JFAL-1594 fix Undo bug; enum EditCommand.Action; basic JUnit

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

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 35d467a..f414d13 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -20,9 +20,12 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.util.ShiftList;
 
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * NOTE: Columns are zero based.
@@ -186,9 +189,9 @@ public class ColumnSelection
    * @param left
    *          shift in edit (+ve for removal, or -ve for inserts)
    */
-  public Vector compensateForEdit(int start, int change)
+  public List<int[]> compensateForEdit(int start, int change)
   {
-    Vector deletedHiddenColumns = null;
+    List<int[]> deletedHiddenColumns = null;
     for (int i = 0; i < size(); i++)
     {
       int temp = columnAt(i);
@@ -201,14 +204,14 @@ public class ColumnSelection
 
     if (hiddenColumns != null)
     {
-      deletedHiddenColumns = new Vector();
+      deletedHiddenColumns = new ArrayList<int[]>();
       int hSize = hiddenColumns.size();
       for (int i = 0; i < hSize; i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
         if (region[0] > start && start + change > region[1])
         {
-          deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
+          deletedHiddenColumns.add(region);
 
           hiddenColumns.removeElementAt(i);
           i--;
@@ -752,6 +755,7 @@ public class ColumnSelection
   public boolean isVisible(int column)
   {
     if (hiddenColumns != null)
+    {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
@@ -760,6 +764,7 @@ public class ColumnSelection
           return false;
         }
       }
+    }
 
     return true;
   }
@@ -1018,7 +1023,9 @@ public class ColumnSelection
         w += els.length;
       }
       if (w == 0)
+      {
         return;
+      }
       Enumeration e = annels.elements();
       alignmentAnnotation.annotations = new Annotation[w];
       w = 0;