X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=a7e93da69579fe8f372ab56cd54d0d5eddba5979;hb=refs%2Fheads%2Ffeatures%2FJAL-1767pcaInProject;hp=0b66b07278a163ff3c327f2f158aaa8633bffcfd;hpb=bab5165f5108cab3cce5b93b60f9ad83b7031b1c;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 0b66b07..a7e93da 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -394,8 +394,6 @@ public class HiddenColumns
             int colsToRemove = region[1] - region[0] + 1;
             hiddenColumns.remove(regionIndex);
             numColumns -= colsToRemove;
-
-            cursor.updateForDeletedRegion(hiddenColumns, colsToRemove);
           }
         }
       }
@@ -684,16 +682,19 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
 
-      int regionindex = cursor.findRegionForColumn(column, false)
-              .getRegionIndex();
-      if (regionindex > -1 && regionindex < hiddenColumns.size())
+      if (!hiddenColumns.isEmpty())
       {
-        int[] region = hiddenColumns.get(regionindex);
-        // already know that column <= region[1] as cursor returns containing
-        // region or region to right
-        if (column >= region[0])
+        int regionindex = cursor.findRegionForColumn(column, false)
+                .getRegionIndex();
+        if (regionindex > -1 && regionindex < hiddenColumns.size())
         {
-          return false;
+          int[] region = hiddenColumns.get(regionindex);
+          // already know that column <= region[1] as cursor returns containing
+          // region or region to right
+          if (column >= region[0])
+          {
+            return false;
+          }
         }
       }
       return true;
@@ -771,15 +772,39 @@ public class HiddenColumns
    */
   public void hideColumns(BitSet inserts)
   {
+    hideColumns(inserts, 0, inserts.length() - 1);
+  }
+
+  /**
+   * Hide columns corresponding to the marked bits, within the range
+   * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+   * 
+   * @param tohide
+   *          columns mapped to bits starting from zero
+   * @param start
+   *          start of range to hide columns within
+   * @param end
+   *          end of range to hide columns within
+   */
+  private void hideColumns(BitSet tohide, int start, int end)
+  {
     try
     {
       LOCK.writeLock().lock();
-      for (int firstSet = inserts
-              .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
+      for (int firstSet = tohide
+              .nextSetBit(start), lastSet = start; firstSet >= start
+                      && lastSet <= end; firstSet = tohide
                       .nextSetBit(lastSet))
       {
-        lastSet = inserts.nextClearBit(firstSet);
-        hideColumns(firstSet, lastSet - 1);
+        lastSet = tohide.nextClearBit(firstSet);
+        if (lastSet <= end)
+        {
+          hideColumns(firstSet, lastSet - 1);
+        }
+        else if (firstSet <= end)
+        {
+          hideColumns(firstSet, end);
+        }
       }
       cursor = new HiddenColumnsCursor(hiddenColumns);
     } finally
@@ -791,6 +816,7 @@ public class HiddenColumns
   /**
    * Hide columns corresponding to the marked bits, within the range
    * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+   * NB Existing entries in [start,end] are cleared.
    * 
    * @param tohide
    *          columns mapped to bits starting from zero
@@ -799,19 +825,10 @@ public class HiddenColumns
    * @param end
    *          end of range to hide columns within
    */
-  public void hideColumns(BitSet tohide, int start, int end)
+  public void clearAndHideColumns(BitSet tohide, int start, int end)
   {
     clearHiddenColumnsInRange(start, end);
-
-    // make sure only bits between start and end are set
-    if (!tohide.isEmpty())
-    {
-      tohide.clear(0, start);
-      tohide.clear(Math.min(end + 1, tohide.length() + 1),
-              tohide.length() + 1);
-    }
-
-    hideColumns(tohide);
+    hideColumns(tohide, start, end);
   }
 
   /**
@@ -991,7 +1008,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      return new HiddenColsIterator(hiddenColumns);
+      return new RangeIterator(hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
@@ -1012,7 +1029,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      return new HiddenColsIterator(start, end, hiddenColumns);
+      return new RangeIterator(start, end, hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
@@ -1028,7 +1045,7 @@ 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
     {
@@ -1045,7 +1062,7 @@ public class HiddenColumns
       HiddenCursorPosition pos = cursor
               .findRegionForColumn(absoluteStart - 1, false);
 
-      return new BoundedStartRegionIterator(pos, start, end,
+      return new StartRegionIterator(pos, start, end,
               hiddenColumns);
     } finally
     {
@@ -1067,7 +1084,8 @@ 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();