X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=d113d92eba43e0940ffefd2f26425bb868d1543f;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=1fa3b96c90f53ae42f0118709fc1b7bb5fde2cf9;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java index 1fa3b96..d113d92 100755 --- a/src/jalview/datamodel/AlignmentOrder.java +++ b/src/jalview/datamodel/AlignmentOrder.java @@ -1,184 +1,275 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.datamodel; - -import java.util.*; - - -/** - *
Title:
- * - *Description:
- * - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 - */ -public class AlignmentOrder -{ - // JBPNote : this method would return a vector containing all sequences in seqset - // with those also contained in order at the beginning of the vector in the order - // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method - // should be here for completeness. - - /* public Vector getOrder(AlignmentI seqset) - { - Vector perm = new Vector(seqset.getHeight()); - for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); iDescription:
+ * + *Copyright: Copyright (c) 2004
+ * + *Company: Dundee University
+ * + * @author not attributable + * @version 1.0 + */ +public class AlignmentOrder +{ + // JBPNote : this method would return a vector containing all sequences in seqset + // with those also contained in order at the beginning of the vector in the order + // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method + // should be here for completeness. + + /* public Vector getOrder(AlignmentI seqset) + { + Vector perm = new Vector(seqset.getHeight()); + for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i