X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=28ec445bc2cc1d1913e13b53d5f47f62a616f152;hb=c16c1633e1a5acc9f44e4de40b9abbb8a59b99b4;hp=c0da1fc80c7dd3ab7cc5cb7479f75b4b77d3c7d1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java index c0da1fc..28ec445 100755 --- a/src/jalview/datamodel/AlignmentOrder.java +++ b/src/jalview/datamodel/AlignmentOrder.java @@ -1,125 +1,349 @@ /* -* 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.*; - - + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 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
- * + *+ * 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) + */ +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