X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=c77fb7b5e6fa56c1bd6eb118063d40dce3cecc40;hb=14aeb3c39e60a604bdeed33949ba05e0c8c8be5d;hp=9722c0a1b12a7bab5685a5e488583f97af91cf74;hpb=5e8ec77d921ff2d604811e5e4ba7e9211b0f48de;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 9722c0a..c77fb7b 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1,38 +1,168 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import jalview.util.Comparison;
-import jalview.util.ShiftList;
 
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
+import java.util.NoSuchElementException;
 import java.util.Vector;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 
-public class HiddenColumns implements Iterable<int[]>
+public class HiddenColumns
 {
-  private static final ReentrantReadWriteLock lock = new ReentrantReadWriteLock();
-  
+  private static final int HASH_MULTIPLIER = 31;
+
+  private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+
   /*
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
    */
-  private Vector<int[]> hiddenColumns;
+  private ArrayList<int[]> hiddenColumns;
+
+  /**
+   * Constructor
+   */
+  public HiddenColumns()
+  {
+  }
+
+  /**
+   * Copy constructor
+   * 
+   * @param copy
+   */
+  public HiddenColumns(HiddenColumns copy)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      if (copy != null)
+      {
+        if (copy.hiddenColumns != null)
+        {
+          hiddenColumns = copy.copyHiddenRegionsToArrayList(0);
+        }
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * Copy constructor within bounds and with offset. Copies hidden column
+   * regions fully contained between start and end, and offsets positions by
+   * subtracting offset.
+   * 
+   * @param copy
+   *          HiddenColumns instance to copy from
+   * @param start
+   *          lower bound to copy from
+   * @param end
+   *          upper bound to copy to
+   * @param offset
+   *          offset to subtract from each region boundary position
+   * 
+   */
+  public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      if (copy != null)
+      {
+        hiddenColumns = new ArrayList<>();
+        Iterator<int[]> it = copy.getBoundedIterator(start, end);
+        while (it.hasNext())
+        {
+          int[] region = it.next();
+          // still need to check boundaries because iterator returns
+          // all overlapping regions and we need contained regions
+          if (region[0] >= start && region[1] <= end)
+          {
+            hiddenColumns.add(
+                    new int[]
+            { region[0] - offset, region[1] - offset });
+          }
+        }
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
 
   /**
-   * This Method is used to return all the HiddenColumn regions
+   * This method is used to return all the HiddenColumn regions and is intended
+   * to remain private. External callers which need a copy of the regions can
+   * call getHiddenColumnsCopyAsList.
    * 
    * @return empty list or List of hidden column intervals
    */
-  public List<int[]> getHiddenRegions()
+  private List<int[]> getHiddenRegions()
   {
     return hiddenColumns == null ? Collections.<int[]> emptyList()
             : hiddenColumns;
   }
 
   /**
+   * Output regions data as a string. String is in the format:
+   * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
+   * 
+   * @param delimiter
+   *          string to delimit regions
+   * @param betweenstring
+   *          to put between start and end region values
+   * @return regions formatted according to delimiter and between strings
+   */
+  public String regionsToString(String delimiter, String between)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      StringBuilder regionBuilder = new StringBuilder();
+      if (hiddenColumns != null)
+      {
+        for (int[] range : hiddenColumns)
+        {
+          regionBuilder.append(delimiter).append(range[0]).append(between)
+                  .append(range[1]);
+        }
+
+        regionBuilder.deleteCharAt(0);
+      }
+      return regionBuilder.toString();
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
    * Find the number of hidden columns
    * 
    * @return number of hidden columns
@@ -41,9 +171,9 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int size = 0;
-      if (hasHidden())
+      if (hasHiddenColumns())
       {
         for (int[] range : hiddenColumns)
         {
@@ -51,29 +181,32 @@ public class HiddenColumns implements Iterable<int[]>
         }
       }
       return size;
-    }
-    finally
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * Answers if there are any hidden columns
+   * Get the number of distinct hidden regions
    * 
-   * @return true if there are hidden columns
+   * @return number of regions
    */
-  public boolean hasHidden()
+  public int getNumberOfRegions()
   {
     try
     {
-      lock.readLock().lock();
-      return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
+      LOCK.readLock().lock();
+      int num = 0;
+      if (hasHiddenColumns())
+      {
+        num = hiddenColumns.size();
+      }
+      return num;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
-
   }
 
   @Override
@@ -81,7 +214,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
       if (!(obj instanceof HiddenColumns))
       {
@@ -113,7 +246,7 @@ public class HiddenColumns implements Iterable<int[]>
       return true;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -128,13 +261,13 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int result = column;
       if (hiddenColumns != null)
       {
         for (int i = 0; i < hiddenColumns.size(); i++)
         {
-          int[] region = hiddenColumns.elementAt(i);
+          int[] region = hiddenColumns.get(i);
           if (result >= region[0])
           {
             result += region[1] - region[0] + 1;
@@ -144,7 +277,7 @@ public class HiddenColumns implements Iterable<int[]>
       return result;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -161,7 +294,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int result = hiddenColumn;
       if (hiddenColumns != null)
       {
@@ -169,7 +302,7 @@ public class HiddenColumns implements Iterable<int[]>
         int[] region;
         do
         {
-          region = hiddenColumns.elementAt(index++);
+          region = hiddenColumns.get(index++);
           if (hiddenColumn > region[1])
           {
             result -= region[1] + 1 - region[0];
@@ -203,7 +336,7 @@ public class HiddenColumns implements Iterable<int[]>
                      // columns.
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -223,93 +356,108 @@ public class HiddenColumns implements Iterable<int[]>
     try
     {
 
-      lock.readLock().lock();
-    int distance = visibleDistance;
+      LOCK.readLock().lock();
+      int distance = visibleDistance;
 
-    // in case startColumn is in a hidden region, move it to the left
-    int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+      // in case startColumn is in a hidden region, move it to the left
+      int start = adjustForHiddenColumns(findColumnPosition(startColumn));
 
-    // get index of hidden region to left of start
-    int index = getHiddenIndexLeft(start);
-    if (index == -1)
-    {
-      // no hidden regions to left of startColumn
-      return start - distance;
-    }
+      // get index of hidden region to left of start
+      int index = getHiddenIndexLeft(start);
+      if (index == -1)
+      {
+        // no hidden regions to left of startColumn
+        return start - distance;
+      }
 
-    // walk backwards through the alignment subtracting the counts of visible
-    // columns from distance
-    int[] region;
-    int gap = 0;
-    int nextstart = start;
+      // walk backwards through the alignment subtracting the counts of visible
+      // columns from distance
+      int[] region;
+      int gap = 0;
+      int nextstart = start;
 
