X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=b214934a34263fb33fbf9aaa36a2b81102619e81;hb=d82d17a7ba88f90e6b8b1b591245a7ee70b3975c;hp=300c950bdb28e09c2a504545e51a6ecc04693724;hpb=2f87d72ea4f1bbf768918a253be05771f9c430cb;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 300c950..b214934 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -125,8 +125,7 @@ public class Alignment implements AlignmentI
   /**
    * Make a new alignment from an array of SeqCigars
    * 
-   * @param seqs
-   *          SeqCigar[]
+   * @param alseqs
    */
   public Alignment(SeqCigar[] alseqs)
   {
@@ -719,6 +718,17 @@ public class Alignment implements AlignmentI
     return maxLength;
   }
 
+  @Override
+  public int getVisibleWidth()
+  {
+    int w = getWidth();
+    if (hiddenCols != null)
+    {
+      w -= hiddenCols.getSize();
+    }
+    return w;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1179,7 +1189,8 @@ public class Alignment implements AlignmentI
     int maxLength = -1;
 
     SequenceI current;
-    for (int i = 0; i < sequences.size(); i++)
+    int nseq = sequences.size();
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       for (int j = current.getLength(); j > maxLength; j--)
@@ -1196,7 +1207,7 @@ public class Alignment implements AlignmentI
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size(); i++)
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();
@@ -1895,9 +1906,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setHiddenColumns(HiddenColumns cols)
+  public boolean setHiddenColumns(HiddenColumns cols)
   {
+    boolean changed = cols == null ? hiddenCols != null
+            : !cols.equals(hiddenCols);
     hiddenCols = cols;
+    return changed;
   }
 
   @Override