X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=b86a1a1086b6ddea1d85185332713f4750cedacd;hb=0c83c631f7d7db0baad3335805c15dd40c0aed59;hp=00364022034ae0e1b508a290cd1e527de27ae78c;hpb=166a912dd82096db2777150675cf115bf8332b6c;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 0036402..b86a1a1 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1,35 +1,123 @@
+/*
+ * 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.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();
+
+  private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
   /*
    * 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 = new ArrayList<>();
+          Iterator<int[]> it = copy.iterator();
+          while (it.hasNext())
+          {
+            hiddenColumns.add(it.next());
+          }
+          cursor.resetCursor(hiddenColumns);
+        }
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
 
   /**
-   * This Method is used to return all the HiddenColumn regions
+   * 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
    * 
-   * @return empty list or List of hidden column intervals
    */
-  public List<int[]> getHiddenRegions()
+  public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
   {
-    return hiddenColumns == null ? Collections.<int[]> emptyList()
-            : hiddenColumns;
+    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 });
+          }
+        }
+        cursor.resetCursor(hiddenColumns);
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
   }
 
   /**
@@ -46,19 +134,26 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       StringBuilder regionBuilder = new StringBuilder();
-      for (int[] range : hiddenColumns)
+      if (hiddenColumns != null)
       {
-        regionBuilder.append(delimiter).append(range[0]).append(between)
-                .append(range[1]);
+        Iterator<int[]> it = hiddenColumns.iterator();
+        while (it.hasNext())
+        {
+          int[] range = it.next();
+          regionBuilder.append(delimiter).append(range[0]).append(between)
+                  .append(range[1]);
+          if (!it.hasNext())
+          {
+            regionBuilder.deleteCharAt(0);
+          }
+        }
       }
-
-      regionBuilder.deleteCharAt(0);
       return regionBuilder.toString();
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -71,39 +166,44 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int size = 0;
-      if (hasHidden())
+      if (hiddenColumns != null)
       {
-        for (int[] range : hiddenColumns)
+        Iterator<int[]> it = hiddenColumns.iterator();
+        while (it.hasNext())
         {
+          int[] range = it.next();
           size += range[1] - range[0] + 1;
         }
       }
       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
@@ -111,7 +211,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
       if (!(obj instanceof HiddenColumns))
       {
@@ -131,10 +231,13 @@ public class HiddenColumns implements Iterable<int[]>
       {
         return false;
       }
-      int i = 0;
-      for (int[] thisRange : hiddenColumns)
+
+      Iterator<int[]> it = hiddenColumns.iterator();
+      Iterator<int[]> thatit = that.iterator();
+      while (it.hasNext())
       {
-        int[] thatRange = that.hiddenColumns.get(i++);
+        int[] thisRange = it.next();
+        int[] thatRange = thatit.next();
         if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
         {
           return false;
@@ -143,7 +246,7 @@ public class HiddenColumns implements Iterable<int[]>
       return true;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -158,23 +261,29 @@ 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++)
+        result += cursor.getHiddenOffset(column);
+
+
+        /*Iterator<int[]> it = hiddenColumns.iterator();
+        while (it.hasNext())
         {
-          int[] region = hiddenColumns.elementAt(i);
+          int[] region = it.next();
           if (result >= region[0])
           {
             result += region[1] - region[0] + 1;
           }
-        }
+        }*/
       }
+
       return result;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -191,31 +300,32 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int result = hiddenColumn;
+      int[] region = null;
       if (hiddenColumns != null)
       {
-        int index = 0;
-        int[] region;
-        do
+        Iterator<int[]> it = new RegionsIterator(0,
+                hiddenColumn, hiddenColumns, cursor);
+        while (it.hasNext())
         {
-          region = hiddenColumns.elementAt(index++);
+          region = it.next();
           if (hiddenColumn > region[1])
           {
             result -= region[1] + 1 - region[0];
           }
-        } while ((hiddenColumn > region[1])
-                && (index < hiddenColumns.size()));
+        }
 
-        if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+        if (region != null && hiddenColumn >= region[0]
+                && hiddenColumn <= region[1])
         {
           // Here the hidden column is within a region, so
           // we want to return the position of region[0]-1, adjusted for any
           // earlier hidden columns.
           // Calculate the difference between the actual hidden col position
           // and region[0]-1, and then subtract from result to convert result
-          // from
-          // the adjusted hiddenColumn value to the adjusted region[0]-1 value
+          // from the adjusted hiddenColumn value to the adjusted region[0]-1
+          // value.
 
