isAligned assertion (bug 0008144)

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index dc70c47..7fb4659 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -607,20 +607,29 @@ public class Alignment implements AlignmentI
     return gapCharacter;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#isAligned()
    */
   public boolean isAligned()
   {
+    return isAligned(false);
+  }
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   */
+  public boolean isAligned(boolean includeHidden) {
     int width = getWidth();
-
+    if (hiddenSequences==null || hiddenSequences.getSize()==0) {
+      includeHidden = true; // no hidden sequences to check against.
+    }
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() != width)
+      if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
       {
-        return false;
+        if (getSequenceAt(i).getLength() != width)
+        {
+          return false;
+        }
       }
     }