JAL-2480 don't allow null type in SequenceFeature

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c0549f2..ae7df53 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -321,6 +321,13 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public synchronized boolean addSequenceFeature(SequenceFeature sf)
   {
+    if (sf.getType() == null)
+    {
+      System.err.println("SequenceFeature type may not be null: "
+              + sf.toString());
+      return false;
+    }
+
     if (sequenceFeatures == null && datasetSequence != null)
     {
       return datasetSequence.addSequenceFeature(sf);

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 1fbc76a..6c82bf3 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -348,7 +348,7 @@ public interface SequenceI extends ASequenceI
 
   /**
    * Adds the given sequence feature and returns true, or returns false if it is
-   * already present on the sequence
+   * already present on the sequence, or if the feature type is null.
    * 
    * @param sf
    * @return

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 08e6f7d..4a208ae 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -340,7 +340,7 @@ public class SequenceTest
     /*
      * SequenceFeature on sequence
      */
-    SequenceFeature sf = new SequenceFeature();
+    SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
     sq.addSequenceFeature(sf);
     SequenceFeature[] sfs = sq.getSequenceFeatures();
     assertEquals(1, sfs.length);
@@ -711,6 +711,36 @@ public class SequenceTest
     assertEquals(' ', sq.getCharAt(-1));
   }
 
+  @Test(groups = { "Functional" })
+  public void testAddSequenceFeatures()
+  {
+    SequenceI sq = new Sequence("", "abcde");
+    // type may not be null
+    assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
+            8, 0f, null)));
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 0f, null)));
+    // can't add a duplicate feature
+    assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
+            4, 8, 0f, null)));
+    // can add a different feature
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
+            8, 0f, null))); // different type
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
+            "description", 4, 8, 0f, null)));// different description
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
+            8, 0f, null))); // different start position
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            9, 0f, null))); // different end position
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 1f, null))); // different score
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, Float.NaN, null))); // score NaN
+    assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
+            8, 0f, "Metal"))); // different group
+    assertEquals(8, sq.getFeatures().getAllFeatures().size());
+  }
+
   /**
    * Tests for adding (or updating) dbrefs
    *