X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=c0a43eea64ba09df70ed8e5686e58334ecb772f0;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
new file mode 100644
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+++ b/src/jalview/datamodel/HiddenColumns.java
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+/*
+ * 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.List;
+import java.util.Vector;
+import java.util.concurrent.locks.ReentrantReadWriteLock;
+
+public class HiddenColumns
+{
+  private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+
+  /*
+   * list of hidden column [start, end] ranges; the list is maintained in
+   * ascending start column order
+   */
+  private ArrayList<int[]> hiddenColumns;
+
+  /**
+   * Constructor
+   */
+  public HiddenColumns()
+  {
+  }
+
+  /**
+   * Copy constructor
+   * 
+   * @param copy
+   */
+  public HiddenColumns(HiddenColumns copy)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      if (copy != null)
+      {
+        if (copy.hiddenColumns != null)
+        {
+          hiddenColumns = copy.copyHiddenRegionsToArrayList();
+        }
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * This method is used to return all the HiddenColumn regions and is intended
+   * to remain private. External callers which need a copy of the regions can
+   * call getHiddenColumnsCopyAsList.
+   * 
+   * @return empty list or List of hidden column intervals
+   */
+  private List<int[]> getHiddenRegions()
+  {
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : hiddenColumns;
+  }
+
+  /**
+   * Output regions data as a string. String is in the format:
+   * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
+   * 
+   * @param delimiter
+   *          string to delimit regions
+   * @param betweenstring
+   *          to put between start and end region values
+   * @return regions formatted according to delimiter and between strings
+   */
+  public String regionsToString(String delimiter, String between)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      StringBuilder regionBuilder = new StringBuilder();
+      if (hiddenColumns != null)
+      {
+        for (int[] range : hiddenColumns)
+        {
+          regionBuilder.append(delimiter).append(range[0]).append(between)
+                  .append(range[1]);
+        }
+
+        regionBuilder.deleteCharAt(0);
+      }
+      return regionBuilder.toString();
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * Find the number of hidden columns
+   * 
+   * @return number of hidden columns
+   */
+  public int getSize()
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int size = 0;
+      if (hasHiddenColumns())
+      {
+        for (int[] range : hiddenColumns)
+        {
+          size += range[1] - range[0] + 1;
+        }
+      }
+      return size;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  @Override
+  public boolean equals(Object obj)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+
+      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;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * 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 int adjustForHiddenColumns(int column)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int result = column;
+      if (hiddenColumns != null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = hiddenColumns.get(i);
+          if (result >= region[0])
+          {
+            result += region[1] - region[0] + 1;
+          }
+        }
+      }
+      return result;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * 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.
+   * 
+   * @param hiddenColumn
+   *          the column index in the full alignment including hidden columns
+   * @return the position of the column in the visible alignment
+   */
+  public int findColumnPosition(int hiddenColumn)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int result = hiddenColumn;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int[] region;
+        do
+        {
+          region = hiddenColumns.get(index++);
+          if (hiddenColumn > region[1])
+          {
+            result -= region[1] + 1 - region[0];
+          }
+        } while ((hiddenColumn > region[1])
+                && (index < hiddenColumns.size()));
+
+        if (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
+
+          // However, if the region begins at 0 we cannot return region[0]-1
+          // just return 0
+          if (region[0] == 0)
+          {
+            return 0;
+          }
+          else
+          {
+            return result - (hiddenColumn - region[0] + 1);
+          }
+        }
+      }
+      return result; // return the shifted position after removing hidden
+                     // columns.
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * 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 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 int subtractVisibleColumns(int visibleDistance, int startColumn)
+  {
+    try
+    {
+
+      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();
+    }
+
+  }
+
+  /**
+   * 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 = null;
+
+      if (hiddenColumns != null)
+      {
+        positions = new ArrayList<>(hiddenColumns.size());
+
+        positions.add(hiddenColumns.get(0)[0]);
+        for (int i = 1; i < hiddenColumns.size(); ++i)
+        {
+
+          int result = 0;
+          if (hiddenColumns != null)
+          {
+            int index = 0;
+            int gaps = 0;
+            do
+            {
+              int[] region = hiddenColumns.get(index);
+              gaps += region[1] + 1 - region[0];
+              result = region[1] + 1;
+              index++;
+            } while (index <= i);
+
+            result -= gaps;
+          }
+          positions.add(result);
+        }
+      }
+      else
+      {
+        positions = new ArrayList<>();
+      }
+
+      return positions;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * This method returns the rightmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the next hidden column.