-    while ((index > -1) && (distance - gap > 0))
-    {
-      // subtract the gap to right of region from distance
-      distance -= gap;
-      start = nextstart;
+      while ((index > -1) && (distance - gap > 0))
+      {
+        // subtract the gap to right of region from distance
+        distance -= gap;
+        start = nextstart;
 
-      // calculate the next gap
-      region = hiddenColumns.get(index);
-      gap = start - region[1];
+        // calculate the next gap
+        region = hiddenColumns.get(index);
+        gap = start - region[1];
 
-      // set start to just to left of current region
-      nextstart = region[0] - 1;
-      index--;
-    }
+        // set start to just to left of current region
+        nextstart = region[0] - 1;
+        index--;
+      }
 
-    if (distance - gap > 0)
-    {
-      // fell out of loop because there are no more hidden regions
-      distance -= gap;
-      return nextstart - distance;
-    }
-    return start - distance;
+      if (distance - gap > 0)
+      {
+        // fell out of loop because there are no more hidden regions
+        distance -= gap;
+        return nextstart - distance;
+      }
+      return start - distance;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
 
   }
 
   /**
-   * Use this method to determine where the next hiddenRegion starts
+   * Use this method to determine the set of hiddenRegion start positions
+   * between absolute position <start> and absolute position <end>
    * 
-   * @param hiddenRegion
-   *          index of hidden region (counts from 0)
-   * @return column number in visible view
+   * @param start
+   *          absolute residue to start from
+   * @param end
+   *          absolute residue to end at
+   * 
+   * @return list of column numbers in *visible* view where hidden regions start
    */
-  public int findHiddenRegionPosition(int hiddenRegion)
+  public List<Integer> findHiddenRegionPositions(int start, int end)
   {
     try
     {
-      lock.readLock().lock();
-      int result = 0;
+      LOCK.readLock().lock();
+      List<Integer> positions = null;
+
       if (hiddenColumns != null)
       {
-        int index = 0;
-        int gaps = 0;
-        do
-        {
-          int[] region = hiddenColumns.elementAt(index);
-          if (hiddenRegion == 0)
-          {
-            return region[0];
-          }
+        positions = new ArrayList<>(hiddenColumns.size());
 
-          gaps += region[1] + 1 - region[0];
-          result = region[1] + 1;
-          index++;
-        } while (index <= hiddenRegion);
+        // navigate to start, keeping count of hidden columns
+        int i = 0;
+        int hiddenSoFar = 0;
+        while ((i < hiddenColumns.size())
+                && (hiddenColumns.get(i)[0] < start))
+        {
+          int[] region = hiddenColumns.get(i);
+          hiddenSoFar += region[1] - region[0] + 1;
+          i++;
+        }
 
-        result -= gaps;
+        // iterate from start to end, adding start positions of each
+        // hidden region. Positions are visible columns count, not absolute
+        while (i < hiddenColumns.size()
+                && (hiddenColumns.get(i)[0] < end))
+        {
+          int[] region = hiddenColumns.get(i);
+          positions.add(region[0] - hiddenSoFar);
+          hiddenSoFar += region[1] - region[0] + 1;
+          i++;
+        }
+      }
+      else
+      {
+        positions = new ArrayList<>();
       }
 
-      return result;
-    }
-    finally
+      return positions;
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -324,13 +472,13 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (hiddenColumns != null)
       {
         int index = 0;
         do
         {
-          int[] region = hiddenColumns.elementAt(index);
+          int[] region = hiddenColumns.get(index);
           if (alPos < region[0])
           {
             return region[0];
@@ -343,7 +491,7 @@ public class HiddenColumns implements Iterable<int[]>
       return alPos;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
 
   }
@@ -359,27 +507,27 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
-    if (hiddenColumns != null)
-    {
-      int index = hiddenColumns.size() - 1;
-      do
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (alPos > region[1])
+        int index = hiddenColumns.size() - 1;
+        do
         {
-          return region[1];
-        }
+          int[] region = hiddenColumns.get(index);
+          if (alPos > region[1])
+          {
+            return region[1];
+          }
 
-        index--;
-      } while (index > -1);
-    }
+          index--;
+        } while (index > -1);
+      }
 
-    return alPos;
+      return alPos;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -396,26 +544,26 @@ public class HiddenColumns implements Iterable<int[]>
     try
     {
 
-      lock.readLock().lock();
-    if (hiddenColumns != null)
-    {
-      int index = hiddenColumns.size() - 1;
-      do
+      LOCK.readLock().lock();
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (pos > region[1])
+        int index = hiddenColumns.size() - 1;
+        do
         {
-          return index;
-        }
+          int[] region = hiddenColumns.get(index);
+          if (pos > region[1])
+          {
+            return index;
+          }
 
-        index--;
-      } while (index > -1);
-    }
+          index--;
+        } while (index > -1);
+      }
 
-    return -1;
+      return -1;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
 
   }
@@ -428,96 +576,91 @@ public class HiddenColumns implements Iterable<int[]>
    */
   public void hideColumns(int start, int end)
   {
-    hideColumns(start, end, false);
-  }
-
-  /**
-   * Adds the specified column range to the hidden columns
-   * 
-   * @param start
-   * @param end
-   */
-  private void hideColumns(int start, int end, boolean alreadyLocked)
-  {
+    boolean wasAlreadyLocked = false;
     try
     {
-
-      if (!alreadyLocked)
+      // check if the write lock was already locked by this thread,
+      // as this method can be called internally in loops within HiddenColumns
+      if (!LOCK.isWriteLockedByCurrentThread())
       {
-        lock.writeLock().lock();
+        LOCK.writeLock().lock();
       }
-
-    if (hiddenColumns == null)
-    {
-      hiddenColumns = new Vector<>();
-    }
-
-    /*
-     * traverse existing hidden ranges and insert / amend / append as
-     * appropriate
-     */
-    for (int i = 0; i < hiddenColumns.size(); i++)
-    {
-      int[] region = hiddenColumns.elementAt(i);
-
-      if (end < region[0] - 1)
+      else
       {
-        /*
-         * insert discontiguous preceding range
-         */
-        hiddenColumns.insertElementAt(new int[] { start, end }, i);
-        return;
+        wasAlreadyLocked = true;
       }
 
-      if (end <= region[1])
+      if (hiddenColumns == null)
       {
-        /*
-         * new range overlaps existing, or is contiguous preceding it - adjust
-         * start column
-         */
-        region[0] = Math.min(region[0], start);
-        return;
+        hiddenColumns = new ArrayList<>();
       }
 
