JAL-2778 Revert back to old synchronisation

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 5733719..8b74129 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -48,7 +48,7 @@ public class Alignment implements AlignmentI
 {
   private Alignment dataset;
 
-  protected List<SequenceI> sequences;
+  private List<SequenceI> sequences;
 
   protected List<SequenceGroup> groups;
 
@@ -197,6 +197,7 @@ public class Alignment implements AlignmentI
         return sequences.get(i);
       }
     }
+
     return null;
   }
 
@@ -705,7 +706,7 @@ public class Alignment implements AlignmentI
   public int getWidth()
   {
     int maxLength = -1;
-
+  
     for (int i = 0; i < sequences.size(); i++)
     {
       if (getSequenceAt(i).getLength() > maxLength)
@@ -713,9 +714,34 @@ public class Alignment implements AlignmentI
         maxLength = getSequenceAt(i).getLength();
       }
     }
-
+  
     return maxLength;
   }
+  /*
+  @Override
+  public int getWidth()
+  {
+    final Wrapper temp = new Wrapper();
+  
+    forEachSequence(new Consumer<SequenceI>()
+    {
+      @Override
+      public void accept(SequenceI s)
+      {
+        if (s.getLength() > temp.inner)
+        {
+          temp.inner = s.getLength();
+        }
+      }
+    }, 0, sequences.size() - 1);
+  
+    return temp.inner;
+  }
+  
+  public static class Wrapper
+  {
+    public int inner;
+  }*/
 
   /**
    * DOCUMENT ME!
@@ -1471,8 +1497,8 @@ public class Alignment implements AlignmentI
   {
     // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
-    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
+    boolean samegap = oldc == getGapCharacter();
     boolean hashidden = toappend.getHiddenSequences() != null
             && toappend.getHiddenSequences().hiddenSequences != null;
     // get all sequences including any hidden ones
@@ -1490,14 +1516,7 @@ public class Alignment implements AlignmentI
         {
           if (!samegap)
           {
-            char[] oldseq = addedsq.getSequence();
-            for (int c = 0; c < oldseq.length; c++)
-            {
-              if (oldseq[c] == oldc)
-              {
-                oldseq[c] = gapCharacter;
-              }
-            }
+            addedsq.replace(oldc, gapCharacter);
           }
           toappendsq.add(addedsq);
         }