X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=9ba85860964dfb646219381de4c8a83af9ca2647;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;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 <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
 import java.util.*;
 
-/**
- * <p>
- * Title:
- * </p>
- * 
- * <p>
- * Description:
- * </p>
- * 
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- * 
- * <p>
- * Company: Dundee University
- * </p>
- * 
- * @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 }
    */
 }