           // However, if the region begins at 0 we cannot return region[0]-1
           // just return 0
@@ -233,7 +343,7 @@ public class HiddenColumns implements Iterable<int[]>
                      // columns.
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -252,96 +362,40 @@ 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));
-
-    // 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;
-
-    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];
-
-      // 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;
-    } finally
-    {
-      lock.readLock().unlock();
-    }
-
-  }
+      // in case startColumn is in a hidden region, move it to the left
+      int start = adjustForHiddenColumns(findColumnPosition(startColumn));
 
-  /**
-   * Use this method to determine the set of hiddenRegion start positions
-   * 
-   * @return list of column number in visible view where hidden regions start
-   */
-  public List<Integer> findHiddenRegionPositions()
-  {
-    try
-    {
-      lock.readLock().lock();
-      List<Integer> positions = new ArrayList<>(
-              hiddenColumns.size());
+      Iterator<int[]> it = new ReverseRegionsIterator(0, start,
+              hiddenColumns);
 
-      positions.add(hiddenColumns.elementAt(0)[0]);
-      for (int i = 1; i < hiddenColumns.size(); ++i)
+      while (it.hasNext() && (distance > 0))
       {
+        int[] region = it.next();
 
-        int result = 0;
-        if (hiddenColumns != null)
+        if (start > region[1])
         {
-          int index = 0;
-          int gaps = 0;
-          do
+          // subtract the gap to right of region from distance
+          if (start - region[1] <= distance)
           {
-            int[] region = hiddenColumns.elementAt(index);
-            gaps += region[1] + 1 - region[0];
-            result = region[1] + 1;
-            index++;
-          } while (index <= i);
-
-          result -= gaps;
+            distance -= start - region[1];
+            start = region[0] - 1;
+          }
+          else
+          {
+            start = start - distance;
+            distance = 0;
+          }
         }
-        positions.add(result);
       }
 
-      return positions;
-    }
-    finally
+      return start - distance;
+
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -349,649 +403,349 @@ public class HiddenColumns implements Iterable<int[]>
    * This method returns the rightmost limit of a region of an alignment with
    * hidden columns. In otherwords, the next hidden column.
    * 
-   * @param index
-   *          int
+   * @param alPos
+   *          the (visible) alignmentPosition to find the next hidden column for
    */
   public int getHiddenBoundaryRight(int alPos)
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (hiddenColumns != null)
       {
-        int index = 0;
-        do
+        Iterator<int[]> it = hiddenColumns.iterator();
+        while (it.hasNext())
         {
-          int[] region = hiddenColumns.elementAt(index);
+          int[] region = it.next();
           if (alPos < region[0])
           {
             return region[0];
           }
-
-          index++;
-        } while (index < hiddenColumns.size());
+        }
       }
-
       return alPos;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
-
   }
 
   /**
    * This method returns the leftmost limit of a region of an alignment with
    * hidden columns. In otherwords, the previous hidden column.
    * 
-   * @param index
-   *          int
+   * @param alPos
+   *          the (visible) alignmentPosition to find the previous hidden column
+   *          for
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
-    if (hiddenColumns != null)
-    {
-      int index = hiddenColumns.size() - 1;
-      do
+      Iterator<int[]> it = new ReverseRegionsIterator(0, alPos,
+              hiddenColumns);
+      while (it.hasNext())
       {
-        int[] region = hiddenColumns.elementAt(index);
+        int[] region = it.next();
         if (alPos > region[1])
         {
           return region[1];
         }
+      }
 
-        index--;
-      } while (index > -1);
-    }
-
-    return alPos;
+      return alPos;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * This method returns the index of the hidden region to the left of a column
-   * position. If the column is in a hidden region it returns the index of the
-   * region to the left. If there is no hidden region to the left it returns -1.
+   * Adds the specified column range to the hidden columns collection
    * 
-   * @param pos
-   *          int
+   * @param start
+   *          start of range to add (absolute position in alignment)
+   * @param end
+   *          end of range to add (absolute position in alignment)
    */
-  private int getHiddenIndexLeft(int pos)
+  public void hideColumns(int start, int end)
   {
+    boolean wasAlreadyLocked = false;
     try
     {
-
-      lock.readLock().lock();
-    if (hiddenColumns != null)
-    {
-      int index = hiddenColumns.size() - 1;
-      do
+      // 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())
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (pos > region[1])
-        {
-          return index;
-        }
+        LOCK.writeLock().lock();
+      }
+      else
+      {
+        wasAlreadyLocked = true;
+      }
 
-        index--;
-      } while (index > -1);
-    }
+      if (hiddenColumns == null)
+      {
+        hiddenColumns = new ArrayList<>();
+      }
 
-    return -1;
+      /*
+       * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
+       */
+      if (hiddenColumns.isEmpty()
+              || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
+      {
+        hiddenColumns.add(new int[] { start, end });
+      }
+      else
+      {
+        /*
+         * traverse existing hidden ranges and insert / amend / append as
+         * appropriate
+         */
+        boolean added = false;
+        for (int i = 0; !added && i < hiddenColumns.size(); i++)
+        {
+          added = insertRangeAtRegion(i, start, end);
+        } // for
+      }
+      if (!wasAlreadyLocked)
+      {
+        cursor.resetCursor(hiddenColumns);
+      }
     } finally
     {
-      lock.readLock().unlock();
+      if (!wasAlreadyLocked)
+      {
+        LOCK.writeLock().unlock();
+      }
     }
-
   }
 
