X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=2b5185fbe5ea7c4f6a2aa2c0f7531205fd68130f;hb=2a66892874abea357a5e5d9ef2f69919453c31d0;hp=1abd04be187a358609df1b297375fca5c183a826;hpb=b70c7ff4b002103401ccceb917114b954e18d50c;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 1abd04b..2b5185f 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1,697 +1,1051 @@
+/*
+ * 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.Collections;
+import java.util.BitSet;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
-
+import java.util.concurrent.locks.ReentrantReadWriteLock;
+
+/**
+ * This class manages the collection of hidden columns associated with an
+ * alignment. To iterate over the collection, or over visible columns/regions,
+ * use an iterator obtained from one of:
+ * 
+ * - getBoundedIterator: iterates over the hidden regions, within some bounds,
+ * returning absolute positions
+ * 
+ * - getBoundedStartIterator: iterates over the start positions of hidden
+ * regions, within some bounds, returning visible positions
+ * 
+ * - getVisContigsIterator: iterates over visible regions in a range, returning
+ * absolute positions
+ * 
+ * - getVisibleColsIterator: iterates over the visible *columns*
+ * 
+ * For performance reasons, provide bounds where possible. Note that column
+ * numbering begins at 0 throughout this class.
+ * 
+ * @author kmourao
+ *
+ */
 public class HiddenColumns
 {
+  private static final int HASH_MULTIPLIER = 31;
+
+  private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+
+  /*
+   * Cursor which tracks the last used hidden columns region, and the number 
+   * of hidden columns up to (but not including) that region.
+   */
+  private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+  /*
+   * cache of the number of hidden columns
+   */
+  private int numColumns = 0;
+
   /*
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
    */
-  private Vector<int[]> hiddenColumns;
+  private List<int[]> hiddenColumns;
 
   /**
-   * This Method is used to return all the HiddenColumn regions
-   * 
-   * @return empty list or List of hidden column intervals
+   * Constructor
    */
-  public List<int[]> getListOfCols()
+  public HiddenColumns()
   {
-    return hiddenColumns == null ? Collections.<int[]> emptyList()
-            : hiddenColumns;
   }
 
-  public boolean hasHidden()
-  {
-    return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
-  }
+  /* 
+   * Methods which change the hiddenColumns collection. These methods should 
+   * use a writeLock to prevent other threads accessing the hiddenColumns
+   * collection while changes are being made. They should also reset the hidden
+   * columns cursor, and either update the hidden columns count, or set it to 0 
+   * (so that it will later be updated when needed).
+   */
 
-  @Override
-  public boolean equals(Object obj)
+  /**
+   * Copy constructor
+   * 
+   * @param copy
+   *          the HiddenColumns object to copy from
+   */
+  public HiddenColumns(HiddenColumns copy)
   {
-    if (!(obj instanceof HiddenColumns))
-    {
-      return false;
-    }
-    HiddenColumns that = (HiddenColumns) obj;
-
-    /*
-     * check hidden columns are either both null, or match
-     */
-    if (this.hiddenColumns == null)
-    {
-      return (that.hiddenColumns == null);
-    }
-    if (that.hiddenColumns == null
-            || that.hiddenColumns.size() != this.hiddenColumns.size())
-    {
-      return false;
-    }
-    int i = 0;
-    for (int[] thisRange : hiddenColumns)
-    {
-      int[] thatRange = that.hiddenColumns.get(i++);
-      if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
-      {
-        return false;
-      }
-    }
-    return true;
+    this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0);
   }
 
   /**
-   * Return absolute column index for a visible column index
+   * 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
    * 
-   * @param column
-   *          int column index in alignment view (count from zero)
-   * @return alignment column index for column
    */
-  public int adjustForHiddenColumns(int column)
+  public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
   {
-    int result = column;
-    if (hiddenColumns != null)
+    try
     {
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      LOCK.writeLock().lock();
+      if (copy != null)
       {
-        int[] region = hiddenColumns.elementAt(i);
-        if (result >= region[0])
+        hiddenColumns = new ArrayList<>();
+        numColumns = 0;
+        Iterator<int[]> it = copy.getBoundedIterator(start, end);
+        while (it.hasNext())
         {
-          result += region[1] - region[0] + 1;
+          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 });
+            numColumns += region[1] - region[0] + 1;
+          }
         }
+        cursor.resetCursor(hiddenColumns);
       }
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
-    return result;
   }
 
   /**
-   * Use this method to find out where a column will appear in the visible
-   * alignment when hidden columns exist. If the column is not visible, then the
-   * left-most visible column will always be returned.
+   * Adds the specified column range to the hidden columns collection
    * 
-   * @param hiddenColumn
-   *          the column index in the full alignment including hidden columns
-   * @return the position of the column in the visible alignment
+   * @param start
+   *          start of range to add (absolute position in alignment)
+   * @param end
+   *          end of range to add (absolute position in alignment)
    */
-  public int findColumnPosition(int hiddenColumn)
+  public void hideColumns(int start, int end)
   {
-    int result = hiddenColumn;
-    if (hiddenColumns != null)
+    boolean wasAlreadyLocked = false;
+    try
     {
-      int index = 0;
-      int[] region;
-      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())
+      {
+        LOCK.writeLock().lock();
+      }
+      else
       {
-        region = hiddenColumns.elementAt(index++);
-        if (hiddenColumn > region[1])
+        wasAlreadyLocked = true;
+      }
+
+      int previndex = 0;
+      int prevHiddenCount = 0;
+      int regionindex = 0;
+      if (hiddenColumns == null)
+      {
+        hiddenColumns = new ArrayList<>();
+      }
+      else
+      {
+        // set up cursor reset values
+        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+        regionindex = cursorPos.getRegionIndex();
+
+        if (regionindex > 0)
         {
-          result -= region[1] + 1 - region[0];
+          // get previous index and hidden count for updating the cursor later
+          previndex = regionindex - 1;
+          int[] prevRegion = hiddenColumns.get(previndex);
+          prevHiddenCount = cursorPos.getHiddenSoFar()
+                  - (prevRegion[1] - prevRegion[0] + 1);
         }
-      } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+      }
 
