X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=7bf20424892c1f0963c789ae8b33c417ee2d724f;hb=1786b6dbaf15f405c2e364f84891612ed0da3405;hp=c0da1fc80c7dd3ab7cc5cb7479f75b4b77d3c7d1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index c0da1fc..7bf2042 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,125 +1,346 @@
/*
-* 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 (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see
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