   /**
-   * Adds the specified column range to the hidden columns
+   * Insert [start, range] at the region at index i in hiddenColumns, if
+   * feasible
    * 
+   * @param i
+   *          index to insert at
    * @param start
+   *          start of range to insert
    * @param end
+   *          end of range to insert
+   * @return true if range was successfully inserted
    */
-  public void hideColumns(int start, int end)
+  private boolean insertRangeAtRegion(int i, int start, int end)
   {
-    hideColumns(start, end, false);
-  }
+    boolean added = false;
 
-  /**
-   * Adds the specified column range to the hidden columns
-   * 
-   * @param start
-   * @param end
-   */
-  private void hideColumns(int start, int end, boolean alreadyLocked)
-  {
-    try
+    int[] region = hiddenColumns.get(i);
+    if (end < region[0] - 1)
     {
-
-      if (!alreadyLocked)
-      {
-        lock.writeLock().lock();
-      }
-
-    if (hiddenColumns == null)
+      /*
+       * insert discontiguous preceding range
+       */
+      hiddenColumns.add(i, new int[] { start, end });
+      added = true;
+    }
+    else if (end <= region[1])
     {
-      hiddenColumns = new Vector<>();
+      /*
+       * new range overlaps existing, or is contiguous preceding it - adjust
+       * start column
+       */
+      region[0] = Math.min(region[0], start);
+      added = true;
     }
-
-    /*
-     * traverse existing hidden ranges and insert / amend / append as
-     * appropriate
-     */
-    for (int i = 0; i < hiddenColumns.size(); i++)
+    else if (start <= region[1] + 1)
     {
-      int[] region = hiddenColumns.elementAt(i);
-
-      if (end < region[0] - 1)
-      {
-        /*
-         * insert discontiguous preceding range
-         */
-        hiddenColumns.insertElementAt(new int[] { start, end }, i);
-        return;
-      }
-
-      if (end <= region[1])
-      {
-        /*
-         * new range overlaps existing, or is contiguous preceding it - adjust
-         * start column
-         */
-        region[0] = Math.min(region[0], start);
-        return;
-      }
+      /*
+       * 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);
 
-      if (start <= region[1] + 1)
+      /*
+       * also update or remove any subsequent ranges 
+       * that are overlapped
+       */
+      while (i < hiddenColumns.size() - 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)
+        int[] nextRegion = hiddenColumns.get(i + 1);
+        if (nextRegion[0] > end + 1)
         {
-          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);
+          /*
+           * gap to next hidden range - no more to update
+           */
+          break;
         }
-        return;
-      }
-    }
-
-    /*
-     * remaining case is that the new range follows everything else
-     */
-    hiddenColumns.addElement(new int[] { start, end });
-    } finally
-    {
-      if (!alreadyLocked)
-      {
-        lock.writeLock().unlock();
+        region[1] = Math.max(nextRegion[1], end);
+        hiddenColumns.subList(i + 1, i + 2).clear();
       }
+      added = true;
     }
+    return added;
   }
 
+  /**
+   * Answers if a column in the alignment is visible
+   * 
+   * @param column
+   *          absolute position of column in the alignment
+   * @return true if column is visible
+   */
   public boolean isVisible(int column)
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
-    if (hiddenColumns != null)
-    {
-      for (int[] region : hiddenColumns)
+      Iterator<int[]> it = new RegionsIterator(column, column,
+              hiddenColumns, cursor);
+      while (it.hasNext())
       {
+        int[] region = it.next();
         if (column >= region[0] && column <= region[1])
         {
           return false;
         }
       }
-    }
 
-    return true;
+      return true;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * ColumnSelection
-   */
-  public HiddenColumns()
-  {
-  }
-
-  /**
-   * Copy constructor
+   * Get the visible sections of a set of sequences
    * 
-   * @param copy
+   * @param start
+   *          sequence position to start from
+   * @param end
+   *          sequence position to end at
+   * @param seqs
+   *          an array of sequences
+   * @return an array of strings encoding the visible parts of each sequence
    */
-  public HiddenColumns(HiddenColumns copy)
+  public String[] getVisibleSequenceStrings(int start, int end,
+          SequenceI[] seqs)
   {
     try
     {
+      LOCK.readLock().lock();
+      int iSize = seqs.length;
+      String[] selections = new String[iSize];
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
+      {
+        for (int i = 0; i < iSize; i++)
+        {
+          StringBuffer visibleSeq = new StringBuffer();
 