-      if (hiddenColumn >= region[0] && hiddenColumn <= region[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])
       {
-        // 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
-
-        // However, if the region begins at 0 we cannot return region[0]-1
-        // just return 0
-        if (region[0] == 0)
+        hiddenColumns.add(new int[] { start, end });
+      }
+      else
+      {
+        /*
+         * traverse existing hidden ranges and insert / amend / append as
+         * appropriate
+         */
+        boolean added = false;
+        if (regionindex > 0)
         {
-          return 0;
+          added = insertRangeAtRegion(regionindex - 1, start, end);
         }
-        else
+        if (!added && regionindex < hiddenColumns.size())
         {
-          return result - (hiddenColumn - region[0] + 1);
+          insertRangeAtRegion(regionindex, start, end);
         }
       }
+
+      // reset the cursor to just before our insertion point: this saves
+      // a lot of reprocessing in large alignments
+      cursor.resetCursor(hiddenColumns, previndex, prevHiddenCount);
+
+      // reset the number of columns so they will be recounted
+      numColumns = 0;
+
+    } finally
+    {
+      if (!wasAlreadyLocked)
+      {
+        LOCK.writeLock().unlock();
+      }
     }
-    return result; // return the shifted position after removing hidden columns.
   }
 
   /**
-   * Find the visible column which is a given visible number of columns to the
-   * left of another visible column. i.e. for a startColumn x, the column which
-   * is distance 1 away will be column x-1.
+   * Insert [start, range] at the region at index i in hiddenColumns, if
+   * feasible
    * 
-   * @param visibleDistance
-   *          the number of visible columns to offset by
-   * @param startColumn
-   *          the column to start from
-   * @return the position of the column in the visible alignment
+   * @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 int subtractVisibleColumns(int visibleDistance, int startColumn)
+  private boolean insertRangeAtRegion(int i, int start, int end)
   {
-    int distance = visibleDistance;
-
-    // in case startColumn is in a hidden region, move it to the left
-    int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+    boolean added = false;
 
-    // get index of hidden region to left of start
-    int index = getHiddenIndexLeft(start);
-    if (index == -1)
+    int[] region = hiddenColumns.get(i);
+    if (end < region[0] - 1)
     {
-      // no hidden regions to left of startColumn
-      return start - distance;
+      /*
+       * insert discontiguous preceding range
+       */
+      hiddenColumns.add(i, new int[] { start, end });
+      added = true;
     }
-
-    // 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))
+    else if (end <= region[1])
     {
-      // 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];
+      /*
+       * new range overlaps existing, or is contiguous preceding it - adjust
+       * start column
+       */
+      region[0] = Math.min(region[0], start);
+      added = true;
+    }
+    else 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)
+      {
+        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);
 
-      // set start to just to left of current region
-      nextstart = region[0] - 1;
-      index--;
+        // in theory this is faster than hiddenColumns.remove(i+1)
+        // benchmarking results a bit ambivalent
+        hiddenColumns.subList(i + 1, i + 2).clear();
+      }
+      added = true;
     }
+    return added;
+  }
 
-    if (distance - gap > 0)
+  /**
+   * mark the columns corresponding to gap characters as hidden in the column
+   * selection
+   * 
+   * @param insertions
+   */
+  public void hideInsertionsFor(List<int[]> inserts)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      for (int[] r : inserts)
+      {
+        hideColumns(r[0], r[1]);
+      }
+      cursor.resetCursor(hiddenColumns);
+      numColumns = 0;
+    } finally
     {
-      // fell out of loop because there are no more hidden regions
-      distance -= gap;
-      return nextstart - distance;
+      LOCK.writeLock().unlock();
     }
-    return start - distance;
-
   }
 
   /**
-   * Use this method to determine where the next hiddenRegion starts
-   * 
-   * @param hiddenRegion
-   *          index of hidden region (counts from 0)
-   * @return column number in visible view
+   * Unhides, and adds to the selection list, all hidden columns
    */
-  public int findHiddenRegionPosition(int hiddenRegion)
+  public void revealAllHiddenColumns(ColumnSelection sel)
   {
-    int result = 0;
-    if (hiddenColumns != null)
+    try
     {
-      int index = 0;
-      int gaps = 0;
-      do
+      LOCK.writeLock().lock();
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (hiddenRegion == 0)
+        Iterator<int[]> it = hiddenColumns.iterator();
+        while (it.hasNext())
         {
-          return region[0];
+          int[] region = it.next();
+          for (int j = region[0]; j < region[1] + 1; j++)
+          {
+            sel.addElement(j);
+          }
         }
+        hiddenColumns = null;
+        cursor.resetCursor(hiddenColumns);
+        numColumns = 0;
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * Reveals, and marks as selected, the hidden column range with the given
+   * start column
+   * 
+   * @param start
+   *          the start column to look for
+   * @param sel
+   *          the column selection to add the hidden column range to
+   */
+  public void revealHiddenColumns(int start, ColumnSelection sel)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
 
-        gaps += region[1] + 1 - region[0];
-        result = region[1] + 1;
-        index++;
-      } while (index <= hiddenRegion);
+      if (hiddenColumns != null)
+      {
+        int regionIndex = cursor.findRegionForColumn(start)
+                .getRegionIndex();
 
