X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=9ba85860964dfb646219381de4c8a83af9ca2647;hb=aeb173dd7daa4559e760548d955ee83aac6828d8;hp=28ec445bc2cc1d1913e13b53d5f47f62a616f152;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 28ec445..9ba8586 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,45 +1,24 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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
+ * 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 - *
- * - * @author not attributable - * @version 1.0 - */ public class AlignmentOrder { // JBPNote : this method would return a vector containing all sequences in @@ -82,7 +61,7 @@ public class AlignmentOrder * AlignmentOrder * * @param anOrder - * Vector + * Vector */ public AlignmentOrder(Vector anOrder) { @@ -93,7 +72,7 @@ public class AlignmentOrder * AlignmentOrder * * @param orderFrom - * AlignmentI + * AlignmentI */ public AlignmentOrder(AlignmentI orderFrom) { @@ -109,7 +88,7 @@ public class AlignmentOrder * Creates a new AlignmentOrder object. * * @param orderFrom - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignmentOrder(SequenceI[] orderFrom) { @@ -125,7 +104,7 @@ public class AlignmentOrder * DOCUMENT ME! * * @param Type - * DOCUMENT ME! + * DOCUMENT ME! */ public void setType(int Type) { @@ -146,7 +125,7 @@ public class AlignmentOrder * DOCUMENT ME! * * @param Name - * DOCUMENT ME! + * DOCUMENT ME! */ public void setName(String Name) { @@ -167,7 +146,7 @@ public class AlignmentOrder * DOCUMENT ME! * * @param Order - * DOCUMENT ME! + * DOCUMENT ME! */ public void setOrder(Vector Order) { @@ -217,9 +196,9 @@ public class AlignmentOrder * equivalence - will throw Error at moment * * @param o - * @param identity - - * false - use weak equivalence (refers to same or different - * parts of same sequence) + * @param identity + * - false - use weak equivalence (refers to same or different parts + * of same sequence) * @return true if o orders equivalent sequenceI objects in the same way */ public boolean equals(AlignmentOrder o, boolean identity) @@ -271,12 +250,11 @@ public class AlignmentOrder /** * Consistency test for alignmentOrders * - * @param o // - * TODO: Weak SequenceI equivalence - will throw Error at - * moment - * @param identity - - * false - use weak equivalence (refers to same or different - * parts of same sequence) + * @param o + * // TODO: Weak SequenceI equivalence - will throw Error at moment + * @param identity + * - false - use weak equivalence (refers to same or different parts + * of same sequence) * @return true if o contains or is contained by this and the common SequenceI * objects are ordered in the same way */ @@ -312,7 +290,7 @@ public class AlignmentOrder for (int i = 0, j = s.size(); i < j; i++) { int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by - // incremental position search + // incremental position search if (pos > last) { last = pos; @@ -335,15 +313,14 @@ public class AlignmentOrder * AlignmentOrder * * @param orderThis - * AlignmentI + * AlignmentI * @param byThat - * AlignmentI + * AlignmentI */ /* * public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat) { // Vector * is an ordering of this alignment using the order of sequence objects in - * byThat, // where ids and unaligned sequences must match - * } + * byThat, // where ids and unaligned sequences must match } */ }