-      lock.readLock().lock();
-      if (copy != null)
+          Iterator<int[]> blocks = new VisibleContigsIterator(start,
+                  end + 1, hiddenColumns);
+
+          while (blocks.hasNext())
+          {
+            int[] block = blocks.next();
+            if (blocks.hasNext())
+            {
+              visibleSeq
+                      .append(seqs[i].getSequence(block[0], block[1] + 1));
+            }
+            else
+            {
+              visibleSeq
+                      .append(seqs[i].getSequence(block[0], block[1]));
+            }
+          }
+
+          selections[i] = visibleSeq.toString();
+        }
+      }
+      else
       {
-        if (copy.hiddenColumns != null)
+        for (int i = 0; i < iSize; i++)
         {
-          hiddenColumns = copy.copyHiddenRegions();
+          selections[i] = seqs[i].getSequenceAsString(start, end);
         }
       }
-    }
-    finally
+
+      return selections;
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
-  private Vector<int[]> copyHiddenRegions()
+  /**
+   * Locate the first position visible for this sequence. If seq isn't visible
+   * then return the position of the left side of the hidden boundary region.
+   * 
+   * @param seq
+   *          sequence to find position for
+   * @return visible start position
+   */
+  public int locateVisibleStartOfSequence(SequenceI seq)
   {
-    Vector<int[]> copy = new Vector<>(hiddenColumns.size());
-    for (int i = 0, j = hiddenColumns.size(); i < j; i++)
+    try
     {
-      int[] rh, cp;
-      rh = hiddenColumns.elementAt(i);
-      if (rh != null)
+      LOCK.readLock().lock();
+      int start = 0;
+
+      if (hiddenColumns == null || hiddenColumns.size() == 0)
       {
-        cp = new int[rh.length];
-        System.arraycopy(rh, 0, cp, 0, rh.length);
-        copy.addElement(cp);
+        return seq.findIndex(seq.getStart()) - 1;
       }
-    }
-    return copy;
-  }
 
-  private ArrayList<int[]> copyHiddenRegionsToArrayList()
-  {
-    ArrayList<int[]> copy = new ArrayList<>(hiddenColumns.size());
-    for (int i = 0, j = hiddenColumns.size(); i < j; i++)
-    {
-      int[] rh, cp;
-      rh = hiddenColumns.elementAt(i);
-      if (rh != null)
+      // Simply walk along the sequence whilst watching for hidden column
+      // boundaries
+      Iterator<int[]> regions = hiddenColumns.iterator();
+      int hideStart = seq.getLength();
+      int hideEnd = -1;
+      int visPrev = 0;
+      int visNext = 0;
+      boolean foundStart = false;
+
+      // step through the non-gapped positions of the sequence
+      for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
       {
-        cp = new int[rh.length];
-        System.arraycopy(rh, 0, cp, 0, rh.length);
-        copy.add(cp);
-      }
-    }
-    return copy;
-  }
+        // get alignment position of this residue in the sequence
+        int p = seq.findIndex(i) - 1;
 
-  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();
-    }
-  }
-
-  /**
-   * propagate shift in alignment columns to column selection
-   * 
-   * @param start
-   *          beginning of edit
-   * @param left
-   *          shift in edit (+ve for removal, or -ve for inserts)
-   */
-  public List<int[]> compensateForEdit(int start, int change,
-          ColumnSelection sel)
-  {
-    try
-    {
-      lock.writeLock().lock();
-      List<int[]> deletedHiddenColumns = null;
-
-      if (hiddenColumns != null)
-      {
-        deletedHiddenColumns = new ArrayList<>();
-        int hSize = hiddenColumns.size();
-        for (int i = 0; i < hSize; i++)
-        {
-          int[] region = hiddenColumns.elementAt(i);
-          if (region[0] > start && start + change > region[1])
-          {
-            deletedHiddenColumns.add(region);
-
-            hiddenColumns.removeElementAt(i);
-            i--;
-            hSize--;
-            continue;
-          }
-
-          if (region[0] > start)
-          {
-            region[0] -= change;
-            region[1] -= change;
-          }
-
-          if (region[0] < 0)
-          {
-            region[0] = 0;
-          }
-
-        }
-
-        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++)
+        // update hidden region start/end
+        while (hideEnd < p && regions.hasNext())
         {
-          region = regions.get(j);
+          int[] region = regions.next();
+          visPrev = visNext;
+          visNext += region[0] - visPrev;
           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[] 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 };
-      }
-    }
-    finally
-    {
-      lock.readLock().unlock();
-    }
-  }
-
-  public String[] getVisibleSequenceStrings(int start, int end,
-          SequenceI[] seqs)
-  {
-    try
-    {
-      lock.readLock().lock();
-      int i, iSize = seqs.length;
-      String selections[] = new String[iSize];
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
-      {
-        for (i = 0; i < iSize; i++)
+        if (hideEnd < p)
         {
-          StringBuffer visibleSeq = new StringBuffer();
-          List<int[]> regions = getHiddenRegions();
-
-          int blockStart = start, blockEnd = end;
-          int[] region;
-          int hideStart, hideEnd;
-
-          for (int j = 0; j < regions.size(); j++)
-          {
-            region = regions.get(j);
-            hideStart = region[0];
-            hideEnd = region[1];
-
-            if (hideStart < start)
-            {
-              continue;
-            }
-
-            blockStart = Math.min(blockStart, hideEnd + 1);
-            blockEnd = Math.min(blockEnd, hideStart);
-
-            if (blockStart > blockEnd)
-            {
-              break;
-            }
-
-            visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
-            blockStart = hideEnd + 1;
-            blockEnd = end;
-          }
-
-          if (end > blockStart)
-          {
-            visibleSeq.append(seqs[i].getSequence(blockStart, end));
-          }
-
-          selections[i] = visibleSeq.toString();
+          hideStart = seq.getLength();
         }
-      }
-      else
-      {
-        for (i = 0; i < iSize; i++)
+        // update visible boundary for sequence
+        if (p < hideStart)
         {
-          selections[i] = seqs[i].getSequenceAsString(start, end);
+          start = p;
+          foundStart = true;
         }
       }
 
