Merge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791

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

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 45dcab2..2d43f02 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -469,6 +469,10 @@ public class HiddenColumns
     }
   }
 
+  /**
+   * Answers true if obj is an instance of HiddenColumns, and holds the same
+   * array of start-end column ranges as this, else answers false
+   */
   @Override
   public boolean equals(Object obj)
   {
@@ -1008,7 +1012,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      return new HiddenColsIterator(hiddenColumns);
+      return new RangeIterator(hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
@@ -1029,7 +1033,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      return new HiddenColsIterator(start, end, hiddenColumns);
+      return new RangeIterator(start, end, hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
@@ -1045,7 +1049,7 @@ public class HiddenColumns
    * @param end
    *          position to end at (inclusive, visible column position)
    */
-  public Iterator<Integer> getBoundedStartIterator(int start, int end)
+  public Iterator<Integer> getStartRegionIterator(int start, int end)
   {
     try
     {
@@ -1062,7 +1066,7 @@ public class HiddenColumns
       HiddenCursorPosition pos = cursor
               .findRegionForColumn(absoluteStart - 1, false);
 
-      return new BoundedStartRegionIterator(pos, start, end,
+      return new StartRegionIterator(pos, start, end,
               hiddenColumns);
     } finally
     {
@@ -1084,7 +1088,8 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      return new VisibleColsIterator(start, end, hiddenColumns);
+      return new RangeElementsIterator(
+              new VisibleContigsIterator(start, end + 1, hiddenColumns));
     } finally
     {
       LOCK.readLock().unlock();