-      if (start <= region[1] + 1)
+      /*
+       * traverse existing hidden ranges and insert / amend / append as
+       * appropriate
+       */
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        /*
-         * new range overlaps existing, or is contiguous following it - adjust
-         * start and end columns
-         */
-        region[0] = Math.min(region[0], start);
-        region[1] = Math.max(region[1], end);
+        int[] region = hiddenColumns.get(i);
+
+        if (end < region[0] - 1)
+        {
+          /*
+           * insert discontiguous preceding range
+           */
+          hiddenColumns.add(i, new int[] { start, end });
+          return;
+        }
 
-        /*
-         * also update or remove any subsequent ranges 
-         * that are overlapped
-         */
-        while (i < hiddenColumns.size() - 1)
+        if (end <= region[1])
         {
-          int[] nextRegion = hiddenColumns.get(i + 1);
-          if (nextRegion[0] > end + 1)
+          /*
+           * new range overlaps existing, or is contiguous preceding it - adjust
+           * start column
+           */
+          region[0] = Math.min(region[0], start);
+          return;
+        }
+
+        if (start <= region[1] + 1)
+        {
+          /*
+           * new range overlaps existing, or is contiguous following it - adjust
+           * start and end columns
+           */
+          region[0] = Math.min(region[0], start);
+          region[1] = Math.max(region[1], end);
+
+          /*
+           * also update or remove any subsequent ranges 
+           * that are overlapped
+           */
+          while (i < hiddenColumns.size() - 1)
           {
-            /*
-             * gap to next hidden range - no more to update
-             */
-            break;
+            int[] nextRegion = hiddenColumns.get(i + 1);
+            if (nextRegion[0] > end + 1)
+            {
+              /*
+               * gap to next hidden range - no more to update
+               */
+              break;
+            }
+            region[1] = Math.max(nextRegion[1], end);
+            hiddenColumns.remove(i + 1);
           }
-          region[1] = Math.max(nextRegion[1], end);
-          hiddenColumns.remove(i + 1);
+          return;
         }
-        return;
       }
-    }
 
-    /*
-     * remaining case is that the new range follows everything else
-     */
-    hiddenColumns.addElement(new int[] { start, end });
+      /*
+       * remaining case is that the new range follows everything else
+       */
+      hiddenColumns.add(new int[] { start, end });
     } finally
     {
-      if (!alreadyLocked)
+      if (!wasAlreadyLocked)
       {
-        lock.writeLock().unlock();
+        LOCK.writeLock().unlock();
       }
     }
   }
@@ -526,82 +669,40 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
-    if (hiddenColumns != null)
-    {
-      for (int[] region : hiddenColumns)
+      if (hiddenColumns != null)
       {
-        if (column >= region[0] && column <= region[1])
+        for (int[] region : hiddenColumns)
         {
-          return false;
+          if (column >= region[0] && column <= region[1])
+          {
+            return false;
+          }
         }
       }
-    }
 
-    return true;
+      return true;
     } finally
     {
-      lock.readLock().unlock();
-    }
-  }
-
-  /**
-   * ColumnSelection
-   */
-  public HiddenColumns()
-  {
-  }
-
-  /**
-   * Copy constructor
-   * 
-   * @param copy
-   */
-  public HiddenColumns(HiddenColumns copy)
-  {
-    try
-    {
-
-      lock.readLock().lock();
-      if (copy != null)
-      {
-        if (copy.hiddenColumns != null)
-        {
-          hiddenColumns = copy.copyHiddenRegions();
-        }
-      }
-    }
-    finally
-    {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
-  private Vector<int[]> copyHiddenRegions()
+  private ArrayList<int[]> copyHiddenRegionsToArrayList(int startIndex)
   {
-    Vector<int[]> copy = new Vector<>(hiddenColumns.size());
-    for (int i = 0, j = hiddenColumns.size(); i < j; i++)
+    int size = 0;
+    if (hiddenColumns != null)
     {
-      int[] rh, cp;
-      rh = hiddenColumns.elementAt(i);
-      if (rh != null)
-      {
-        cp = new int[rh.length];
-        System.arraycopy(rh, 0, cp, 0, rh.length);
-        copy.addElement(cp);
-      }
+      size = hiddenColumns.size();
     }
-    return copy;
-  }
+    ArrayList<int[]> copy = new ArrayList<>(size);
 
-  private ArrayList<int[]> copyHiddenRegionsToArrayList()
-  {
-    ArrayList<int[]> copy = new ArrayList<>(hiddenColumns.size());
-    for (int i = 0, j = hiddenColumns.size(); i < j; i++)
+    for (int i = startIndex, j = size; i < j; i++)
     {
-      int[] rh, cp;
-      rh = hiddenColumns.elementAt(i);
+      int[] rh;
+      int[] cp;
+      rh = hiddenColumns.get(i);
       if (rh != null)
       {
         cp = new int[rh.length];
@@ -609,202 +710,71 @@ public class HiddenColumns implements Iterable<int[]>
         copy.add(cp);
       }
     }
-    return copy;
-  }
-
-  public void getHiddenColumnsCopy(Vector<int[]> copy)
-  {
-    try
-    {
-      lock.readLock().lock();
-      copy = copyHiddenRegions();
-    } finally
-    {
-      lock.readLock().unlock();
-    }
-  }
 
-  public void getHiddenColumnsCopy(ArrayList<int[]> copy)
-  {
-    try
-    {
-      lock.readLock().lock();
-      copy = copyHiddenRegionsToArrayList();
-    } finally
-    {
-      lock.readLock().unlock();
-    }
+    return copy;
   }
 
   /**
-   * propagate shift in alignment columns to column selection
+   * return all visible segments between the given start and end boundaries
    * 
    * @param start
-   *          beginning of edit
-   * @param left
-   *          shift in edit (+ve for removal, or -ve for inserts)
+   *          (first column inclusive from 0)
+   * @param end
+   *          (last column - not inclusive)
+   * @return List<int[]> {[i_start, i_end], ..} where intervals lie in
+   *         start<=i_start<=i_end<end
    */
-  public List<int[]> compensateForEdit(int start, int change,
-          ColumnSelection sel)
+  public List<int[]> getVisibleContigs(int start, int end)
   {
     try
     {
-      lock.writeLock().lock();
-      List<int[]> deletedHiddenColumns = null;
-
-      if (hiddenColumns != null)
+      LOCK.readLock().lock();
+      List<int[]> vcontigs = new ArrayList<>();
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
-        deletedHiddenColumns = new ArrayList<>();
-        int hSize = hiddenColumns.size();
-        for (int i = 0; i < hSize; i++)
+        int vstart = start;
+        int hideStart;
+        int hideEnd;
+
+        for (int[] region : hiddenColumns)
         {
-          int[] region = hiddenColumns.elementAt(i);
-          if (region[0] > start && start + change > region[1])
-          {
-            deletedHiddenColumns.add(region);
+          hideStart = region[0];
+          hideEnd = region[1];
 
