X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=42303660de8a07b5f50bd7454509edaf43460a2d;hb=bbc8fc127287ad3a11f0b470d37d741ddca162ff;hp=bb9c0f53ca9158052315ed9a6c808fa6d4c571a7;hpb=ceba202c97c435a5a0f70307961ba74316bd8312;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index bb9c0f5..4230366 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -86,7 +86,6 @@ public class Sequence extends ASequence implements SequenceI
   HiddenMarkovModel hmm;
 
   boolean isHMMConsensusSequence = false;
-
   private DBModList<DBRefEntry> dbrefs; // controlled access
 
   /**
@@ -385,7 +384,6 @@ public class Sequence extends ASequence implements SequenceI
     {
       this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
     }
-
   }
 
   @Override
@@ -1441,6 +1439,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
+    // TODO JAL-3980 maintain as sorted list
     if (datasetSequence != null)
     {
       datasetSequence.addDBRef(entry);
@@ -1451,6 +1450,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       dbrefs = new DBModList<>();
     }
+    // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
 
     for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
     {
@@ -1825,14 +1825,30 @@ 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)
       {
         String id = ann.getCalcId();
-        if (id != null && id.equals(calcId)
-                && ann.label != null && ann.label.equals(label))
+        if ((id != null && id.equals(calcId))
+                && (ann.label != null && ann.label.equals(label))
+                && ((ignoreDescription && description == null)
+                        || (ann.description != null
+                                && ann.description.equals(description))))
         {
           result.add(ann);
         }
@@ -1978,7 +1994,6 @@ public class Sequence extends ASequence implements SequenceI
     }
     return false;
   }
-
   /**
    * {@inheritDoc}
    */