apply version 2.7 copyright

[jalview.git] / src / jalview / datamodel / HiddenSequences.java

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 21dcce1..901cf35 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,22 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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 <http://www.gnu.org/licenses/>.
  */
-
 package jalview.datamodel;
 
 import java.util.*;
@@ -27,6 +25,7 @@ public class HiddenSequences
    * holds a list of hidden sequences associated with an alignment.
    */
   public SequenceI[] hiddenSequences;
+
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -57,7 +56,8 @@ public class HiddenSequences
     int width = 0;
     for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
+      if (hiddenSequences[i] != null
+              && hiddenSequences[i].getLength() > width)
       {
         width = hiddenSequences[i].getLength();
       }
@@ -67,8 +67,7 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are removed from the
-   * main alignment
+   * Call this method if sequences are removed from the main alignment
    */
   public void adjustHeightSequenceDeleted(int seqIndex)
   {
@@ -104,8 +103,8 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are added to or removed from the
-   * main alignment
+   * Call this method if sequences are added to or removed from the main
+   * alignment
    */
   public void adjustHeightSequenceAdded()
   {
@@ -162,9 +161,8 @@ public class HiddenSequences
   {
     Vector revealedSeqs = new Vector();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
-    if (repSequence != null &&
-        hiddenReps != null
-        && hiddenReps.containsKey(repSequence))
+    if (repSequence != null && hiddenReps != null
+            && hiddenReps.containsKey(repSequence))
     {
       hiddenReps.remove(repSequence);
       revealedSeqs.addElement(repSequence);
@@ -191,7 +189,8 @@ public class HiddenSequences
         }
         else
         {
-          System.out.println(seq.getName() + " has been deleted whilst hidden");
+          System.out.println(seq.getName()
+                  + " has been deleted whilst hidden");
         }
       }