-            hiddenColumns.removeElementAt(i);
-            i--;
-            hSize--;
+          // navigate to start
+          if (hideEnd < vstart)
+          {
             continue;
           }
-
-          if (region[0] > start)
+          if (hideStart > vstart)
           {
-            region[0] -= change;
-            region[1] -= change;
+            int[] contig = new int[] { vstart, hideStart - 1 };
+            vcontigs.add(contig);
           }
+          vstart = hideEnd + 1;
 
-          if (region[0] < 0)
+          // exit if we're past the end
+          if (vstart >= end)
           {
-            region[0] = 0;
+            break;
           }
-
-        }
-
-        this.revealHiddenColumns(0, sel);
-      }
-
-      return deletedHiddenColumns;
-    } finally
-    {
-      lock.writeLock().unlock();
-    }
-  }
-
-  /**
-   * propagate shift in alignment columns to column selection special version of
-   * compensateForEdit - allowing for edits within hidden regions
-   * 
-   * @param start
-   *          beginning of edit
-   * @param left
-   *          shift in edit (+ve for removal, or -ve for inserts)
-   */
-  public void compensateForDelEdits(int start, int change)
-  {
-    try
-    {
-      lock.writeLock().lock();
-      if (hiddenColumns != null)
-      {
-        for (int i = 0; i < hiddenColumns.size(); i++)
-        {
-          int[] region = hiddenColumns.elementAt(i);
-          if (region[0] >= start)
-          {
-            region[0] -= change;
-          }
-          if (region[1] >= start)
-          {
-            region[1] -= change;
-          }
-          if (region[1] < region[0])
-          {
-            hiddenColumns.removeElementAt(i--);
-          }
-
-          if (region[0] < 0)
-          {
-            region[0] = 0;
-          }
-          if (region[1] < 0)
-          {
-            region[1] = 0;
-          }
-        }
-      }
-    }
-    finally
-    {
-      lock.writeLock().unlock();
-    }
-  }
-
-  /**
-   * return all visible segments between the given start and end boundaries
-   * 
-   * @param start
-   *          (first column inclusive from 0)
-   * @param end
-   *          (last column - not inclusive)
-   * @return int[] {i_start, i_end, ..} where intervals lie in
-   *         start<=i_start<=i_end<end
-   */
-  public int[] getVisibleContigs(int start, int end)
-  {
-    try
-    {
-      lock.readLock().lock();
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
-      {
-        List<int[]> visiblecontigs = new ArrayList<>();
-        List<int[]> regions = getHiddenRegions();
-
-        int vstart = start;
-        int[] region;
-        int hideStart, hideEnd;
-
-        for (int j = 0; vstart < end && j < regions.size(); j++)
-        {
-          region = regions.get(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-
-          if (hideEnd < vstart)
-          {
-            continue;
-          }
-          if (hideStart > vstart)
-          {
-            visiblecontigs.add(new int[] { vstart, hideStart - 1 });
-          }
-          vstart = hideEnd + 1;
         }
 
         if (vstart < end)
         {
-          visiblecontigs.add(new int[] { vstart, end - 1 });
+          int[] contig = new int[] { vstart, end - 1 };
+          vcontigs.add(contig);
         }
-        int[] vcontigs = new int[visiblecontigs.size() * 2];
-        for (int i = 0, j = visiblecontigs.size(); i < j; i++)
-        {
-          int[] vc = visiblecontigs.get(i);
-          visiblecontigs.set(i, null);
-          vcontigs[i * 2] = vc[0];
-          vcontigs[i * 2 + 1] = vc[1];
-        }
-        visiblecontigs.clear();
-        return vcontigs;
       }
       else
       {
-        return new int[] { start, end - 1 };
+        int[] contig = new int[] { start, end - 1 };
+        vcontigs.add(contig);
       }
-    }
-    finally
+      return vcontigs;
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -813,23 +783,22 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
-      int i, iSize = seqs.length;
-      String selections[] = new String[iSize];
+      LOCK.readLock().lock();
+      int iSize = seqs.length;
+      String[] selections = new String[iSize];
       if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
-        for (i = 0; i < iSize; i++)
+        for (int i = 0; i < iSize; i++)
         {
           StringBuffer visibleSeq = new StringBuffer();
-          List<int[]> regions = getHiddenRegions();
 
-          int blockStart = start, blockEnd = end;
-          int[] region;
-          int hideStart, hideEnd;
+          int blockStart = start;
+          int blockEnd = end;
+          int hideStart;
+          int hideEnd;
 
-          for (int j = 0; j < regions.size(); j++)
+          for (int[] region : hiddenColumns)
           {
-            region = regions.get(j);
             hideStart = region[0];
             hideEnd = region[1];
 
@@ -862,17 +831,16 @@ public class HiddenColumns implements Iterable<int[]>
       }
       else
       {
-        for (i = 0; i < iSize; i++)
+        for (int i = 0; i < iSize; i++)
         {
           selections[i] = seqs[i].getSequenceAsString(start, end);
         }
       }
 
       return selections;
-    }
-    finally
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -890,23 +858,29 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
-      int fpos = seq.getStart(), lpos = seq.getEnd();
+      LOCK.readLock().lock();
+      int fpos = seq.getStart();
+      int lpos = seq.getEnd();
       int start = 0;
 
       if (hiddenColumns == null || hiddenColumns.size() == 0)
       {
-        int ifpos = seq.findIndex(fpos) - 1,
-                ilpos = seq.findIndex(lpos) - 1;
-        return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
+        int ifpos = seq.findIndex(fpos) - 1;
+        int ilpos = seq.findIndex(lpos) - 1;
+        return new int[] { ifpos, ifpos, ilpos };
       }
 