-      return selections;
-    }
-    finally
-    {
-      lock.readLock().unlock();
-    }
-  }
-
-  /**
-   * Locate the first and last position visible for this sequence. if seq isn't
-   * visible then return the position of the left and right of the hidden
-   * boundary region, and the corresponding alignment column indices for the
-   * extent of the sequence
-   * 
-   * @param seq
-   * @return int[] { visible start, visible end, first seqpos, last seqpos,
-   *         alignment index for seq start, alignment index for seq end }
-   */
-  public int[] locateVisibleBoundsOfSequence(SequenceI seq)
-  {
-    try
-    {
-      lock.readLock().lock();
-      int fpos = seq.getStart(), 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 };
-      }
-
-      // 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;
-      boolean foundStart = false;
-      for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
-              && p < pLen; p++)
-      {
-        if (!Comparison.isGap(seq.getCharAt(p)))
-        {
-          // keep track of first/last column
-          // containing sequence data regardless of visibility
-          if (firstP == -1)
-          {
-            firstP = p;
-          }
-          lastP = p;
-          // update hidden region start/end
-          while (hideEnd < p && rcount < regions.size())
-          {
-            int[] region = regions.get(rcount++);
-            visPrev = visNext;
-            visNext += region[0] - visPrev;
-            hideStart = region[0];
-            hideEnd = region[1];
-          }
-          if (hideEnd < p)
-          {
-            hideStart = seq.getLength();
-          }
-          // update visible boundary for sequence
-          if (p < hideStart)
-          {
-            if (!foundStart)
-            {
-              fpos = spos;
-              start = p;
-              foundStart = true;
-            }
-            lastvispos = p;
-            lpos = spos;
-          }
-          // look for next sequence position
-          spos++;
-        }
-      }
       if (foundStart)
       {
-        return new int[] { findColumnPosition(start),
-            findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+        return findColumnPosition(start);
       }
       // otherwise, sequence was completely hidden
-      return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
-    }
-    finally
+      return visPrev;
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1003,7 +757,8 @@ public class HiddenColumns implements Iterable<int[]>
    */
   public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
   {
-    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+    makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+            alignmentAnnotation);
   }
 
   /**
@@ -1022,95 +777,84 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
-      if (alignmentAnnotation.annotations == null)
-      {
-        return;
-      }
-      if (start == end && end == -1)
-      {
-        start = 0;
-        end = alignmentAnnotation.annotations.length;
-      }
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
-      {
-        // 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;
-
-        for (int j = 0; j < regions.size(); j++)
-        {
-          region = regions.get(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-
-          if (hideStart < start)
-          {
-            continue;
-          }
-
-          blockStart = Math.min(blockStart, hideEnd + 1);
-          blockEnd = Math.min(blockEnd, hideStart);
-
-          if (blockStart > blockEnd)
-          {
-            break;
-          }
+      LOCK.readLock().lock();
 
-          annels.addElement(els = new Annotation[blockEnd - blockStart]);
-          System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
-                  0, els.length);
-          w += els.length;
-          blockStart = hideEnd + 1;
-          blockEnd = end;
-        }
+      int startFrom = start;
+      int endAt = end;
 
-        if (end > blockStart)
+      if (alignmentAnnotation.annotations != null)
+      {
+        if (hiddenColumns != null && hiddenColumns.size() > 0)
         {
-          annels.addElement(els = new Annotation[end - blockStart + 1]);
-          if ((els.length
-                  + blockStart) <= alignmentAnnotation.annotations.length)
-          {
-            // copy just the visible segment of the annotation row
-            System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                    els, 0, els.length);
-          }
-          else
-          {
-            // copy to the end of the annotation row
-            System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                    els, 0,
-                    (alignmentAnnotation.annotations.length - blockStart));
-          }
-          w += els.length;
+          removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
         }
-        if (w == 0)
+        else
         {
-          return;
+          alignmentAnnotation.restrict(startFrom, endAt);
         }
+      }
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
 
