- // JBPNote : this method would return a vector containing all sequences in seqset\r
- // with those also contained in order at the beginning of the vector in the order\r
- // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method\r
- // should be here for completeness.\r
-\r
- /* public Vector getOrder(AlignmentI seqset)\r
- {\r
- Vector perm = new Vector(seqset.getHeight());\r
- for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)\r
- perm.setElement(i,...).\r
- return Order;\r
- }\r
- */\r
-\r
- /** DOCUMENT ME!! */\r
- public static final int FILE = 0;\r
-\r
- /** DOCUMENT ME!! */\r
- public static final int MSA = 1;\r
-\r
- /** DOCUMENT ME!! */\r
- public static final int USER = 2;\r
- private int Type = 0;\r
- private String Name;\r
- private Vector Order = null;\r
-\r
- /**\r
- * Creates a new AlignmentOrder object.\r
- */\r
- public AlignmentOrder()\r
- {\r
- }\r
+ // JBPNote : this method would return a vector containing all sequences in seqset\r
+ // with those also contained in order at the beginning of the vector in the order\r
+ // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method\r
+ // should be here for completeness.\r