-      result -= gaps;
+        if (regionIndex != -1 && regionIndex != hiddenColumns.size())
+        {
+          // regionIndex is the region which either contains start
+          // or lies to the right of start
+          int[] region = hiddenColumns.get(regionIndex);
+          if (start == region[0])
+          {
+            for (int j = region[0]; j < region[1] + 1; j++)
+            {
+              sel.addElement(j);
+            }
+            int colsToRemove = region[1] - region[0] + 1;
+            hiddenColumns.remove(regionIndex);
+
+            if (hiddenColumns.isEmpty())
+            {
+              hiddenColumns = null;
+              numColumns = 0;
+            }
+            else
+            {
+              numColumns -= colsToRemove;
+            }
+            cursor.updateForDeletedRegion(hiddenColumns);
+          }
+        }
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
+  }
+
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   *          sequence in al which sequences are aligned to
+   * @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)
+  {
+    int profsqpos = 0;
 
-    return result;
+    char gc = al.getGapCharacter();
+    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+    HiddenColumns nview = (HiddenColumns) alandhidden[1];
+    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+    nview.propagateInsertions(profileseq, al, origseq);
+    return nview;
   }
 
   /**
-   * 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 profileseq
+   *          sequence in al which corresponds to origseq
+   * @param al
+   *          alignment which is to have gaps inserted into it
+   * @param origseq
+   *          sequence corresponding to profileseq which defines gap map for
+   *          modifying al
    */
-  public int getHiddenBoundaryRight(int alPos)
+  private void propagateInsertions(SequenceI profileseq, AlignmentI al,
+          SequenceI origseq)
   {
-    if (hiddenColumns != null)
+    try
     {
-      int index = 0;
-      do
+      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.hideColumns(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();
+      List<int[]> newhidden = new ArrayList<>();
+
+      int numGapsBefore = 0;
+      int gapPosition = 0;
+      while (regions.hasNext())
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (alPos < region[0])
+        // 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])
         {
-          return region[0];
+          gapPosition++;
+          if (gaps.get(gapPosition))
+          {
+            numGapsBefore++;
+          }
         }
 
-        index++;
-      } while (index < hiddenColumns.size());
-    }
+        int left = region[0] - numGapsBefore;
+        int right = region[1] - numGapsBefore;
+        newhidden.add(new int[] { left, right });
 
-    return alPos;
+        // 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);
 
+      }
+      hiddenColumns = newhidden;
+      cursor.resetCursor(hiddenColumns);
+      numColumns = 0;
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
   }
 
   /**
-   * This method returns the leftmost limit of a region of an alignment with
-   * hidden columns. In otherwords, the previous hidden column.
+   * Pad gaps in all sequences in alignment except profileseq
    * 
-   * @param index
-   *          int
+   * @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
    */
-  public int getHiddenBoundaryLeft(int alPos)
+  private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+          AlignmentI al)
   {
-    if (hiddenColumns != null)
+    // loop over the sequences and pad with gaps where required
+    for (int s = 0, ns = al.getHeight(); s < ns; s++)
     {
-      int index = hiddenColumns.size() - 1;
-      do
+      SequenceI sqobj = al.getSequenceAt(s);
+      if (sqobj != profileseq)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (alPos > region[1])
+        String sq = al.getSequenceAt(s).getSequenceAsString();
+        if (sq.length() <= pos)
         {
-          return region[1];
+          // 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();
         }
-
-        index--;
-      } while (index > -1);
+        else
+        {
+          al.getSequenceAt(s).setSequence(
+                  sq.substring(0, pos) + sb.toString() + sq.substring(pos));
+        }
+      }
     }
+  }
 
-    return alPos;
+  /*
+   * Methods which only need read access to the hidden columns collection. 
+   * These methods should use a readLock to prevent other threads changing
+   * the hidden columns collection while it is in use.
+   */
 
+  /**
+   * 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)
+      {
+        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);
+          }
+        }
+      }
+      return regionBuilder.toString();
+    } finally
+    {
+      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.
+   * Find the number of hidden columns
    * 
-   * @param pos
-   *          int
+   * @return number of hidden columns
    */
-  private int getHiddenIndexLeft(int pos)
+  public int getSize()
   {
-    if (hiddenColumns != null)
+    try
     {
-      int index = hiddenColumns.size() - 1;
-      do
+      LOCK.readLock().lock();
+
+      if (numColumns == 0 && hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (pos > region[1])
+        // numColumns is out of date, so recalculate
+        int size = 0;
+
+        Iterator<int[]> it = hiddenColumns.iterator();
+        while (it.hasNext())
         {
-          return index;
+          int[] range = it.next();
+          size += range[1] - range[0] + 1;
         }
 
-        index--;
-      } while (index > -1);
-    }
-
-    return -1;
+        numColumns = size;
+      }
 
+      return numColumns;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
-   * Adds the specified column range to the hidden columns
+   * Get the number of distinct hidden regions
    * 
-   * @param start
-   * @param end
+   * @return number of regions
    */
-  public void hideColumns(int start, int end)
+  public int getNumberOfRegions()
   {
-    if (hiddenColumns == null)
+    try
+    {
+      LOCK.readLock().lock();
+      int num = 0;
+      if (hasHiddenColumns())
+      {
+        num = hiddenColumns.size();
+      }
+      return num;
+    } finally
     {
-      hiddenColumns = new Vector<int[]>();
+      LOCK.readLock().unlock();
     }
+  }
 
-    /*
-     * traverse existing hidden ranges and insert / amend / append as
-     * appropriate
-     */
-    for (int i = 0; i < hiddenColumns.size(); i++)
+  @Override
+  public boolean equals(Object obj)
+  {
+    try
     {
-      int[] region = hiddenColumns.elementAt(i);
+      LOCK.readLock().lock();
 