       // Simply walk along the sequence whilst watching for hidden column
       // boundaries
       List<int[]> regions = getHiddenRegions();
-      int spos = fpos, lastvispos = -1, rcount = 0,
-              hideStart = seq.getLength(), hideEnd = -1;
-      int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
+      int spos = fpos;
+      int rcount = 0;
+      int hideStart = seq.getLength();
+      int hideEnd = -1;
+      int visPrev = 0;
+      int visNext = 0;
+      int firstP = -1;
+      int lastP = -1;
       boolean foundStart = false;
       for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
               && p < pLen; p++)
@@ -942,7 +916,6 @@ public class HiddenColumns implements Iterable<int[]>
               start = p;
               foundStart = true;
             }
-            lastvispos = p;
             lpos = spos;
           }
           // look for next sequence position
@@ -951,15 +924,13 @@ public class HiddenColumns implements Iterable<int[]>
       }
       if (foundStart)
       {
-        return new int[] { findColumnPosition(start),
-            findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+        return new int[] { findColumnPosition(start), firstP, lastP };
       }
       // otherwise, sequence was completely hidden
-      return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
-    }
-    finally
+      return new int[] { visPrev, firstP, lastP };
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -990,7 +961,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (alignmentAnnotation.annotations == null)
       {
         return;
@@ -1005,14 +976,14 @@ public class HiddenColumns implements Iterable<int[]>
         // then mangle the alignmentAnnotation annotation array
         Vector<Annotation[]> annels = new Vector<>();
         Annotation[] els = null;
-        List<int[]> regions = getHiddenRegions();
-        int blockStart = start, blockEnd = end;
-        int[] region;
-        int hideStart, hideEnd, w = 0;
+        int blockStart = start;
+        int blockEnd = end;
+        int hideStart;
+        int hideEnd;
+        int w = 0;
 
-        for (int j = 0; j < regions.size(); j++)
+        for (int[] region : hiddenColumns)
         {
-          region = regions.get(j);
           hideStart = region[0];
           hideEnd = region[1];
 
@@ -1029,7 +1000,8 @@ public class HiddenColumns implements Iterable<int[]>
             break;
           }
 
-          annels.addElement(els = new Annotation[blockEnd - blockStart]);
+          els = new Annotation[blockEnd - blockStart];
+          annels.addElement(els);
           System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
                   0, els.length);
           w += els.length;
@@ -1039,7 +1011,8 @@ public class HiddenColumns implements Iterable<int[]>
 
         if (end > blockStart)
         {
-          annels.addElement(els = new Annotation[end - blockStart + 1]);
+          els = new Annotation[end - blockStart + 1];
+          annels.addElement(els);
           if ((els.length
                   + blockStart) <= alignmentAnnotation.annotations.length)
           {
@@ -1075,10 +1048,9 @@ public class HiddenColumns implements Iterable<int[]>
       {
         alignmentAnnotation.restrict(start, end);
       }
-    }
-    finally
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1090,11 +1062,11 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       return hiddenColumns != null && hiddenColumns.size() > 0;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1106,11 +1078,11 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       return hiddenColumns != null && hiddenColumns.size() > 1;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1124,15 +1096,15 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       List<int[]> inserts = sr.getInsertions();
       for (int[] r : inserts)
       {
-        hideColumns(r[0], r[1], true);
+        hideColumns(r[0], r[1]);
       }
     } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1143,12 +1115,12 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       if (hiddenColumns != null)
       {
         for (int i = 0; i < hiddenColumns.size(); i++)
         {
-          int[] region = hiddenColumns.elementAt(i);
+          int[] region = hiddenColumns.get(i);
           for (int j = region[0]; j < region[1] + 1; j++)
           {
             sel.addElement(j);
@@ -1157,10 +1129,9 @@ public class HiddenColumns implements Iterable<int[]>
       }
 
       hiddenColumns = null;
-    }
-    finally
+    } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1174,10 +1145,10 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.get(i);
         if (start == region[0])
         {
           for (int j = region[0]; j < region[1] + 1; j++)
@@ -1185,7 +1156,7 @@ public class HiddenColumns implements Iterable<int[]>
             sel.addElement(j);
           }
 
-          hiddenColumns.removeElement(region);
+          hiddenColumns.remove(region);
           break;
         }
       }
@@ -1193,132 +1164,9 @@ public class HiddenColumns implements Iterable<int[]>
       {
         hiddenColumns = null;
       }
-    }
-    finally
-    {
-      lock.writeLock().unlock();
-    }
-  }
-
-  /**
-   * removes intersection of position,length ranges in deletions from the
-   * start,end regions marked in intervals.
-   * 
-   * @param shifts
-   * @param intervals
-   * @return
-   */
-  private boolean pruneIntervalVector(final List<int[]> shifts,
-          Vector<int[]> intervals)
-  {
-    boolean pruned = false;
-    int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
-    int hr[] = intervals.elementAt(i);
-    int sr[] = shifts.get(s);
-    while (i <= j && s <= t)
-    {
-      boolean trailinghn = hr[1] >= sr[0];
-      if (!trailinghn)
-      {
-        if (i < j)
-        {
-          hr = intervals.elementAt(++i);
-        }
-        else
-        {
-          i++;
-        }
-        continue;
-      }
-      int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
-      if (endshift < hr[0] || endshift < sr[0])
-      { // leadinghc disjoint or not a deletion
-        if (s < t)
-        {
-          sr = shifts.get(++s);
-        }
-        else
-        {
-          s++;
-        }
-        continue;
-      }
-      boolean leadinghn = hr[0] >= sr[0];
-      boolean leadinghc = hr[0] < endshift;
-      boolean trailinghc = hr[1] < endshift;
-      if (leadinghn)
-      {
-        if (trailinghc)
-        { // deleted hidden region.
-          intervals.removeElementAt(i);
-          pruned = true;
-          j--;
-          if (i <= j)
-          {
-            hr = intervals.elementAt(i);
-          }
-          continue;
-        }
-        if (leadinghc)
-        {
-          hr[0] = endshift; // clip c terminal region
-          leadinghn = !leadinghn;
-          pruned = true;
-        }
-      }
-      if (!leadinghn)
-      {
-        if (trailinghc)
-        {
-          if (trailinghn)
-          {
-            hr[1] = sr[0] - 1;
-            pruned = true;
-          }
-        }
-        else
-        {
-          // sr contained in hr
-          if (s < t)
-          {
-            sr = shifts.get(++s);
-          }
-          else
-          {
-            s++;
-          }
-          continue;
-        }
-      }
-    }
-    return pruned; // true if any interval was removed or modified by
-    // operations.
-  }
-
-  /**
-   * remove any hiddenColumns or selected columns and shift remaining based on a
-   * series of position, range deletions.
-   * 
-   * @param deletions
-   */
-  public void pruneDeletions(List<int[]> shifts)
-  {
-    try
-    {
-      lock.writeLock().lock();
-      // delete any intervals intersecting.
-      if (hiddenColumns != null)
-      {
-        pruneIntervalVector(shifts, hiddenColumns);
-        if (hiddenColumns != null && hiddenColumns.size() == 0)
-        {
-          hiddenColumns = null;
-        }
-      }
-    }
-    finally
+    } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1362,154 +1210,114 @@ public class HiddenColumns implements Iterable<int[]>
           SequenceI origseq)
   {
     char gc = al.getGapCharacter();
-    // recover mapping between sequence's non-gap positions and positions
-    // mapping to view.
-    pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
-    int[] viscontigs = al.getHiddenColumns().getVisibleContigs(0,
-            profileseq.getLength());
-    int spos = 0;
-    int offset = 0;
 
