* 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)
{
/*
* 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
* 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
{
if (newAnnot.sequenceRef != null)
{
- SequenceI dsseq = newAnnot.sequenceRef.getDatasetSequence();
+ SequenceI dsseq = newAnnot.sequenceRef;
while (dsseq.getDatasetSequence() != null)
{
dsseq = dsseq.getDatasetSequence();