From ca47e4d0e1176893b414fba3fbe8a308e24cc52e Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 17 Sep 2021 13:12:34 +0100
Subject: [PATCH] JAL-2226 new method to search for annotation matching
 particular description as well as calcId and label

---
 src/jalview/datamodel/Sequence.java      |   23 +++++++++++++++++++++--
 src/jalview/datamodel/SequenceI.java     |   11 +++++++++++
 test/jalview/datamodel/SequenceTest.java |   29 +++++++++++++++++++++++++++++
 3 files changed, 61 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 552349f..3bd7b4b 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1799,13 +1799,32 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
+    return getAlignmentAnnotations(calcId, label, null, true);
+  }
+
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description)
+  {
+    return getAlignmentAnnotations(calcId, label, description, false);
+  }
+
+  private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description, boolean nullWildcard)
+  {
     List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
-                && ann.label != null && ann.label.equals(label))
+        if (((nullWildcard && calcId == null)
+                || (ann.calcId != null && ann.calcId.equals(calcId)))
+                && ((nullWildcard && label == null)
+                        || (ann.label != null && ann.label.equals(label)))
+                && ((nullWildcard && description == null)
+                        || (ann.description != null
+                                && ann.description.equals(description))))
+
         {
           result.add(ann);
         }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 933f332..7c3eb41 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -446,6 +446,17 @@ public interface SequenceI extends ASequenceI
           String label);
 
   /**
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source), label (type) and description (observation instance).
+   * Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   * @param description
+   */
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description);
+  /**
    * create a new dataset sequence (if necessary) for this sequence and sets
    * this sequence to refer to it. This call will move any features or
    * references on the sequence onto the dataset. It will also make a duplicate
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 6d07113..eb75645 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -192,6 +192,35 @@ public class SequenceTest
     assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
   }
 
+
+  @Test(groups = { "Functional" })
+  public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
+  {
+    addAnnotation("label1", "desc1", "calcId1", 1f);
+    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
+            1f);
+    addAnnotation("label2", "desc3", "calcId3", 1f);
+    AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
+            1f);
+    addAnnotation("label5", "desc3", null, 1f);
+    addAnnotation(null, "desc3", "calcId3", 1f);
+
+    List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
+            "label2", "desc3");
+    assertEquals(1, anns.size());
+    assertSame(ann4, anns.get(0));
+    /**
+     * null matching should fail
+     */
+    assertTrue(seq.getAlignmentAnnotations("calcId3", "label2",null).isEmpty());
+    
+    assertTrue(seq.getAlignmentAnnotations("calcId2", "label3",null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations("calcId3", "label5",null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations("calcId2", null,null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations(null, "label3",null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations(null, null,null).isEmpty());
+  }
+
   /**
    * Tests for addAlignmentAnnotation. Note this method has the side-effect of
    * setting the sequenceRef on the annotation. Adding the same annotation twice
-- 
1.7.10.2