merge from 2_4_Release branch

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 21dcce1..22fe523 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
@@ -27,6 +26,7 @@ public class HiddenSequences
    * holds a list of hidden sequences associated with an alignment.
    */
   public SequenceI[] hiddenSequences;
+
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -57,7 +57,8 @@ 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 +68,7 @@ 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 +104,8 @@ 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 +162,8 @@ 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 +190,8 @@ public class HiddenSequences
         }
         else
         {
-          System.out.println(seq.getName() + " has been deleted whilst hidden");
+          System.out.println(seq.getName()
+                  + " has been deleted whilst hidden");
         }
       }