-    // add profile to visible contigs
-    for (int v = 0; v < viscontigs.length; v += 2)
-    {
-      if (viscontigs[v] > spos)
+    // take the set of hidden columns, and the set of gaps in origseq,
+    // and remove all the hidden gaps from hiddenColumns
+
+    // first get the gaps as a Bitset
+    BitSet gaps = origseq.gapBitset();
+
+    // now calculate hidden ^ not(gap)
+    BitSet hidden = new BitSet();
+    markHiddenRegions(hidden);
+    hidden.andNot(gaps);
+    hiddenColumns = null;
+    this.hideMarkedBits(hidden);
+
+    // for each sequence in the alignment, except the profile sequence,
+    // insert gaps corresponding to each hidden region
+    // but where each hidden column region is shifted backwards by the number of
+    // preceding visible gaps
+    // update hidden columns at the same time
+    Iterator<int[]> regions = iterator();
+    ArrayList<int[]> newhidden = new ArrayList<>();
+
+    int numGapsBefore = 0;
+    int gapPosition = 0;
+    while (regions.hasNext())
+    {
+      // get region coordinates accounting for gaps
+      // we can rely on gaps not being *in* hidden regions because we already
+      // removed those
+      int[] region = regions.next();
+      while (gapPosition < region[0])
       {
-        StringBuffer sb = new StringBuffer();
-        for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+        gapPosition++;
+        if (gaps.get(gapPosition))
         {
-          sb.append(gc);
+          numGapsBefore++;
         }
-        for (int s = 0, ns = al.getHeight(); s < ns; s++)
-        {
-          SequenceI sqobj = al.getSequenceAt(s);
-          if (sqobj != profileseq)
-          {
-            String sq = al.getSequenceAt(s).getSequenceAsString();
-            if (sq.length() <= spos + offset)
-            {
-              // pad sequence
-              int diff = spos + offset - sq.length() - 1;
-              if (diff > 0)
-              {
-                // pad gaps
-                sq = sq + sb;
-                while ((diff = spos + offset - sq.length() - 1) > 0)
-                {
-                  // sq = sq
-                  // + ((diff >= sb.length()) ? sb.toString() : sb
-                  // .substring(0, diff));
-                  if (diff >= sb.length())
-                  {
-                    sq += sb.toString();
-                  }
-                  else
-                  {
-                    char[] buf = new char[diff];
-                    sb.getChars(0, diff, buf, 0);
-                    sq += buf.toString();
-                  }
-                }
-              }
-              sq += sb.toString();
-            }
-            else
-            {
-              al.getSequenceAt(s).setSequence(
-                      sq.substring(0, spos + offset) + sb.toString()
-                              + sq.substring(spos + offset));
-            }
-          }
-        }
-        // offset+=sb.length();
       }
-      spos = viscontigs[v + 1] + 1;
-    }
-    if ((offset + spos) < profileseq.getLength())
-    {
-      // pad the final region with gaps.
+
+      int left = region[0] - numGapsBefore;
+      int right = region[1] - numGapsBefore;
+      newhidden.add(new int[] { left, right });
+
+      // make a string with number of gaps = length of hidden region
       StringBuffer sb = new StringBuffer();
-      for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+      for (int s = 0; s < right - left + 1; s++)
       {
         sb.append(gc);
       }
-      for (int s = 0, ns = al.getHeight(); s < ns; s++)
-      {
-        SequenceI sqobj = al.getSequenceAt(s);
-        if (sqobj == profileseq)
-        {
-          continue;
-        }
-        String sq = sqobj.getSequenceAsString();
-        // pad sequence
-        int diff = origseq.getLength() - sq.length();
-        while (diff > 0)
-        {
-          // sq = sq
-          // + ((diff >= sb.length()) ? sb.toString() : sb
-          // .substring(0, diff));
-          if (diff >= sb.length())
-          {
-            sq += sb.toString();
-          }
-          else
-          {
-            char[] buf = new char[diff];
-            sb.getChars(0, diff, buf, 0);
-            sq += buf.toString();
-          }
-          diff = origseq.getLength() - sq.length();
-        }
-      }
-    }
-  }
+      padGaps(sb, left, profileseq, al);
 
-  /**
-   * remove any hiddenColumns or selected columns and shift remaining based on a
-   * series of position, range deletions.
-   * 
-   * @param deletions
-   */
-  private void pruneDeletions(ShiftList deletions)
-  {
-    if (deletions != null)
-    {
-      final List<int[]> shifts = deletions.getShifts();
-      if (shifts != null && shifts.size() > 0)
-      {
-        pruneDeletions(shifts);
-
-        // and shift the rest.
-        this.compensateForEdits(deletions);
-      }
     }
+    hiddenColumns = newhidden;
   }
 
   /**
-   * Adjust hidden column boundaries based on a series of column additions or
-   * deletions in visible regions.
+   * Pad gaps in all sequences in alignment except profileseq
    * 
-   * @param shiftrecord
-   * @return
+   * @param sb
+   *          gap string to insert
+   * @param left
+   *          position to insert at
+   * @param profileseq
+   *          sequence not to pad
+   * @param al
+   *          alignment to pad sequences in
    */
-  private ShiftList compensateForEdits(ShiftList shiftrecord)
+  private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+          AlignmentI al)
   {
-    if (shiftrecord != null)
+    // loop over the sequences and pad with gaps where required
+    for (int s = 0, ns = al.getHeight(); s < ns; s++)
     {
-      final List<int[]> shifts = shiftrecord.getShifts();
-      if (shifts != null && shifts.size() > 0)
+      SequenceI sqobj = al.getSequenceAt(s);
+      if (sqobj != profileseq)
       {
-        int shifted = 0;
-        for (int i = 0, j = shifts.size(); i < j; i++)
+        String sq = al.getSequenceAt(s).getSequenceAsString();
+        if (sq.length() <= pos)
+        {
+          // pad sequence
+          int diff = pos - sq.length() - 1;
+          if (diff > 0)
+          {
+            // pad gaps
+            sq = sq + sb;
+            while ((diff = pos - sq.length() - 1) > 0)
+            {
+              if (diff >= sb.length())
+              {
+                sq += sb.toString();
+              }
+              else
+              {
+                char[] buf = new char[diff];
+                sb.getChars(0, diff, buf, 0);
+                sq += buf.toString();
+              }
+            }
+          }
+          sq += sb.toString();
+        }
+        else
         {
-          int[] sh = shifts.get(i);
-          compensateForDelEdits(shifted + sh[0], sh[1]);
-          shifted -= sh[1];
+          al.getSequenceAt(s).setSequence(
+                  sq.substring(0, pos) + sb.toString() + sq.substring(pos));
         }
       }
-      return shiftrecord.getInverse();
     }
-    return null;
   }
 
