X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=9b60e566929ade7150328476a74cacf45f8557dd;hb=fbb18baad3919cbf94fcb5159bbd5269d6af18b4;hp=b8cdf52232e2d6aee46e05d608609bf8c0abb160;hpb=98a71b36e29f88a1aba4b00c1f8c7099152c7307;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index b8cdf52..9b60e56 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 public class CigarArray extends CigarBase
@@ -118,7 +136,7 @@ public class CigarArray extends CigarBase
    * applyDeletions
    * edits underlying refCigars to propagate deleted regions, and removes deletion
    * operations from CigarArray operation list.
-   * @return int[] position where deletion occured in cigarArray or null if none occured
+   * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured
    */
   public int[] applyDeletions()
   {
@@ -127,31 +145,45 @@ public class CigarArray extends CigarBase
       return null;
     int cursor=0; // range counter for deletions
     int vcursor=0; // visible column index
-    for (int i=0; i<length; i++) {
+    int offset=0; // shift in visible column index as deletions are made
+    int i=0;
+    while (i<length) {
       if (operation[i]!=D) {
         if (operation[i]==M)
           cursor+=range[i];
-        vcursor+=range[i];
+        vcursor+=range[i++];
       }
       else
       {
         if (delpos==null)
           delpos=new java.util.Vector();
         int delstart=cursor, delend=cursor+range[i]-1; // inclusive
-        delpos.addElement(new Integer(vcursor-1)); // index of left hand column of hidden region boundary
+        delpos.addElement(new int[] { vcursor+offset, range[i]}); // index of right hand column after hidden region boundary
+        offset+=range[i]-1; // shift in visible column coordinates
         System.arraycopy(operation, i+1, operation, i, length-i);
         System.arraycopy(range, i+1, range, i, length-i);
         length--;
+        /*        int dmax=0;
+         for (int s=0; s<refCigars.length; s++) {
+           int d = refCigars[s].deleteRange(delstart, delend);
+           if (d>dmax)
+             dmax=d;
+         }
+         offset+=dmax; // shift in visible column coordinates
+         */
         for (int s=0; s<refCigars.length; s++) {
-          refCigars[s].deleteRange(delstart, delend);
+          int d = refCigars[s].deleteRange(delstart, delend);
         }
+
       }
     }
     if (delpos!=null)
     {
-      int[] pos=new int[delpos.size()];
+      int[] pos=new int[delpos.size()*2];
       for (int k = 0, l = delpos.size(); k < l; k++) {
-        pos[k] = ((Integer) delpos.elementAt(k)).intValue();
+        int[] dr = ((int[]) delpos.elementAt(k));
+        pos[k*2] = dr[0];
+        pos[k*2+1] = dr[1];
         delpos.setElementAt(null,k);
       }
       delpos=null;