JAL-3621 corrected sequence feature sort and test

[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 32987b0..56512cd 100644 (file)
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -5,8 +5,6 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
-import jalview.datamodel.SequenceFeature;
-
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -15,6 +13,7 @@ import java.util.Set;
 
 import org.testng.annotations.Test;
 
+import jalview.datamodel.SequenceFeature;
 import junit.extensions.PA;
 
 public class SequenceFeaturesTest
@@ -940,14 +939,14 @@ public class SequenceFeaturesTest
     assertFalse(iterator.hasNext());
 
     /*
-     * two types specified - get sorted alphabetically
+     * two types specified - order is preserved
      */
     types = sf.varargToTypes("Metal", "Cath");
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertSame(iterator.next(), featureStores.get("Cath"));
-    assertTrue(iterator.hasNext());
     assertSame(iterator.next(), featureStores.get("Metal"));
+    assertTrue(iterator.hasNext());
+    assertSame(iterator.next(), featureStores.get("Cath"));
     assertFalse(iterator.hasNext());
 
     /*
@@ -1052,7 +1051,8 @@ public class SequenceFeaturesTest
   public void testSortFeatures()
   {
     List<SequenceFeature> sfs = new ArrayList<>();
-    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80,
+    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30,
+            60,
             Float.NaN, null);
     sfs.add(sf1);
     SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
@@ -1061,18 +1061,34 @@ public class SequenceFeaturesTest
     SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
             Float.NaN, null);
     sfs.add(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30,
+            80,
+            Float.NaN, null);
+    sfs.add(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30,
+            90,
+            Float.NaN, null);
+    sfs.add(sf5);
 
-    // sort by end position descending
+    /*
+     * sort by end position descending, order unchanged if matched
+     */
     SequenceFeatures.sortFeatures(sfs, false);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf3);
-    assertSame(sfs.get(2), sf2);
+    assertSame(sfs.get(0), sf5); // end 90
+    assertSame(sfs.get(1), sf4); // end 80
+    assertSame(sfs.get(2), sf1); // end 60, start 50
+    assertSame(sfs.get(3), sf3); // end 60, start 30
+    assertSame(sfs.get(4), sf2); // end 50
 
-    // sort by start position ascending
+    /*
+     * resort {5, 4, 1, 3, 2} by start position ascending, end descending
+     */
     SequenceFeatures.sortFeatures(sfs, true);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf2);
-    assertSame(sfs.get(2), sf3);
+    assertSame(sfs.get(0), sf5); // start 30, end 90
+    assertSame(sfs.get(1), sf4); // start 30, end 80
+    assertSame(sfs.get(2), sf1); // start 30, end 60
+    assertSame(sfs.get(3), sf2); // start 40
+    assertSame(sfs.get(4), sf3); // start 50
   }
 
   @Test(groups = "Functional")
@@ -1161,7 +1177,7 @@ public class SequenceFeaturesTest
   public void testShiftFeatures()
   {
     SequenceFeatures store = new SequenceFeatures();
-    assertFalse(store.shiftFeatures(1));
+    assertFalse(store.shiftFeatures(0, 1));
 
     SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
     store.add(sf1);
@@ -1179,7 +1195,7 @@ public class SequenceFeaturesTest
     /*
      * shift features right by 5
      */
-    assertTrue(store.shiftFeatures(5));
+    assertTrue(store.shiftFeatures(0, 5));
   
     // non-positional features untouched:
     List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
@@ -1208,7 +1224,7 @@ public class SequenceFeaturesTest
      * feature at [7-10] should be removed
      * feature at [13-19] should become [1-4] 
      */
-    assertTrue(store.shiftFeatures(-15));
+    assertTrue(store.shiftFeatures(0, -15));
     pos = store.getPositionalFeatures();
     assertEquals(pos.size(), 2);
     SequenceFeatures.sortFeatures(pos, true);
@@ -1218,6 +1234,35 @@ public class SequenceFeaturesTest
     assertEquals(pos.get(1).getBegin(), 13);
     assertEquals(pos.get(1).getEnd(), 22);
     assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+    /*
+     * shift right by 4 from column 2
+     * feature at [1-4] should be unchanged
+     * feature at [13-22] should become [17-26] 
+     */
+    assertTrue(store.shiftFeatures(2, 4));
+    pos = store.getPositionalFeatures();
+    assertEquals(pos.size(), 2);
+    SequenceFeatures.sortFeatures(pos, true);
+    assertEquals(pos.get(0).getBegin(), 1);
+    assertEquals(pos.get(0).getEnd(), 4);
+    assertEquals(pos.get(0).getType(), "Metal");
+    assertEquals(pos.get(1).getBegin(), 17);
+    assertEquals(pos.get(1).getEnd(), 26);
+    assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+    /*
+     * shift right from column 18
+     * should be no updates
+     */
+    SequenceFeature f1 = pos.get(0);
+    SequenceFeature f2 = pos.get(1);
+    assertFalse(store.shiftFeatures(18, 6));
+    pos = store.getPositionalFeatures();
+    assertEquals(pos.size(), 2);
+    SequenceFeatures.sortFeatures(pos, true);
+    assertSame(pos.get(0), f1);
+    assertSame(pos.get(1), f2);
   }
 
   @Test(groups = "Functional")
@@ -1232,4 +1277,18 @@ public class SequenceFeaturesTest
     assertTrue(store.isOntologyTerm("junk", new String[] {}));
     assertTrue(store.isOntologyTerm("junk", (String[]) null));
   }
+
+  @Test(groups = "Functional")
+  public void testDeleteAll()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+    assertFalse(store.hasFeatures());
+    store.deleteAll();
+    assertFalse(store.hasFeatures());
+    store.add(new SequenceFeature("Cath", "Desc", 12, 20, 0f, "Group"));
+    store.add(new SequenceFeature("Pfam", "Desc", 6, 12, 2f, "Group2"));
+    assertTrue(store.hasFeatures());
+    store.deleteAll();
+    assertFalse(store.hasFeatures());
+  }
 }