-      if (end < region[0] - 1)
+      if (!(obj instanceof HiddenColumns))
       {
-        /*
-         * insert discontiguous preceding range
-         */
-        hiddenColumns.insertElementAt(new int[] { start, end }, i);
-        return;
+        return false;
       }
+      HiddenColumns that = (HiddenColumns) obj;
 
-      if (end <= region[1])
+      /*
+       * check hidden columns are either both null, or match
+       */
+      if (this.hiddenColumns == null)
       {
-        /*
-         * new range overlaps existing, or is contiguous preceding it - adjust
-         * start column
-         */
-        region[0] = Math.min(region[0], start);
-        return;
+        return (that.hiddenColumns == null);
       }
-
-      if (start <= region[1] + 1)
+      if (that.hiddenColumns == null
+              || that.hiddenColumns.size() != this.hiddenColumns.size())
       {
-        /*
-         * 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)
-          {
-            /*
-             * gap to next hidden range - no more to update
-             */
-            break;
-          }
-          region[1] = Math.max(nextRegion[1], end);
-          hiddenColumns.remove(i + 1);
-        }
-        return;
+        return false;
       }
-    }
-
-    /*
-     * remaining case is that the new range follows everything else
-     */
-    hiddenColumns.addElement(new int[] { start, end });
-  }
 
-  public boolean isVisible(int column)
-  {
-    if (hiddenColumns != null)
-    {
-      for (int[] region : hiddenColumns)
+      Iterator<int[]> it = hiddenColumns.iterator();
+      Iterator<int[]> thatit = that.iterator();
+      while (it.hasNext())
       {
-        if (column >= region[0] && column <= region[1])
+        int[] thisRange = it.next();
+        int[] thatRange = thatit.next();
+        if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
         {
           return false;
         }
       }
+      return true;
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-
-    return true;
   }
 
   /**
-   * ColumnSelection
+   * Return absolute column index for a visible column index
+   * 
+   * @param column
+   *          int column index in alignment view (count from zero)
+   * @return alignment column index for column
    */
-  public HiddenColumns()
+  public int visibleToAbsoluteColumn(int column)
   {
+    try
+    {
+      LOCK.readLock().lock();
+      int result = column;
+
+      if (hiddenColumns != null)
+      {
+        result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
+      }
+
+      return result;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
-   * Copy constructor
+   * Use this method to find out where a column will appear in the visible
+   * alignment when hidden columns exist. If the column is not visible, then the
+   * index of the next visible column on the left will be returned (or 0 if
+   * there is no visible column on the left)
    * 
-   * @param copy
+   * @param hiddenColumn
+   *          the column index in the full alignment including hidden columns
+   * @return the position of the column in the visible alignment
    */
-  public HiddenColumns(HiddenColumns copy)
+  public int absoluteToVisibleColumn(int hiddenColumn)
   {
-    if (copy != null)
+    try
     {
-      if (copy.hiddenColumns != null)
+      LOCK.readLock().lock();
+      int result = hiddenColumn;
+
+      if (hiddenColumns != null)
       {
-        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
-        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+        HiddenCursorPosition cursorPos = cursor
+                .findRegionForColumn(hiddenColumn);
+        int index = cursorPos.getRegionIndex();
+        int hiddenBeforeCol = cursorPos.getHiddenSoFar();
+    
+        // just subtract hidden cols count - this works fine if column is
+        // visible
+        result = hiddenColumn - hiddenBeforeCol;
+    
+        // now check in case column is hidden - it will be in the returned
+        // hidden region
+        if (index < hiddenColumns.size())
         {
-          int[] rh, cp;
-          rh = copy.hiddenColumns.elementAt(i);
-          if (rh != null)
+          int[] region = hiddenColumns.get(index);
+          if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
           {
-            cp = new int[rh.length];
-            System.arraycopy(rh, 0, cp, 0, rh.length);
-            hiddenColumns.addElement(cp);
+            // actually col is hidden, return region[0]-1
+            // unless region[0]==0 in which case return 0
+            if (region[0] == 0)
+            {
+              result = 0;
+            }
+            else
+            {
+              result = region[0] - 1 - hiddenBeforeCol;
+            }
           }
         }
       }
+
+      return result; // return the shifted position after removing hidden
+                     // columns.
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * propagate shift in alignment columns to column selection
+   * Find the visible column which is a given visible number of columns to the
+   * left of another visible column. i.e. for a startColumn x, the column which
+   * is distance 1 away will be column x-1.
    * 
-   * @param start
-   *          beginning of edit
-   * @param left
-   *          shift in edit (+ve for removal, or -ve for inserts)
+   * @param visibleDistance
+   *          the number of visible columns to offset by
+   * @param startColumn
+   *          the column to start from
+   * @return the position of the column in the visible alignment
    */
-  public List<int[]> compensateForEdit(int start, int change,
-          ColumnSelection sel)
+  public int subtractVisibleColumns(int visibleDistance, int startColumn)
   {
-    List<int[]> deletedHiddenColumns = null;
-
-    if (hiddenColumns != null)
+    try
     {
-      deletedHiddenColumns = new ArrayList<int[]>();
-      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);
+      LOCK.readLock().lock();
+      int distance = visibleDistance;
 
-          hiddenColumns.removeElementAt(i);
-          i--;
-          hSize--;
-          continue;
-        }
+      // in case startColumn is in a hidden region, move it to the left
+      int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn));
 
-        if (region[0] > start)
-        {
-          region[0] -= change;
-          region[1] -= change;
-        }
+      Iterator<int[]> it = new ReverseRegionsIterator(0, start,
+              hiddenColumns);
+
+      while (it.hasNext() && (distance > 0))
+      {
+        int[] region = it.next();
 
