- /**
- * Consistency test for alignmentOrders
- * @param o
- * // TODO: Weak SequenceI equivalence - will throw Error at moment
- * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
- * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
- */
- public boolean isConsistent(AlignmentOrder o, boolean identity) {
- if (o!=this) {
- if (o==null)
- return false;
- if (Order!=null && o.Order!=null) {
- Vector c,s;
- if (o.Order.size()>Order.size()) {
- c = o.Order;
- s = Order;
- } else {
- c = Order;
- s = o.Order;
- }
- if (!identity) {
- throw new Error("Weak sequenceI equivalence not yet implemented.");
- } else {
- // test if c contains s and order in s is conserved in c
- int last=-1;
- for (int i=0,j=s.size(); i<j; i++) {
- int pos=c.indexOf(s.get(i)); // JBPNote - optimize by incremental position search
- if (pos>last) {
- last=pos;
- } else
- return false;
+ return true;
+ }
+
+ /**
+ * Consistency test for alignmentOrders
+ *
+ * @param o
+ * @return true if o contains or is contained by this and the common SequenceI
+ * objects are ordered in the same way
+ */
+ public boolean isConsistent(AlignmentOrder o)
+ {
+ return isConsistent(o, true);
+ }
+
+ /**
+ * Consistency test for alignmentOrders
+ *
+ * @param o
+ * // TODO: Weak SequenceI equivalence - will throw Error at moment
+ * @param identity
+ * - false - use weak equivalence (refers to same or different parts
+ * of same sequence)
+ * @return true if o contains or is contained by this and the common SequenceI
+ * objects are ordered in the same way
+ */
+ public boolean isConsistent(AlignmentOrder o, boolean identity)
+ {
+ if (o != this)
+ {
+ if (o == null)
+ {
+ return false;
+ }
+ if (Order != null && o.Order != null)
+ {
+ List<SequenceI> c, s;
+ if (o.Order.size() > Order.size())
+ {
+ c = o.Order;
+ s = Order;
+ }
+ else
+ {
+ c = Order;
+ s = o.Order;
+ }
+ if (!identity)
+ {
+ throw new Error("Weak sequenceI equivalence not yet implemented.");
+ }
+ else
+ {
+ // test if c contains s and order in s is conserved in c
+ int last = -1;
+ for (int i = 0, j = s.size(); i < j; i++)
+ {
+ int pos = c.indexOf(s.get(i)); // JBPNote - optimize by
+ // incremental position search
+ if (pos > last)
+ {
+ last = pos;
+ }
+ else
+ {
+ return false;