From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 23 May 2017 12:52:39 +0000 (+0100)
Subject: JAL-2490 unit tests for getFeaturesForGroup
X-Git-Tag: Release_2_10_3b1~245
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=7ed8fecb051ef29c364a45ee6ae6244a7da7275b

JAL-2490 unit tests for getFeaturesForGroup
---

diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java
index d2893e5..00a57b6 100644
--- a/test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreTest.java
@@ -711,4 +711,62 @@ public class FeatureStoreTest
     assertTrue(FeatureStore.contains(features, sf2));
     assertFalse(FeatureStore.contains(features, sf3));
   }
+
+  @Test(groups = "Functional")
+  public void testGetFeaturesForGroup()
+  {
+    FeatureStore fs = new FeatureStore();
+
+    /*
+     * with no features
+     */
+    assertTrue(fs.getFeaturesForGroup(true, null).isEmpty());
+    assertTrue(fs.getFeaturesForGroup(false, null).isEmpty());
+    assertTrue(fs.getFeaturesForGroup(true, "uniprot").isEmpty());
+    assertTrue(fs.getFeaturesForGroup(false, "uniprot").isEmpty());
+
+    /*
+     * sf1: positional feature in the null group
+     */
+    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+            null);
+    fs.addFeature(sf1);
+    assertTrue(fs.getFeaturesForGroup(true, "uniprot").isEmpty());
+    assertTrue(fs.getFeaturesForGroup(false, "uniprot").isEmpty());
+    assertTrue(fs.getFeaturesForGroup(false, null).isEmpty());
+    List<SequenceFeature> features = fs.getFeaturesForGroup(true, null);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf1));
+
+    /*
+     * sf2: non-positional feature in the null group
+     * sf3: positional feature in a non-null group
+     * sf4: non-positional feature in a non-null group
+     */
+    SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
+            null);
+    SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+            "Uniprot");
+    SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
+            "Rfam");
+    fs.addFeature(sf2);
+    fs.addFeature(sf3);
+    fs.addFeature(sf4);
+
+    features = fs.getFeaturesForGroup(true, null);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf1));
+
+    features = fs.getFeaturesForGroup(false, null);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+
+    features = fs.getFeaturesForGroup(true, "Uniprot");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf3));
+
+    features = fs.getFeaturesForGroup(false, "Rfam");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf4));
+  }
 }
diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index eaa5276..e3d587f 100644
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -1018,4 +1018,86 @@ public class SequenceFeaturesTest
     assertSame(sfs.get(1), sf2);
     assertSame(sfs.get(2), sf3);
   }
+
+  @Test(groups = "Functional")
+  public void testGetFeaturesForGroup()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+
+    List<SequenceFeature> features = store.getFeaturesForGroup(true, null);
+    assertTrue(features.isEmpty());
+    assertTrue(store.getFeaturesForGroup(false, null).isEmpty());
+    assertTrue(store.getFeaturesForGroup(true, "Uniprot").isEmpty());
+    assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
+
+    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+            null);
+    SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
+            null);
+    SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+            "Uniprot");
+    SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 0, 0, 0f,
+            "Rfam");
+    SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 5, 15, 0f,
+            null);
+    store.add(sf1);
+    store.add(sf2);
+    store.add(sf3);
+    store.add(sf4);
+    store.add(sf5);
+
+    // positional features for null group, any type
+    features = store.getFeaturesForGroup(true, null);
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf5));
+
+    // positional features for null group, specified type
+    features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
+        "Xfam" });
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf1));
+    features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
+        "Xfam", "Cath" });
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf5));
+
+    // positional features for non-null group, any type
+    features = store.getFeaturesForGroup(true, "Uniprot");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf3));
+    assertTrue(store.getFeaturesForGroup(true, "Rfam").isEmpty());
+
+    // positional features for non-null group, specified type
+    features = store.getFeaturesForGroup(true, "Uniprot", "Pfam", "Xfam",
+            "Rfam");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf3));
+    assertTrue(store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty());
+
+    // non-positional features for null group, any type
+    features = store.getFeaturesForGroup(false, null);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+
+    // non-positional features for null group, specified type
+    features = store.getFeaturesForGroup(false, null, "Pfam", "Xfam");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+    assertTrue(store.getFeaturesForGroup(false, null, "Cath").isEmpty());
+
+    // non-positional features for non-null group, any type
+    features = store.getFeaturesForGroup(false, "Rfam");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf4));
+    assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
+
+    // non-positional features for non-null group, specified type
+    features = store.getFeaturesForGroup(false, "Rfam", "Pfam", "Metal");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf4));
+    assertTrue(store.getFeaturesForGroup(false, "Rfam", "Cath", "Pfam")
+            .isEmpty());
+  }
 }