      * they are returned in keyset (alphabetical) order
      */
-    Iterable<String> types = sf.varargToTypes();
-    Iterator<String> iterator = types.iterator();
+    Map<String, FeatureStore> featureStores = (Map<String, FeatureStore>) PA
+            .getValue(sf, "featureStore");
+
+    Iterable<FeatureStore> types = sf.varargToTypes();
+    Iterator<FeatureStore> iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Cath");
+    assertSame(iterator.next(), featureStores.get("Cath"));
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
+    assertSame(iterator.next(), featureStores.get("Metal"));
     assertFalse(iterator.hasNext());
 
     /*
@@ -863,9 +907,9 @@ public class SequenceFeaturesTest
     types = sf.varargToTypes(new String[] {});
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Cath");
+    assertSame(iterator.next(), featureStores.get("Cath"));
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
+    assertSame(iterator.next(), featureStores.get("Metal"));
     assertFalse(iterator.hasNext());
 
     /*
@@ -881,9 +925,9 @@ public class SequenceFeaturesTest
     types = sf.varargToTypes((String[]) null);
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Cath");
+    assertSame(iterator.next(), featureStores.get("Cath"));
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
+    assertSame(iterator.next(), featureStores.get("Metal"));
     assertFalse(iterator.hasNext());
 
     /*
@@ -892,29 +936,27 @@ public class SequenceFeaturesTest
     types = sf.varargToTypes("Metal");
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
+    assertSame(iterator.next(), featureStores.get("Metal"));
     assertFalse(iterator.hasNext());
 
     /*
      * two types specified - get sorted alphabetically
      */
-    types = sf.varargToTypes("Metal", "Helix");
+    types = sf.varargToTypes("Metal", "Cath");
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Helix");
+    assertSame(iterator.next(), featureStores.get("Cath"));
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
+    assertSame(iterator.next(), featureStores.get("Metal"));
     assertFalse(iterator.hasNext());
 
     /*
-     * null type included - should get removed
+     * null type included - should be ignored
      */
     types = sf.varargToTypes("Metal", null, "Helix");
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Helix");
-    assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
+    assertSame(iterator.next(), featureStores.get("Metal"));
     assertFalse(iterator.hasNext());
   }
 
@@ -990,6 +1032,9 @@ public class SequenceFeaturesTest
     assertEquals(features.size(), 2);
     assertTrue(features.contains(sf2));
     assertTrue(features.contains(sf3));
+
+    features = store.getFeaturesByOntology("sequence_variant");
+    assertTrue(features.isEmpty());
   }
 
   @Test(groups = "Functional")
@@ -1163,4 +1208,17 @@ public class SequenceFeaturesTest
     assertEquals(pos.get(1).getEnd(), 22);
     assertEquals(pos.get(1).getType(), "Disulfide bond");
   }
+
+  @Test(groups = "Functional")
+  public void testIsOntologyTerm()
+  {
+    SequenceFeatures store = new SequenceFeatures();
+    assertTrue(store.isOntologyTerm("gobbledygook"));
+    assertTrue(store.isOntologyTerm("transcript", "transcript"));
+    assertTrue(store.isOntologyTerm("mRNA", "transcript"));
+    assertFalse(store.isOntologyTerm("transcript", "mRNA"));
+    assertTrue(store.isOntologyTerm("junk", "transcript", "junk"));
+    assertTrue(store.isOntologyTerm("junk", new String[] {}));
+    assertTrue(store.isOntologyTerm("junk", (String[]) null));
+  }
 }