return (anns == null ? Collections.<AlignmentAnnotation> emptyList()
: Arrays.asList(anns));
}
+
+ /**
+ * replace an existing sequence associated annotation with another, creating
+ * association as necessary.
+ *
+ * @param newAnnot
+ * - annotation row associated with an alignment sequence to be
+ * propagated to its dataset sequence.
+ * @param typeName
+ * - label used to match existing row
+ * @param calcId
+ * - calcId for existing row
+ */
+ public static void replaceAnnotationOnAlignmentWith(
+ AlignmentAnnotation newAnnot, String typeName, String calcId)
+ {
+ if (newAnnot.sequenceRef != null)
+ {
+ SequenceI dsseq = newAnnot.sequenceRef.getDatasetSequence();
+ while (dsseq.getDatasetSequence() != null)
+ {
+ dsseq = dsseq.getDatasetSequence();
+ }
+ // look for same annotation on dataset and lift this one over
+ List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+ typeName);
+ if (dsan != null && dsan.size() > 0)
+ {
+ for (AlignmentAnnotation dssan : dsan)
+ {
+ dsseq.removeAlignmentAnnotation(dssan);
+ }
+ }
+ AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+ dsseq.addAlignmentAnnotation(dssan);
+ dssan.adjustForAlignment();
+ }
+ }
}