Merge branch 'develop' into releases/Release_2_11_2_Branch

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index e0a9d35..d52e049 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -523,6 +523,7 @@ public class Sequence extends ASequence implements SequenceI
   public void setStart(int start)
   {
     this.start = start;
+    sequenceChanged();
   }
 
   /**
@@ -1798,13 +1799,30 @@ 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 ignoreDescription)
+  {
     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 ((ann.calcId != null && ann.calcId.equals(calcId))
+                && (ann.label != null && ann.label.equals(label))
+                && ((ignoreDescription && description == null)
+                        || (ann.description != null
+                                && ann.description.equals(description))))
+
         {
           result.add(ann);
         }