   /**
@@ -1520,21 +1328,20 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int hashCode = 1;
       if (hiddenColumns != null)
       {
         for (int[] hidden : hiddenColumns)
         {
-          hashCode = 31 * hashCode + hidden[0];
-          hashCode = 31 * hashCode + hidden[1];
+          hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+          hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
         }
       }
       return hashCode;
-    }
-    finally
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1548,17 +1355,17 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       for (int firstSet = inserts
               .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
                       .nextSetBit(lastSet))
       {
         lastSet = inserts.nextClearBit(firstSet);
-        hideColumns(firstSet, lastSet - 1, true);
+        hideColumns(firstSet, lastSet - 1);
       }
     } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1571,7 +1378,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (hiddenColumns == null)
       {
         return;
@@ -1580,21 +1387,455 @@ public class HiddenColumns implements Iterable<int[]>
       {
         inserts.set(range[0], range[1] + 1);
       }
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-    finally
+  }
+
+  /**
+   * Calculate the visible start and end index of an alignment.
+   * 
+   * @param width
+   *          full alignment width
+   * @return integer array where: int[0] = startIndex, and int[1] = endIndex
+   */
+  public int[] getVisibleStartAndEndIndex(int width)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int[] alignmentStartEnd = new int[] { 0, width - 1 };
+      int startPos = alignmentStartEnd[0];
+      int endPos = alignmentStartEnd[1];
+
+      int[] lowestRange = new int[] { -1, -1 };
+      int[] higestRange = new int[] { -1, -1 };
+
+      if (hiddenColumns == null)
+      {
+        return new int[] { startPos, endPos };
+      }
+
+      for (int[] hiddenCol : hiddenColumns)
+      {
+        lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+        higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+      }
+
+      if (lowestRange[0] == -1 && lowestRange[1] == -1)
+      {
+        startPos = alignmentStartEnd[0];
+      }
+      else
+      {
+        startPos = lowestRange[1] + 1;
+      }
+
+      if (higestRange[0] == -1 && higestRange[1] == -1)
+      {
+        endPos = alignmentStartEnd[1];
+      }
+      else
+      {
+        endPos = higestRange[0] - 1;
+      }
+      return new int[] { startPos, endPos };
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
+    }
+
+  }
+
+  /**
+   * Finds the hidden region (if any) which starts or ends at res
+   * 
+   * @param res
+   *          visible residue position, unadjusted for hidden columns
+   * @return region as [start,end] or null if no matching region is found
+   */
+  public int[] getRegionWithEdgeAtRes(int res)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int adjres = adjustForHiddenColumns(res);
+
+      int[] reveal = null;
+      if (hiddenColumns != null)
+      {
+        for (int[] region : hiddenColumns)
+        {
+          if (adjres + 1 == region[0] || adjres - 1 == region[1])
+          {
+            reveal = region;
+            break;
+          }
+        }
+      }
+      return reveal;
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
   }
 
-  @Override
   public Iterator<int[]> iterator()
   {
-    if (hiddenColumns == null)
+    if (hiddenColumns != null)
     {
-      return Collections.<int[]> emptyList().iterator();
+      int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
+      return new BoundedHiddenColsIterator(0, last, true);
+    }
+    else
+    {
+      return new BoundedHiddenColsIterator(0, 0, true);
     }
-    return hiddenColumns.iterator();
   }
 
