-// if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
-// System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
+ // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
+ // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
+ }
+
+ /**
+ * references to entities that this sequence cigar is associated with.
+ */
+ private Hashtable selGroups = null;
+
+ public void setGroupMembership(Object group)
+ {
+ if (selGroups == null)
+ {
+ selGroups = new Hashtable();
+ }
+ selGroups.put(group, new int[0]);
+ }
+
+ /**
+ * Test for and if present remove association to group.
+ *
+ * @param group
+ * @return true if group was associated and it was removed
+ */
+ public boolean removeGroupMembership(Object group)
+ {
+ if (selGroups != null && selGroups.containsKey(group))
+ {
+ selGroups.remove(group);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * forget all associations for this sequence.
+ */
+ public void clearMemberships()
+ {
+ if (selGroups != null)
+ {
+ selGroups.clear();
+ }
+ selGroups = null;
+ }
+
+ /**
+ *
+ * @return null or array of all associated entities
+ */
+ public Object[] getAllMemberships()
+ {
+ if (selGroups == null)
+ {
+ return null;
+ }
+ Object[] mmbs = new Object[selGroups.size()];
+ Enumeration en = selGroups.keys();
+ for (int i = 0; en.hasMoreElements(); i++)
+ {
+ mmbs[i] = en.nextElement();
+ }
+ return mmbs;