-        if (region[0] < 0)
+        if (start > region[1])
         {
-          region[0] = 0;
+          // subtract the gap to right of region from distance
+          if (start - region[1] <= distance)
+          {
+            distance -= start - region[1];
+            start = region[0] - 1;
+          }
+          else
+          {
+            start = start - distance;
+            distance = 0;
+          }
         }
-
       }
+      return start - distance;
 
-      this.revealHiddenColumns(0, sel);
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-
-    return deletedHiddenColumns;
   }
 
   /**
-   * propagate shift in alignment columns to column selection special version of
-   * compensateForEdit - allowing for edits within hidden regions
+   * This method returns the rightmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the next hidden column.
    * 
-   * @param start
-   *          beginning of edit
-   * @param left
-   *          shift in edit (+ve for removal, or -ve for inserts)
+   * @param alPos
+   *          the absolute (visible) alignmentPosition to find the next hidden
+   *          column for
+   * @return the index of the next hidden column, or alPos if there is no next
+   *         hidden column
    */
-  public void compensateForDelEdits(int start, int change)
+  public int getHiddenBoundaryRight(int alPos)
   {
-    if (hiddenColumns != null)
+    try
     {
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      LOCK.readLock().lock();
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(i);
-        if (region[0] >= start)
+        int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+        if (index < hiddenColumns.size())
         {
-          region[0] -= change;
-        }
-        if (region[1] >= start)
-        {
-          region[1] -= change;
-        }
-        if (region[1] < region[0])
-        {
-          hiddenColumns.removeElementAt(i--);
+          int[] region = hiddenColumns.get(index);
+          if (alPos < region[0])
+          {
+            return region[0];
+          }
+          else if ((alPos <= region[1])
+                  && (index + 1 < hiddenColumns.size()))
+          {
+            // alPos is within a hidden region, return the next one
+            // if there is one
+            region = hiddenColumns.get(index + 1);
+            return region[0];
+          }
         }
+      }
+      return alPos;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
 
-        if (region[0] < 0)
-        {
-          region[0] = 0;
-        }
-        if (region[1] < 0)
+  /**
+   * This method returns the leftmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the previous hidden column.
+   * 
+   * @param alPos
+   *          the absolute (visible) alignmentPosition to find the previous
+   *          hidden column for
+   */
+  public int getHiddenBoundaryLeft(int alPos)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+
+      if (hiddenColumns != null)
+      {
+        int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+
+        if (index > 0)
         {
-          region[1] = 0;
+          int[] region = hiddenColumns.get(index - 1);
+          return region[1];
         }
       }
+      return alPos;
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
   }
 
+
   /**
-   * return all visible segments between the given start and end boundaries
+   * Answers if a column in the alignment is visible
    * 
-   * @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
+   * @param column
+   *          absolute position of column in the alignment
+   * @return true if column is visible
    */
-  public int[] getVisibleContigs(int start, int end)
+  public boolean isVisible(int column)
   {
-    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    try
     {
-      List<int[]> visiblecontigs = new ArrayList<int[]>();
-      List<int[]> regions = getListOfCols();
+      LOCK.readLock().lock();
 
-      int vstart = start;
-      int[] region;
-      int hideStart, hideEnd;
-
-      for (int j = 0; vstart < end && j < regions.size(); j++)
+      int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+      if (regionindex > -1 && regionindex < hiddenColumns.size())
       {
-        region = regions.get(j);
-        hideStart = region[0];
-        hideEnd = region[1];
-
-        if (hideEnd < vstart)
+        int[] region = hiddenColumns.get(regionindex);
+        // already know that column <= region[1] as cursor returns containing
+        // region or region to right
+        if (column >= region[0])
         {
-          continue;
-        }
-        if (hideStart > vstart)
-        {
-          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
+          return false;
         }
-        vstart = hideEnd + 1;
       }
+      return true;
 
-      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
+    } finally
     {
-      return new int[] { start, end - 1 };
+      LOCK.readLock().unlock();
     }
   }
 
+  /**
+   * Get the visible sections of a set of sequences
+   * 
+   * @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 String[] getVisibleSequenceStrings(int start, int end,
           SequenceI[] seqs)
   {
-    int i, iSize = seqs.length;
-    String selections[] = new String[iSize];
-    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    try
     {
-      for (i = 0; i < iSize; i++)
+      LOCK.readLock().lock();
+      int iSize = seqs.length;
+      String[] selections = new String[iSize];
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
-        StringBuffer visibleSeq = new StringBuffer();
-        List<int[]> regions = getListOfCols();
-
-        int blockStart = start, blockEnd = end;
-        int[] region;
-        int hideStart, hideEnd;
-
-        for (int j = 0; j < regions.size(); j++)
+        for (int i = 0; i < iSize; i++)
         {
-          region = regions.get(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-
-          if (hideStart < start)
-          {
-            continue;
-          }
+          StringBuffer visibleSeq = new StringBuffer();
 
-          blockStart = Math.min(blockStart, hideEnd + 1);
-          blockEnd = Math.min(blockEnd, hideStart);
+          Iterator<int[]> blocks = new VisibleContigsIterator(start,
+                  end + 1, hiddenColumns);
 
-          if (blockStart > blockEnd)
+          while (blocks.hasNext())
           {
-            break;
+            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]));
+            }
           }
 
-          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
-          blockStart = hideEnd + 1;
-          blockEnd = end;
+          selections[i] = visibleSeq.toString();
         }
-
-        if (end > blockStart)
+      }
+      else
+      {
+        for (int i = 0; i < iSize; i++)
         {
-          visibleSeq.append(seqs[i].getSequence(blockStart, end));
+          selections[i] = seqs[i].getSequenceAsString(start, end);
         }
-
-        selections[i] = visibleSeq.toString();
       }
-    }
-    else
+
+      return selections;
+    } finally
     {
-      for (i = 0; i < iSize; i++)
-      {
-        selections[i] = seqs[i].getSequenceAsString(start, end);
-      }
+      LOCK.readLock().unlock();
     }
-
-    return selections;
   }
 