+  public Iterator<int[]> getBoundedIterator(int start, int end)
+  {
+    return new BoundedHiddenColsIterator(start, end, true);
+  }
+
+  public Iterator<Integer> getBoundedStartIterator(int start, int end)
+  {
+    return new BoundedStartRegionIterator(start, end, true);
+  }
+
+  public Iterator<Integer> getVisibleColsIterator(int start, int end)
+  {
+    return new VisibleColsIterator(start, end, true);
+  }
+
+  /**
+   * An iterator which iterates over hidden column regions in a range.
+   * 
+   * @author kmourao
+   *
+   */
+  class BoundedHiddenColsIterator implements Iterator<int[]>
+  {
+    private int start; // start position to iterate from
+
+    private int end; // end position to iterate to
+
+    // current index in hiddenColumns
+    private int currentPosition = 0;
+
+    // current column in hiddenColumns
+    private int[] currentRegion;
+
+    // whether to make a local copy of hiddenColumns
+    private final boolean useCopy;
+
+    // local copy or reference to hiddenColumns
+    private List<int[]> localHidden;
+
+    /**
+     * Construct an iterator over hiddenColums bounded at
+     * [lowerBound,upperBound]
+     * 
+     * @param lowerBound
+     *          lower bound to iterate from
+     * @param upperBound
+     *          upper bound to iterate to
+     * @param useCopyCols
+     *          whether to make a local copy of hiddenColumns for iteration (set
+     *          to true if calling from outwith the HiddenColumns class)
+     */
+    BoundedHiddenColsIterator(int lowerBound, int upperBound,
+            boolean useCopyCols)
+    {
+      start = lowerBound;
+      end = upperBound;
+      useCopy = useCopyCols;
+
+      try
+      {
+        if (useCopy)
+        {
+          // assume that if useCopy is false the calling code has locked
+          // hiddenColumns
+          LOCK.readLock().lock();
+        }
+        
+        if (hiddenColumns != null)
+        {
+          localHidden = new ArrayList<>();
+
+          // iterate until a region overlaps with [start,end]
+          int i = 0;
+          while ((i < hiddenColumns.size())
+                  && (hiddenColumns.get(i)[1] < start))
+          {
+            i++;
+          }
+
+          // iterate from start to end, adding each hidden region. Positions are
+          // absolute, and all regions which *overlap* [start,end] are added.
+          while (i < hiddenColumns.size()
+                  && (hiddenColumns.get(i)[0] <= end))
+          {
+            int[] rh;
+            int[] cp;
+            rh = hiddenColumns.get(i);
+            if (rh != null)
+            {
+              cp = new int[rh.length];
+              System.arraycopy(rh, 0, cp, 0, rh.length);
+              localHidden.add(cp);
+            }
+            i++;
+          }
+        }
+      }
+      finally
+      {
+        if (useCopy)
+        {
+          LOCK.readLock().unlock();
+        }
+      }
+    }
+
+    @Override
+    public boolean hasNext()
+    {
+      return (localHidden != null)
+              && (currentPosition < localHidden.size());
+    }
+
+    @Override
+    public int[] next()
+    {
+      currentRegion = localHidden.get(currentPosition);
+      currentPosition++;
+      return currentRegion;
+    }
+  }
+
+  class BoundedStartRegionIterator implements Iterator<Integer>
+  {
+
+    private int start; // start position to iterate from
+
+    private int end; // end position to iterate to
+
+    // current index in hiddenColumns
+    private int currentPosition = 0;
+
+    // local copy or reference to hiddenColumns
+    private List<Integer> positions = null;
+
+    /**
+     * Construct an iterator over hiddenColums bounded at
+     * [lowerBound,upperBound]
+     * 
+     * @param lowerBound
+     *          lower bound to iterate from
+     * @param upperBound
+     *          upper bound to iterate to
+     * @param useCopyCols
+     *          whether to make a local copy of hiddenColumns for iteration (set
+     *          to true if calling from outwith the HiddenColumns class)
+     */
+    BoundedStartRegionIterator(int lowerBound, int upperBound,
+            boolean useCopy)
+    {
+      start = lowerBound;
+      end = upperBound;
+      
+      try
+      {
+        if (useCopy)
+        {
+          // assume that if useCopy is false the calling code has locked
+          // hiddenColumns
+          LOCK.readLock().lock();
+        }
+
+        if (hiddenColumns != null)
+        {
+          positions = new ArrayList<>(hiddenColumns.size());
+
+          // navigate to start, keeping count of hidden columns
+          int i = 0;
+          int hiddenSoFar = 0;
+          while ((i < hiddenColumns.size())
+                  && (hiddenColumns.get(i)[0] < start + hiddenSoFar))
+          {
+            int[] region = hiddenColumns.get(i);
+            hiddenSoFar += region[1] - region[0] + 1;
+            i++;
+          }
+
+          // iterate from start to end, adding start positions of each
+          // hidden region. Positions are visible columns count, not absolute
+          while (i < hiddenColumns.size()
+                  && (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
+          {
+            int[] region = hiddenColumns.get(i);
+            positions.add(region[0] - hiddenSoFar);
+            hiddenSoFar += region[1] - region[0] + 1;
+            i++;
+          }
+        }
+        else
+        {
+          positions = new ArrayList<>();
+        }
+      } finally
+      {
+        if (useCopy)
+        {
+          LOCK.readLock().unlock();
+        }
+      }
+    }
+
+    @Override
+    public boolean hasNext()
+    {
+      return (currentPosition < positions.size());
+    }
+
+    @Override
+    public Integer next()
+    {
+      int result = positions.get(currentPosition);
+      currentPosition++;
+      return result;
+    }
+  }
+
+  public class VisibleColsIterator implements Iterator<Integer>
+  {
+    private int last;
+
+    private int current;
+
+    private int next;
+
+    private List<int[]> localHidden = new ArrayList<>();
+
+    private int lasthiddenregion;
+
+    public VisibleColsIterator(int firstcol, int lastcol, boolean useCopy)
+    {
+      last = lastcol;
+      current = firstcol;
+      next = firstcol;
+      lasthiddenregion = -1;
+
+      try
+      {
+        if (useCopy)
+        {
+          // assume that if useCopy is false the calling code has locked
+          // hiddenColumns
+          LOCK.readLock().lock();
+        }
+
+        if (hiddenColumns != null)
+        {
+          int i = 0;
+          for (i = 0; i < hiddenColumns.size(); ++i)
+          {
+            if (current >= hiddenColumns.get(i)[0]
+                    && current <= hiddenColumns.get(i)[1])
+            {
+              // current is hidden, move to right
+              current = hiddenColumns.get(i)[1] + 1;
+              next = current;
+            }
+            if (current < hiddenColumns.get(i)[0])
+            {
+              break;
+            }
+          }
+
+          lasthiddenregion = i - 1;
+
+          for (i = hiddenColumns.size() - 1; i >= 0; --i)
+          {
+            if (last >= hiddenColumns.get(i)[0]
+                    && last <= hiddenColumns.get(i)[1])
+            {
+              // last is hidden, move to left
+              last = hiddenColumns.get(i)[0] - 1;
+            }
+            if (last > hiddenColumns.get(i)[1])
+            {
+              break;
+            }
+          }
+
+          // make a local copy of the bit we need
+          i = lasthiddenregion + 1;
+          while (i < hiddenColumns.size()
+                  && hiddenColumns.get(i)[0] <= last)
+          {
+            int[] region = new int[] { hiddenColumns.get(i)[0],
+                hiddenColumns.get(i)[1] };
+            localHidden.add(region);
+            i++;
+          }
+          lasthiddenregion = -1;
+        }
+      } finally
+      {
+        if (useCopy)
+        {
+          LOCK.readLock().unlock();
+        }
+      }
+    }
+
+    @Override
+    public boolean hasNext()
+    {
+      return next <= last;
+    }
+
+    @Override
+    public Integer next()
+    {
+      if (next > last)
+      {
+        throw new NoSuchElementException();
+      }
+      current = next;
+      if ((localHidden != null)
+              && (lasthiddenregion + 1 < localHidden.size()))
+      {
+        // still some more hidden regions
+        if (next + 1 < localHidden.get(lasthiddenregion + 1)[0])
+        {
+          // next+1 is still before the next hidden region
+          next++;
+        }
+        else if ((next + 1 >= localHidden.get(lasthiddenregion + 1)[0])
+                && (next + 1 <= localHidden.get(lasthiddenregion + 1)[1]))
+        {
+          // next + 1 is in the next hidden region
+          next = localHidden.get(lasthiddenregion + 1)[1] + 1;
+          lasthiddenregion++;
+        }
+      }
+      else
+      {
+        // finished with hidden regions, just increment normally
+        next++;
+      }
+      return current;
+    }
+
+    @Override
+    public void remove()
+    {
+      throw new UnsupportedOperationException();
+    }
+  }
 }