-        alignmentAnnotation.annotations = new Annotation[w];
-        w = 0;
-
-        for (Annotation[] chnk : annels)
-        {
-          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
-                  chnk.length);
-          w += chnk.length;
-        }
+  private void removeHiddenAnnotation(int start, int end,
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    // mangle the alignmentAnnotation annotation array
+    ArrayList<Annotation[]> annels = new ArrayList<>();
+    Annotation[] els = null;
+
+    int w = 0;
+    
+    Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
+            hiddenColumns);
+
+    int copylength;
+    int annotationLength;
+    while (blocks.hasNext())
+    {
+      int[] block = blocks.next();
+      annotationLength = block[1] - block[0] + 1;
+    
+      if (blocks.hasNext())
+      {
+        // copy just the visible segment of the annotation row
+        copylength = annotationLength;
       }
       else
       {
-        alignmentAnnotation.restrict(start, end);
+        if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
+        {
+          // copy just the visible segment of the annotation row
+          copylength = annotationLength;
+        }
+        else
+        {
+          // copy to the end of the annotation row
+          copylength = alignmentAnnotation.annotations.length - block[0];
+        }
       }
+      
+      els = new Annotation[annotationLength];
+      annels.add(els);
+      System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
+              copylength);
+      w += annotationLength;
     }
-    finally
+    
+    if (w != 0)
     {
-      lock.readLock().unlock();
+      alignmentAnnotation.annotations = new Annotation[w];
+
+      w = 0;
+      for (Annotation[] chnk : annels)
+      {
+        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                chnk.length);
+        w += chnk.length;
+      }
     }
   }
 
@@ -1122,11 +866,11 @@ 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();
     }
   }
 
@@ -1138,11 +882,11 @@ 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();
     }
   }
 
@@ -1156,15 +900,16 @@ 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]);
       }
+      cursor.resetCursor(hiddenColumns);
     } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1175,24 +920,24 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       if (hiddenColumns != null)
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
+        Iterator<int[]> it = hiddenColumns.iterator();
+        while (it.hasNext())
         {
-          int[] region = hiddenColumns.elementAt(i);
+          int[] region = it.next();
           for (int j = region[0]; j < region[1] + 1; j++)
           {
             sel.addElement(j);
           }
         }
+        hiddenColumns = null;
+        cursor.resetCursor(hiddenColumns);
       }
-
-      hiddenColumns = null;
-    }
-    finally
+    } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1206,169 +951,53 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      LOCK.writeLock().lock();
+      Iterator<int[]> it = new RegionsIterator(start, start, hiddenColumns,
+              cursor);
+      while (it.hasNext())
       {
-        int[] region = hiddenColumns.elementAt(i);
+        int[] region = it.next();
         if (start == region[0])
         {
           for (int j = region[0]; j < region[1] + 1; j++)
           {
             sel.addElement(j);
           }
-
-          hiddenColumns.removeElement(region);
+          it.remove();
           break;
         }
+        else if (start < region[0])
+        {
+          break; // passed all possible matching regions
+        }
       }
+
       if (hiddenColumns.size() == 0)
       {
         hiddenColumns = null;
       }
-    }
-    finally
+      cursor.resetCursor(hiddenColumns);
+    } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
   /**
-   * removes intersection of position,length ranges in deletions from the
-   * start,end regions marked in intervals.
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
    * 
-   * @param shifts
-   * @param intervals
-   * @return
+   * @param profileseq
+   * @param al
+   *          - alignment to have gaps inserted into it
+   * @param input
+   *          - alignment view where sequence corresponding to profileseq is
+   *          first entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
    */
-  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
-    {
-      lock.writeLock().unlock();
-    }
-  }
-
-  /**
-   * Add gaps into the sequences aligned to profileseq under the given
-   * AlignmentView
-   * 
-   * @param profileseq
-   * @param al
-   *          - alignment to have gaps inserted into it
-   * @param input
-   *          - alignment view where sequence corresponding to profileseq is
-   *          first entry
-   * @return new HiddenColumns for new alignment view, with insertions into
-   *         profileseq marked as hidden.
-   */
-  public static HiddenColumns propagateInsertions(SequenceI profileseq,
-          AlignmentI al, AlignmentView input)
+  public static HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentI al, AlignmentView input)
   {
     int profsqpos = 0;
 
