HiddenSequences now array, not hashtable

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 62852a2..5f60530 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -146,8 +146,9 @@ public class Alignment implements AlignmentI
           getDataset().addSequence(ds);
         }
       }
-
       sequences.addElement(snew);
+
+      hiddenSequences.adjustHeightSequenceAdded();
     }
 
 
@@ -310,13 +311,7 @@ public class Alignment implements AlignmentI
      */
     public void deleteSequence(SequenceI s)
     {
-        for (int i = 0; i < getHeight(); i++)
-        {
-            if (getSequenceAt(i) == s)
-            {
-                deleteSequence(i);
-            }
-        }
+      deleteSequence(findIndex(s));
     }
 
     /**
@@ -327,6 +322,7 @@ public class Alignment implements AlignmentI
     public void deleteSequence(int i)
     {
         sequences.removeElementAt(i);
+        hiddenSequences.adjustHeightSequenceDeleted(i);
     }
 
 
@@ -565,15 +561,6 @@ public class Alignment implements AlignmentI
         return gapCharacter;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getAAFrequency()
-    {
-        return AAFrequency.calculate(sequences, 0, getWidth());
-    }
 
     /**
      * DOCUMENT ME!
@@ -844,7 +831,9 @@ public class Alignment implements AlignmentI
     for (int i=0; i<sequences.size(); i++) {
       alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
     }
-    return new CigarArray(alseqs);
+    CigarArray cal = new CigarArray(alseqs);
+    cal.addOperation(CigarArray.M, getWidth());
+    return cal;
   }
 
 }