/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
AlignmentAnnotation[] getAlignmentAnnotation();
- Iterable<AlignmentAnnotation> findAnnotation(String calcId);
-
/**
- * context for this annotated collection
+ * Returns a list of annotations matching the given calc id, or an empty list
+ * if calcId is null
*
- * @return null or the collection upon which this collection is defined (e.g.
- * alignment, parent group).
+ * @param calcId
+ * @return
*/
- AnnotatedCollectionI getContext();
+ Iterable<AlignmentAnnotation> findAnnotation(String calcId);
/**
- * Return an iterable set of any annotations in the collection that match the
- * provided criteria, i.e.
- * <ul>
- * <li>reference the same sequence datasequence</li>
- * <li>have the same calcId (source of annotation)</li>
- * <li>have the same label (type of annotation)</li>
- * </ul>
+ * Returns an iterable collection of any annotations that match on given
+ * sequence ref, calcId and label (ignoring null values).
*
- * @param datasequence
+ * @param seq
+ * null or reference sequence to select annotation for
* @param calcId
+ * null or the calcId to select annotation for
* @param label
- * @return
+ * null or the label to select annotation for
*/
- Iterable<AlignmentAnnotation> findAnnotation(SequenceI datasequence,
+ Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label);
+
+ /**
+ * context for this annotated collection
+ *
+ * @return null or the collection upon which this collection is defined (e.g.
+ * alignment, parent group).
+ */
+ AnnotatedCollectionI getContext();
+
+
}