X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=e4bc25e0910a0cab4b8057c01da79f5662729d88;hb=3193f6774b111974d609ea5d5adc95ff50f92b68;hp=86c140f0a8071566edb454d883f52c1e3b0caa0b;hpb=12aa3352bd2981b8aa86d9d28e4c405fa56a2c29;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 86c140f..e4bc25e 100755
--- 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
@@ -172,11 +172,17 @@ public class Alignment implements AlignmentI
     {
         return groups;
     }
-
     /** Takes out columns consisting entirely of gaps (-,.," ")
      */
-    public void removeGaps()
-    {
+    public void removeGaps() {
+      removeGaps((ShiftList)null);
+    }
+    /**
+     * remove gaps in alignment - recording any frame shifts in shiftrecord
+     * intended to be passed to ColumnSelection.compensateForEdits(shiftrecord)
+     * @param shiftrecord
+     */
+    public void removeGaps(ShiftList shiftrecord) {
         SequenceI[] seqs = getVisibleAndRepresentedSeqs();
         int j, jSize = seqs.length;
 
@@ -219,6 +225,9 @@ public class Alignment implements AlignmentI
             if (!delete && startCol > -1)
             {
               deleteColumns(seqs, startCol, endCol);
+              if (shiftrecord!=null) {
+                shiftrecord.addShift(startCol, 1+endCol-startCol);
+              }
               width -= (endCol - startCol);
               i -= (endCol - startCol);
               startCol = -1;
@@ -229,6 +238,9 @@ public class Alignment implements AlignmentI
         if (delete && startCol > -1)
         {
           deleteColumns(seqs, startCol, endCol);
+          if (shiftrecord!=null) {
+            shiftrecord.addShift(startCol, 1+endCol-startCol);
+          }
         }
     }
 
@@ -394,8 +406,7 @@ public class Alignment implements AlignmentI
 
         while (i < sequences.size())
         {
-            Sequence s = (Sequence)getSequenceAt(i);
-            s.hiddenSequences = null;
+            SequenceI s = getSequenceAt(i);
             s.setColor(java.awt.Color.white);
             i++;
         }
@@ -406,9 +417,6 @@ public class Alignment implements AlignmentI
     {
         if (groups.contains(g))
         {
-          //remove any hidden representatives
-        //  for(int i=0; i<g.getsiz
-         //   g.getSequences()
             groups.removeElement(g);
         }
     }
@@ -557,15 +565,6 @@ public class Alignment implements AlignmentI
         return gapCharacter;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getAAFrequency()
-    {
-        return AAFrequency.calculate(sequences, 0, getWidth());
-    }
 
     /**
      * DOCUMENT ME!
@@ -836,7 +835,9 @@ 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;
   }
 
 }