X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=8b741290bc8e878154d9cb4b6d8e0108e8b7ffbb;hb=f67e3c63a48403f4bbb9066595e4cb5a00089234;hp=baa8e831a82293a46c7298fb88db3a0fc486150c;hpb=621b23ed6783d2c4c7caaf6d58151217b2fa4f1d;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index baa8e83..8b74129 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -36,7 +36,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
-import java.util.function.Consumer;
 
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
@@ -49,7 +48,7 @@ public class Alignment implements AlignmentI
 {
   private Alignment dataset;
 
-  protected List<SequenceI> sequences;
+  private List<SequenceI> sequences;
 
   protected List<SequenceGroup> groups;
 
@@ -191,10 +190,12 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceI getSequenceAt(int i)
   {
-    // don't need to synchronise here as sequences is a synchronizedList
-    if (i > -1 && i < sequences.size())
+    synchronized (sequences)
     {
-      return sequences.get(i);
+      if (i > -1 && i < sequences.size())
+      {
+        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!
@@ -1913,11 +1939,4 @@ public class Alignment implements AlignmentI
   {
     hiddenCols = cols;
   }
-
-  @Override
-  public void forEachSequence(Consumer<SequenceI> c, int start, int end)
-  {
-    sequences.subList(start, end).forEach(c);
-  }
-
 }