X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=e51afd041569e75f35083707253061e153e672b9;hb=0c355acb1b5ddab95961d703ca6bc383a4464def;hp=c35ff4628bdb4058b869c2b2da840643353812e0;hpb=8b08ad675b71e43e127d7be3b65c6d2f9d9094db;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index c35ff46..e51afd0 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -175,8 +175,9 @@ public class ColumnSelection
    * @param start beginning of edit
    * @param left shift in edit (+ve for removal, or -ve for inserts)
    */
-  public void compensateForEdit(int start, int change)
+  public Vector compensateForEdit(int start, int change)
   {
+    Vector deletedHiddenColumns = null;
     for (int i = 0; i < size(); i++)
     {
       int temp = columnAt(i);
@@ -189,20 +190,37 @@ public class ColumnSelection
 
     if(hiddenColumns!=null)
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      deletedHiddenColumns = new Vector();
+      int hSize = hiddenColumns.size();
+      for(int i=0; i<hSize; i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
-        if(region[0] > start)
+        if ( region[0]>start && start+change>region[1] )
+        {
+          deletedHiddenColumns.addElement(
+              hiddenColumns.elementAt(i));
+
+          hiddenColumns.removeElementAt(i);
+          i--;
+          hSize--;
+          continue;
+        }
+
+        if(region[0]>start)
         {
           region[0] -= change;
           region[1] -= change;
         }
+
         if(region[0]<0)
           region[0] = 0;
-        if(region[1] <0)
-          region[1] = 0;
+
       }
+
+      this.revealHiddenColumns(0);
     }
+
+    return deletedHiddenColumns;
   }
   /**
    * propagate shift in alignment columns to column selection
@@ -582,6 +600,8 @@ public class ColumnSelection
     { removeElement(max);  max ++;  }
 
     min++; max--;
+    if(min>max)
+      min = max;
 
     hideColumns(min, max);
   }
@@ -644,18 +664,18 @@ public class ColumnSelection
       if (copy.selected!=null) {
         selected = new Vector();
         for (int i=0,j=copy.selected.size(); i<j; i++) {
-          selected.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
+          selected.addElement(copy.selected.elementAt(i));
         }
       }
       if (copy.hiddenColumns!=null) {
-        hiddenColumns=new Vector();
+        hiddenColumns=new Vector(copy.hiddenColumns.size());
         for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
           int[] rh,cp;
           rh = (int[])copy.hiddenColumns.elementAt(i);
           if (rh!=null) {
             cp = new int[rh.length];
             System.arraycopy(rh, 0, cp, 0, rh.length);
-            hiddenColumns.setElementAt(cp, i);
+            hiddenColumns.addElement(cp);
           }
         }
       }
@@ -717,7 +737,7 @@ public class ColumnSelection
     {
       for(i=0; i<iSize; i++)
       {
-        selection[i] = seqs[i].getSequence(start, end);
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
     }