   /**
-   * 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
+   * 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
-   * @return int[] { visible start, visible end, first seqpos, last seqpos,
-   *         alignment index for seq start, alignment index for seq end }
+   *          sequence to find position for
+   * @return visible start position
    */
-  public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+  public int locateVisibleStartOfSequence(SequenceI seq)
   {
-    int fpos = seq.getStart(), lpos = seq.getEnd();
-    int start = 0;
-
-    if (hiddenColumns == null || hiddenColumns.size() == 0)
+    try
     {
-      int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
-      return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
-    }
+      LOCK.readLock().lock();
+      int start = 0;
 
-    // Simply walk along the sequence whilst watching for hidden column
-    // boundaries
-    List<int[]> regions = getListOfCols();
-    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)))
+      if (hiddenColumns == null || hiddenColumns.size() == 0)
       {
-        // keep track of first/last column
-        // containing sequence data regardless of visibility
-        if (firstP == -1)
-        {
-          firstP = p;
-        }
-        lastP = p;
+        return seq.findIndex(seq.getStart()) - 1;
+      }
+
+      // 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++)
+      {
+        // get alignment position of this residue in the sequence
+        int p = seq.findIndex(i) - 1;
+
         // update hidden region start/end
-        while (hideEnd < p && rcount < regions.size())
+        while (hideEnd < p && regions.hasNext())
         {
-          int[] region = regions.get(rcount++);
+          int[] region = regions.next();
           visPrev = visNext;
           visNext += region[0] - visPrev;
           hideStart = region[0];
@@ -704,26 +1058,21 @@ public class HiddenColumns
         // update visible boundary for sequence
         if (p < hideStart)
         {
-          if (!foundStart)
-          {
-            fpos = spos;
-            start = p;
-            foundStart = true;
-          }
-          lastvispos = p;
-          lpos = spos;
+          start = p;
+          foundStart = true;
         }
-        // look for next sequence position
-        spos++;
       }
-    }
-    if (foundStart)
+
+      if (foundStart)
+      {
+        return absoluteToVisibleColumn(start);
+      }
+      // otherwise, sequence was completely hidden
+      return visPrev;
+    } finally
     {
-      return new int[] { findColumnPosition(start),
-          findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+      LOCK.readLock().unlock();
     }
-    // otherwise, sequence was completely hidden
-    return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
   }
 
   /**
@@ -734,7 +1083,12 @@ public class HiddenColumns
    */
   public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
   {
-    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+    if (alignmentAnnotation != null
+            && alignmentAnnotation.annotations != null)
+    {
+      makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+            alignmentAnnotation);
+    }
   }
 
   /**
@@ -751,78 +1105,81 @@ public class HiddenColumns
   public void makeVisibleAnnotation(int start, int end,
           AlignmentAnnotation alignmentAnnotation)
   {
-    if (alignmentAnnotation.annotations == null)
-    {
-      return;
-    }
-    if (start == end && end == -1)
-    {
-      start = 0;
-      end = alignmentAnnotation.annotations.length;
-    }
-    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    try
     {
-      // then mangle the alignmentAnnotation annotation array
-      Vector<Annotation[]> annels = new Vector<Annotation[]>();
-      Annotation[] els = null;
-      List<int[]> regions = getListOfCols();
-      int blockStart = start, blockEnd = end;
-      int[] region;
-      int hideStart, hideEnd, w = 0;
+      LOCK.readLock().lock();
 
-      for (int j = 0; j < regions.size(); j++)
-      {
-        region = regions.get(j);
-        hideStart = region[0];
-        hideEnd = region[1];
+      int startFrom = start;
+      int endAt = end;
 
-        if (hideStart < start)
+      if (alignmentAnnotation != null
+              && alignmentAnnotation.annotations != null)
+      {
+        if (hiddenColumns != null && hiddenColumns.size() > 0)
         {
-          continue;
+          removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
         }
-
-        blockStart = Math.min(blockStart, hideEnd + 1);
-        blockEnd = Math.min(blockEnd, hideStart);
-
-        if (blockStart > blockEnd)
+        else
         {
-          break;
+          alignmentAnnotation.restrict(startFrom, endAt);
         }
-
-        annels.addElement(els = new Annotation[blockEnd - blockStart]);
-        System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
-                0, els.length);
-        w += els.length;
-        blockStart = hideEnd + 1;
-        blockEnd = end;
       }
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
 
-      if (end > blockStart)
+  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())
       {
-        annels.addElement(els = new Annotation[end - blockStart + 1]);
-        if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+        // copy just the visible segment of the annotation row
+        copylength = annotationLength;
+      }
+      else
+      {
+        if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
         {
           // copy just the visible segment of the annotation row
-          System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                  els, 0, els.length);
+          copylength = annotationLength;
         }
         else
         {
           // copy to the end of the annotation row
-          System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                  els, 0,
-                  (alignmentAnnotation.annotations.length - blockStart));
+          copylength = alignmentAnnotation.annotations.length - block[0];
         }
-        w += els.length;
-      }
-      if (w == 0)
-      {
-        return;
       }
-
+      
+      els = new Annotation[annotationLength];
+      annels.add(els);
+      System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
+              copylength);
+      w += annotationLength;
+    }
+    
+    if (w != 0)
+    {
       alignmentAnnotation.annotations = new Annotation[w];
-      w = 0;
 
+      w = 0;
       for (Annotation[] chnk : annels)
       {
         System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
@@ -830,10 +1187,6 @@ public class HiddenColumns
         w += chnk.length;
       }
     }
-    else
-    {
-      alignmentAnnotation.restrict(start, end);
-    }
   }
 