@@ -1393,155 +1022,125 @@ public class HiddenColumns implements Iterable<int[]>
   private void propagateInsertions(SequenceI profileseq, AlignmentI al,
           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)
-      {
-        StringBuffer sb = new StringBuffer();
-        for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
-        {
-          sb.append(gc);
-        }
-        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())
+    try
     {
-      // pad the final region with gaps.
-      StringBuffer sb = new StringBuffer();
-      for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
-      {
-        sb.append(gc);
-      }
-      for (int s = 0, ns = al.getHeight(); s < ns; s++)
+      LOCK.writeLock().lock();
+
+      char gc = al.getGapCharacter();
+
+      // 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 = hiddenColumns.iterator();
+      ArrayList<int[]> newhidden = new ArrayList<>();
+
+      int numGapsBefore = 0;
+      int gapPosition = 0;
+      while (regions.hasNext())
       {
-        SequenceI sqobj = al.getSequenceAt(s);
-        if (sqobj == profileseq)
+        // 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])
         {
-          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())
+          gapPosition++;
+          if (gaps.get(gapPosition))
           {
-            sq += sb.toString();
+            numGapsBefore++;
           }
-          else
-          {
-            char[] buf = new char[diff];
-            sb.getChars(0, diff, buf, 0);
-            sq += buf.toString();
-          }
-          diff = origseq.getLength() - sq.length();
         }
-      }
-    }
-  }
 
-  /**
-   * 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);
+        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; s < right - left + 1; s++)
+        {
+          sb.append(gc);
+        }
+        padGaps(sb, left, profileseq, al);
 
-        // and shift the rest.
-        this.compensateForEdits(deletions);
       }
+      hiddenColumns = newhidden;
+      cursor.resetCursor(hiddenColumns);
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
   }
 
   /**
-   * 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;
   }
 
   /**
@@ -1552,21 +1151,19 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int hashCode = 1;
-      if (hiddenColumns != null)
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
       {
-        for (int[] hidden : hiddenColumns)
-        {
-          hashCode = 31 * hashCode + hidden[0];
-          hashCode = 31 * hashCode + hidden[1];
-        }
+        int[] hidden = it.next();
+        hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+        hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
       }
       return hashCode;
-    }
-    finally
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1580,17 +1177,18 @@ 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);
       }
+      cursor.resetCursor(hiddenColumns);
     } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1603,30 +1201,381 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (hiddenColumns == null)
       {
         return;
       }
-      for (int[] range : hiddenColumns)
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
       {
+        int[] range = it.next();
         inserts.set(range[0], range[1] + 1);
       }
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * 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 };
+      }
+
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
+      {
+        int[] range = it.next();
+        lowestRange = (range[0] <= startPos) ? range : lowestRange;
+        higestRange = (range[1] >= endPos) ? range : 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();
     }
-    finally
+  }
+
+  /**
+   * 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;
+      Iterator<int[]> it = new RegionsIterator(adjres - 2,
+              adjres + 2, hiddenColumns, cursor);
+      while (it.hasNext())
+      {
+        int[] region = it.next();
+        if (adjres + 1 == region[0] || adjres - 1 == region[1])
+        {
+          reveal = region;
+          break;
+        }
+      }
+      return reveal;
+    } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
-  @Override
+  /**
+   * Return an iterator over the hidden regions
+   */
   public Iterator<int[]> iterator()
   {
-    if (hiddenColumns == null)
+    try
     {
-      return Collections.<int[]> emptyList().iterator();
+      LOCK.readLock().lock();
+      return new BoundedHiddenColsIterator(hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-    return hiddenColumns.iterator();
   }
 
