JAL-3070 JAL-3066 fix initialisation of slivka ServiceWithParameters

[jalview.git] / src / jalview / analysis / AlignmentAnnotationUtils.java

diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index 194ef80..5c2d936 100644 (file)
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -75,11 +75,11 @@ public class AlignmentAnnotationUtils
      * Build a lookup, by calcId (annotation source), of all annotation types in
      * each graph group.
      */
-    Map<String, Map<Integer, List<String>>> groupLabels = new HashMap<String, Map<Integer, List<String>>>();
+    Map<String, Map<Integer, List<String>>> groupLabels = new HashMap<>();
 
     // trackers for which calcId!label combinations we have dealt with
-    List<String> addedToShown = new ArrayList<String>();
-    List<String> addedToHidden = new ArrayList<String>();
+    List<String> addedToShown = new ArrayList<>();
+    List<String> addedToHidden = new ArrayList<>();
 
     for (AlignmentAnnotation aa : annotations)
     {
@@ -99,7 +99,7 @@ public class AlignmentAnnotationUtils
         /*
          * Build a 'composite label' for types in line graph groups.
          */
-        final List<String> labelAsList = new ArrayList<String>();
+        final List<String> labelAsList = new ArrayList<>();
         final String displayLabel = aa.label;
         labelAsList.add(displayLabel);
         if (aa.graph == AlignmentAnnotation.LINE_GRAPH
@@ -245,8 +245,8 @@ public class AlignmentAnnotationUtils
    * association as necessary.
    * 
    * @param newAnnot
-   *          - annotation row associated with an alignment sequence to be
-   *          propagated to its dataset sequence.
+   *          - annotation row associated with a sequence to be propagated to
+   *          its reference annotation
    * @param typeName
    *          - label used to match existing row
    * @param calcId
@@ -257,7 +257,7 @@ public class AlignmentAnnotationUtils
   {
     if (newAnnot.sequenceRef != null)
     {
-      SequenceI dsseq = newAnnot.sequenceRef.getDatasetSequence();
+      SequenceI dsseq = newAnnot.sequenceRef;
       while (dsseq.getDatasetSequence() != null)
       {
         dsseq = dsseq.getDatasetSequence();