From 06775313266c93eba687d73df794eba606145048 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 21 Dec 2016 14:39:19 +0000
Subject: [PATCH] JAL-2360 Javadoc and test cases for findAnnotation

---
 src/jalview/datamodel/AnnotatedCollectionI.java |    7 +++++++
 src/jalview/datamodel/SequenceGroup.java        |    8 ++++++--
 test/jalview/datamodel/AlignmentTest.java       |    6 ++++++
 3 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index 74568e4..3f6c515 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -31,6 +31,13 @@ public interface AnnotatedCollectionI extends SequenceCollectionI
    */
   AlignmentAnnotation[] getAlignmentAnnotation();
 
+  /**
+   * Returns a list of annotations matching the given calc id, or an empty list
+   * if calcId is null
+   * 
+   * @param calcId
+   * @return
+   */
   Iterable<AlignmentAnnotation> findAnnotation(String calcId);
 
   Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 9245761..da47a89 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1269,10 +1269,14 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    if (calcId == null)
+    {
+      return aa;
+    }
     for (AlignmentAnnotation a : getAlignmentAnnotation())
     {
-      if (a.getCalcId() == calcId)
+      if (calcId.equals(a.getCalcId()))
       {
         aa.add(a);
       }
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index d2f4b4d..0d6c8ae 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -611,6 +611,12 @@ public class AlignmentTest
     AlignmentAnnotation ann = iter.next();
     assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
     assertFalse(iter.hasNext());
+
+    // invalid id
+    anns = al.findAnnotation("CalcIdForD.melanogaster.?");
+    assertFalse(iter.hasNext());
+    anns = al.findAnnotation(null);
+    assertFalse(iter.hasNext());
   }
 
   @Test(groups = { "Functional" })
-- 
1.7.10.2