+  /**
+   * Return a bounded iterator over the hidden regions
+   * 
+   * @param start
+   *          position to start from (inclusive, absolute column position)
+   * @param end
+   *          position to end at (inclusive, absolute column position)
+   * @return
+   */
+  public Iterator<int[]> getBoundedIterator(int start, int end)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      return new BoundedHiddenColsIterator(start, end, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * Return a bounded iterator over the *visible* start positions of hidden
+   * regions
+   * 
+   * @param start
+   *          position to start from (inclusive, visible column position)
+   * @param end
+   *          position to end at (inclusive, visible column position)
+   */
+  public Iterator<Integer> getBoundedStartIterator(int start, int end)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      return new BoundedStartRegionIterator(start, end, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * Return an iterator over visible *columns* (not regions) between the given
+   * start and end boundaries
+   * 
+   * @param start
+   *          first column (inclusive)
+   * @param end
+   *          last column (inclusive)
+   */
+  public Iterator<Integer> getVisibleColsIterator(int start, int end)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      return new VisibleColsIterator(start, end, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * return an iterator over visible segments between the given start and end
+   * boundaries
+   * 
+   * @param start
+   *          (first column inclusive from 0)
+   * @param end
+   *          (last column - not inclusive)
+   */
+  public Iterator<int[]> getVisContigsIterator(int start, int end)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      return new VisibleContigsIterator(start, end, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * return an iterator over visible segments between the given start and end
+   * boundaries
+   * 
+   * @param start
+   *          (first column - inclusive from 0)
+   * @param end
+   *          (last column - inclusive)
+   * @param useVisibleCoords
+   *          if true, start and end are visible column positions, not absolute
+   *          positions
+   */
+  public Iterator<int[]> getVisibleBlocksIterator(int start, int end,
+          boolean useVisibleCoords)
+  {
+    if (useVisibleCoords)
+    {
+      // TODO
+      // we should really just convert start and end here with
+      // adjustForHiddenColumns
+      // and then create a VisibleContigsIterator
+      // but without a cursor this will be horribly slow in some situations
+      // ... so until then...
+      return new VisibleBlocksVisBoundsIterator(start, end, true);
+    }
+    else
+    {
+      try
+      {
+        LOCK.readLock().lock();
+        return new VisibleContigsIterator(start, end + 1, hiddenColumns);
+      } finally
+    {
+        LOCK.readLock().unlock();
+      }
+    }
+  }
+
+  /**
+   * An iterator which iterates over visible regions in a range. The range is
+   * specified in terms of visible column positions. Provides a special
+   * "endsAtHidden" indicator to allow callers to determine if the final visible
+   * column is adjacent to a hidden region.
+   */
+  public class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
+  {
+    private List<int[]> vcontigs = new ArrayList<>();
+
+    private int currentPosition = 0;
+
+    private boolean endsAtHidden = false;
+
+    /**
+     * Constructor for iterator over visible regions in a range.
+     * 
+     * @param start
+     *          start position in terms of visible column position
+     * @param end
+     *          end position in terms of visible column position
+     * @param usecopy
+     *          whether to use a local copy of hidden columns
+     */
+    VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy)
+    {
+      /* actually this implementation always uses a local copy but this may change in future */
+      try
+      {
+        if (usecopy)
+        {
+          LOCK.readLock().lock();
+        }
+
+        if (hiddenColumns != null && hiddenColumns.size() > 0)
+        {
+          int blockStart = start;
+          int blockEnd = end;
+          int hiddenSoFar = 0;
+          int visSoFar = 0;
+
+          // iterate until a region begins within (start,end]
+          int i = 0;
+          while ((i < hiddenColumns.size())
+                  && (hiddenColumns.get(i)[0] <= blockStart + hiddenSoFar))
+          {
+            hiddenSoFar += hiddenColumns.get(i)[1] - hiddenColumns.get(i)[0]
+                    + 1;
+            i++;
+          }
+
+          blockStart += hiddenSoFar; // convert start to absolute position
+          blockEnd += hiddenSoFar; // convert end to absolute position
+
+          // iterate from start to end, adding each visible region. Positions
+          // are
+          // absolute, and all hidden regions which overlap [start,end] are
+          // used.
+          while (i < hiddenColumns.size()
+                  && (hiddenColumns.get(i)[0] <= blockEnd))
+          {
+            int[] region = hiddenColumns.get(i);
+
+            // end position of this visible region is either just before the
+            // start of the next hidden region, or the absolute position of
+            // 'end', whichever is lowest
+            blockEnd = Math.min(blockEnd, region[0] - 1);
+
+            vcontigs.add(new int[] { blockStart, blockEnd });
+
+            visSoFar += blockEnd - blockStart + 1;
+
+            // next visible region starts after this hidden region
+            blockStart = region[1] + 1;
+
+            hiddenSoFar += region[1] - region[0] + 1;
+
+            // reset blockEnd to absolute position of 'end', assuming we've now
+            // passed all hidden regions before end
+            blockEnd = end + hiddenSoFar;
+
+            i++;
+          }
+          if (visSoFar < end - start)
+          {
+            // the number of visible columns we've accounted for is less than
+            // the number specified by end-start; work out the end position of
+            // the last visible region
+            blockEnd = blockStart + end - start - visSoFar;
+            vcontigs.add(new int[] { blockStart, blockEnd });
+
+            // if the last visible region ends at the next hidden region, set
+            // endsAtHidden=true
+            if (i < hiddenColumns.size()
+                    && hiddenColumns.get(i)[0] - 1 == blockEnd)
+            {
+              endsAtHidden = true;
+            }
+          }
+        }
+        else
+        {
+          // there are no hidden columns, return a single visible contig
+          vcontigs.add(new int[] { start, end });
+          endsAtHidden = false;
+        }
+      } finally
+      {
+        if (usecopy)
+        {
+          LOCK.readLock().unlock();
+        }
+      }
+    }
+
+    @Override
+    public boolean hasNext()
+    {
+      return (currentPosition < vcontigs.size());
+    }
+
+    @Override
+    public int[] next()
+    {
+      int[] result = vcontigs.get(currentPosition);
+      currentPosition++;
+      return result;
+    }
+
+    public boolean endsAtHidden()
+    {
+      return endsAtHidden;
+    }
+  }
 }