{\r
return Order;\r
}\r
-\r
+ /**\r
+ * replaces oldref with newref in the alignment order.\r
+ * @param oldref\r
+ * @param newref\r
+ * @return\r
+ */\r
+ public boolean updateSequence(SequenceI oldref, SequenceI newref) {\r
+ int found=Order.indexOf(oldref);\r
+ if (found>-1) {\r
+ Order.setElementAt(newref, found);\r
+ }\r
+ return found>-1;\r
+ }\r
/**\r
* AlignmentOrder\r
*\r