+ public void removeSingleReadAlignment(SingleReadAlignment singleReadAlignment) {
+ this.singleReadAlignments.remove(singleReadAlignment);
+ if (this.equals(singleReadAlignment.getConsensusSequence())){
+ singleReadAlignment.setConsensusAlignment(null);
+ }
+ }
+// /**
+// * @see #getSingleReads()
+// */
+// //TODO private as long it is unclear how bidirectionality is handled
+// @SuppressWarnings("unused")
+// private void setSingleReadAlignments(Set<SingleReadAlignment> singleReadAlignments) {
+// this.singleReadAlignments = singleReadAlignments;
+// }
+
+// *********************** CONVENIENCE ***********************************/
+
+ /**
+ * Convenience method to add a single read to a consensus sequence
+ * by creating a {@link SingleReadAlignment}.
+ * @param singleRead the {@link SingleRead} to add
+ * @return the created SingleReadAlignment
+ */
+ public SingleReadAlignment addSingleRead(SingleRead singleRead) {
+ SingleReadAlignment alignment = SingleReadAlignment.NewInstance(this, singleRead);
+ return alignment;
+ }
+