   /**
@@ -842,400 +1195,331 @@ public class HiddenColumns
    */
   public boolean hasHiddenColumns()
   {
-    return hiddenColumns != null && hiddenColumns.size() > 0;
+    try
+    {
+      LOCK.readLock().lock();
+
+      // we don't use getSize()>0 here because it has to iterate over
+      // the full hiddenColumns collection and so will be much slower
+      return hiddenColumns != null && hiddenColumns.size() > 0;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
    * 
-   * @return true if there are more than one set of columns hidden
+   * @return true if there is more than one hidden column region
    */
-  public boolean hasManyHiddenColumns()
+  public boolean hasMultiHiddenColumnRegions()
   {
-    return hiddenColumns != null && hiddenColumns.size() > 1;
+    try
+    {
+      LOCK.readLock().lock();
+      return hiddenColumns != null && hiddenColumns.size() > 1;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
+
   /**
-   * mark the columns corresponding to gap characters as hidden in the column
-   * selection
-   * 
-   * @param sr
+   * Returns a hashCode built from hidden column ranges
    */
-  public void hideInsertionsFor(SequenceI sr)
+  @Override
+  public int hashCode()
   {
-    List<int[]> inserts = sr.getInsertions();
-    for (int[] r : inserts)
+    try
+    {
+      LOCK.readLock().lock();
+      int hashCode = 1;
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
+      {
+        int[] hidden = it.next();
+        hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+        hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
+      }
+      return hashCode;
+    } finally
     {
-      hideColumns(r[0], r[1]);
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * Unhides, and adds to the selection list, all hidden columns
+   * Hide columns corresponding to the marked bits
+   * 
+   * @param inserts
+   *          - columns map to bits starting from zero
    */
-  public void revealAllHiddenColumns(ColumnSelection sel)
+  public void hideColumns(BitSet inserts)
   {
-    if (hiddenColumns != null)
+    try
     {
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      LOCK.writeLock().lock();
+      for (int firstSet = inserts
+              .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
+                      .nextSetBit(lastSet))
       {
-        int[] region = hiddenColumns.elementAt(i);
-        for (int j = region[0]; j < region[1] + 1; j++)
-        {
-          sel.addElement(j);
-        }
+        lastSet = inserts.nextClearBit(firstSet);
+        hideColumns(firstSet, lastSet - 1);
       }
+      cursor.resetCursor(hiddenColumns);
+      numColumns = 0;
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
-
-    hiddenColumns = null;
   }
 
