JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 3bd7b4b..f8e70b1 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1415,6 +1415,7 @@ 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);
@@ -1425,6 +1426,7 @@ 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++)
     {
@@ -1810,18 +1812,16 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
-          String label, String description, boolean nullWildcard)
+          String label, String description, boolean ignoreDescription)
   {
     List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (((nullWildcard && calcId == null)
-                || (ann.calcId != null && ann.calcId.equals(calcId)))
-                && ((nullWildcard && label == null)
-                        || (ann.label != null && ann.label.equals(label)))
-                && ((nullWildcard && description == null)
+        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))))