   /**
-   * Reveals, and marks as selected, the hidden column range with the given
-   * start column
    * 
-   * @param start
+   * @param inserts
+   *          BitSet where hidden columns will be marked
    */
-  public void revealHiddenColumns(int start, ColumnSelection sel)
+  public void markHiddenRegions(BitSet inserts)
   {
-    for (int i = 0; i < hiddenColumns.size(); i++)
+    try
     {
-      int[] region = hiddenColumns.elementAt(i);
-      if (start == region[0])
+      LOCK.readLock().lock();
+      if (hiddenColumns == null)
       {
-        for (int j = region[0]; j < region[1] + 1; j++)
-        {
-          sel.addElement(j);
-        }
-
-        hiddenColumns.removeElement(region);
-        break;
+        return;
       }
-    }
-    if (hiddenColumns.size() == 0)
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
+      {
+        int[] range = it.next();
+        inserts.set(range[0], range[1] + 1);
+      }
+    } finally
     {
-      hiddenColumns = null;
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * removes intersection of position,length ranges in deletions from the
-   * start,end regions marked in intervals.
+   * Calculate the visible start and end index of an alignment.
    * 
-   * @param shifts
-   * @param intervals
-   * @return
+   * @param width
+   *          full alignment width
+   * @return integer array where: int[0] = startIndex, and int[1] = endIndex
    */
-  private boolean pruneIntervalVector(final List<int[]> shifts,
-          Vector<int[]> intervals)
+  public int[] getVisibleStartAndEndIndex(int width)
   {
-    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)
+    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)
       {
-        if (i < j)
-        {
-          hr = intervals.elementAt(++i);
-        }
-        else
-        {
-          i++;
-        }
-        continue;
+        return new int[] { startPos, endPos };
       }
-      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;
+
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
+      {
+        int[] range = it.next();
+        lowestRange = (range[0] <= startPos) ? range : lowestRange;
+        higestRange = (range[1] >= endPos) ? range : higestRange;
       }
-      boolean leadinghn = hr[0] >= sr[0];
-      boolean leadinghc = hr[0] < endshift;
-      boolean trailinghc = hr[1] < endshift;
-      if (leadinghn)
+
+      if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
       {
-        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;
-        }
+        startPos = alignmentStartEnd[0];
       }
-      if (!leadinghn)
+      else
       {
-        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;
-        }
+        startPos = lowestRange[1] + 1;
+      }
+
+      if (higestRange[0] == -1) // includes (higestRange[1] == -1)
+      {
+        endPos = alignmentStartEnd[1];
       }
+      else
+      {
+        endPos = higestRange[0] - 1;
+      }
+      return new int[] { startPos, endPos };
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-    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.
+   * Finds the hidden region (if any) which starts or ends at res
    * 
-   * @param deletions
+   * @param res
+   *          visible residue position, unadjusted for hidden columns
+   * @return region as [start,end] or null if no matching region is found. If
+   *         res is adjacent to two regions, returns the left region.
    */
-  public void pruneDeletions(List<int[]> shifts)
+  public int[] getRegionWithEdgeAtRes(int res)
   {
-    // delete any intervals intersecting.
-    if (hiddenColumns != null)
+    try
     {
-      pruneIntervalVector(shifts, hiddenColumns);
-      if (hiddenColumns != null && hiddenColumns.size() == 0)
+      LOCK.readLock().lock();
+      int adjres = visibleToAbsoluteColumn(res);
+
+      int[] reveal = null;
+
+      if (hiddenColumns != null)
       {
-        hiddenColumns = null;
+        // look for a region ending just before adjres
+        int regionindex = cursor.findRegionForColumn(adjres - 1)
+                .getRegionIndex();
+        if (regionindex < hiddenColumns.size()
+                && hiddenColumns.get(regionindex)[1] == adjres - 1)
+        {
+          reveal = hiddenColumns.get(regionindex);
+        }
+        // check if the region ends just after adjres
+        else if (regionindex < hiddenColumns.size()
+                && hiddenColumns.get(regionindex)[0] == adjres + 1)
+        {
+          reveal = hiddenColumns.get(regionindex);
+        }
       }
+      return reveal;
+
+    } finally
+    {
+      LOCK.readLock().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.
+   * Return an iterator over the hidden regions
    */
-  public static HiddenColumns propagateInsertions(SequenceI profileseq,
-          AlignmentI al, AlignmentView input)
+  public Iterator<int[]> iterator()
   {
-    int profsqpos = 0;
-
-    char gc = al.getGapCharacter();
-    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
-    HiddenColumns nview = (HiddenColumns) alandhidden[1];
-    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
-    nview.propagateInsertions(profileseq, al, origseq);
-    return nview;
+    try
+    {
+      LOCK.readLock().lock();
+      return new HiddenColsIterator(hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
+   * Return a bounded iterator over the hidden regions
    * 
-   * @param profileseq
-   *          - sequence in al which corresponds to origseq
-   * @param al
-   *          - alignment which is to have gaps inserted into it
-   * @param origseq
-   *          - sequence corresponding to profileseq which defines gap map for
-   *          modifying al
+   * @param start
+   *          position to start from (inclusive, absolute column position)
+   * @param end
+   *          position to end at (inclusive, absolute column position)
+   * @return
    */
-  private void propagateInsertions(SequenceI profileseq, AlignmentI al,
-          SequenceI origseq)
+  public Iterator<int[]> getBoundedIterator(int start, int end)
   {
-    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++)
-      {
-        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();
-        }
-      }
+      LOCK.readLock().lock();
+      return new HiddenColsIterator(start, end, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * remove any hiddenColumns or selected columns and shift remaining based on a
-   * series of position, range deletions.
+   * Return a bounded iterator over the *visible* start positions of hidden
+   * regions
    * 
-   * @param deletions
+   * @param start
+   *          position to start from (inclusive, visible column position)
+   * @param end
+   *          position to end at (inclusive, visible column position)
    */
-  private void pruneDeletions(ShiftList deletions)
+  public Iterator<Integer> getBoundedStartIterator(int start, int end)
   {
-    if (deletions != null)
+    try
     {
-      final List<int[]> shifts = deletions.getShifts();
-      if (shifts != null && shifts.size() > 0)
-      {
-        pruneDeletions(shifts);
-
-        // and shift the rest.
-        this.compensateForEdits(deletions);
-      }
+      LOCK.readLock().lock();
+
+      // get absolute position of column in alignment
+      int absoluteStart = visibleToAbsoluteColumn(start);
+
+      // Get cursor position and supply it to the iterator:
+      // Since we want visible region start, we look for a cursor for the
+      // (absoluteStart-1), then if absoluteStart is the start of a visible
+      // region we'll get the cursor pointing to the region before, which is
+      // what we want
+      HiddenCursorPosition pos = cursor
+              .findRegionForColumn(absoluteStart - 1);
+
+      return new BoundedStartRegionIterator(pos, start, end,
+              hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
   }
 
   /**
-   * Adjust hidden column boundaries based on a series of column additions or
-   * deletions in visible regions.
+   * Return an iterator over visible *columns* (not regions) between the given
+   * start and end boundaries
    * 
-   * @param shiftrecord
-   * @return
+   * @param start
+   *          first column (inclusive)
+   * @param end
+   *          last column (inclusive)
    */
-  private ShiftList compensateForEdits(ShiftList shiftrecord)
+  public Iterator<Integer> getVisibleColsIterator(int start, int end)
   {
-    if (shiftrecord != null)
+    try
     {
-      final List<int[]> shifts = shiftrecord.getShifts();
-      if (shifts != null && shifts.size() > 0)
-      {
-        int shifted = 0;
-        for (int i = 0, j = shifts.size(); i < j; i++)
-        {
-          int[] sh = shifts.get(i);
-          compensateForDelEdits(shifted + sh[0], sh[1]);
-          shifted -= sh[1];
-        }
-      }
-      return shiftrecord.getInverse();
+      LOCK.readLock().lock();
+      return new VisibleColsIterator(start, end, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-    return null;
   }
 
   /**
-   * Returns a hashCode built from hidden column ranges
+   * 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
+   * @param useVisibleCoords
+   *          if true, start and end are visible column positions, not absolute
+   *          positions*
    */
-  public int hashCode(int hc)
+  public Iterator<int[]> getVisContigsIterator(int start, int end,
+          boolean useVisibleCoords)
   {
-    int hashCode = hc;
-    if (hiddenColumns != null)
+    int adjstart = start;
+    int adjend = end;
+    if (useVisibleCoords)
     {
-      for (int[] hidden : hiddenColumns)
-      {
-        hashCode = 31 * hashCode + hidden[0];
-        hashCode = 31 * hashCode + hidden[1];
-      }
+      adjstart = visibleToAbsoluteColumn(start);
+      adjend = visibleToAbsoluteColumn(end);
     }
-    return hashCode;
-  }
 
+    try
+    {
+      LOCK.readLock().lock();
+      return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
 }