+   * 
+   * @param index
+   *          int
+   */
+  public int getHiddenBoundaryRight(int alPos)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        do
+        {
+          int[] region = hiddenColumns.get(index);
+          if (alPos < region[0])
+          {
+            return region[0];
+          }
+
+          index++;
+        } while (index < hiddenColumns.size());
+      }
+
+      return alPos;
+    } finally
+    {
+      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
+   */
+  public int getHiddenBoundaryLeft(int alPos)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+
+      if (hiddenColumns != null)
+      {
+        int index = hiddenColumns.size() - 1;
+        do
+        {
+          int[] region = hiddenColumns.get(index);
+          if (alPos > region[1])
+          {
+            return region[1];
+          }
+
+          index--;
+        } while (index > -1);
+      }
+
+      return alPos;
+    } 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.
+   * 
+   * @param pos
+   *          int
+   */
+  private int getHiddenIndexLeft(int pos)
+  {
+    try
+    {
+
+      LOCK.readLock().lock();
+      if (hiddenColumns != null)
+      {
+        int index = hiddenColumns.size() - 1;
+        do
+        {
+          int[] region = hiddenColumns.get(index);
+          if (pos > region[1])
+          {
+            return index;
+          }
+
+          index--;
+        } while (index > -1);
+      }
+
+      return -1;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+
+  }
+
+  /**
+   * Adds the specified column range to the hidden columns
+   * 
+   * @param start
+   * @param end
+   */
+  public void hideColumns(int start, int end)
+  {
+    boolean wasAlreadyLocked = false;
+    try
+    {
+      // 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
+      {
+        wasAlreadyLocked = true;
+      }
+
+      if (hiddenColumns == null)
+      {
+        hiddenColumns = new ArrayList<>();
+      }
+
+      /*
+       * traverse existing hidden ranges and insert / amend / append as
+       * appropriate
+       */
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = hiddenColumns.get(i);
+
+        if (end < region[0] - 1)
+        {
+          /*
+           * insert discontiguous preceding range
+           */
+          hiddenColumns.add(i, new int[] { start, end });
+          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;
+        }
+
+        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);
+            hiddenColumns.remove(i + 1);
+          }
+          return;
+        }
+      }
+
+      /*
+       * remaining case is that the new range follows everything else
+       */
+      hiddenColumns.add(new int[] { start, end });
+    } finally
+    {
+      if (!wasAlreadyLocked)
+      {
+        LOCK.writeLock().unlock();
+      }
+    }
+  }
+
+  public boolean isVisible(int column)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+
+      if (hiddenColumns != null)
+      {
+        for (int[] region : hiddenColumns)
+        {
+          if (column >= region[0] && column <= region[1])
+          {
+            return false;
+          }
+        }
+      }
+
+      return true;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  private ArrayList<int[]> copyHiddenRegionsToArrayList()
+  {
+    int size = 0;
+    if (hiddenColumns != null)
+    {
+      size = hiddenColumns.size();
+    }
+    ArrayList<int[]> copy = new ArrayList<>(size);
+
+    for (int i = 0, j = size; i < j; i++)
+    {
+      int[] rh;
+      int[] cp;
+      rh = hiddenColumns.get(i);
+      if (rh != null)
+      {
+        cp = new int[rh.length];
+        System.arraycopy(rh, 0, cp, 0, rh.length);
+        copy.add(cp);
+      }
+    }
+
+    return copy;
+  }
+
+  /**
+   * Returns a copy of the vector of hidden regions, as an ArrayList. Before
+   * using this method please consider if you really need access to the hidden
+   * regions - a new (or existing!) method on HiddenColumns might be more
+   * appropriate.
+   * 
+   * @return hidden regions as an ArrayList of [start,end] pairs
+   */
+  public ArrayList<int[]> getHiddenColumnsCopy()
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      return 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.get(i);
+          if (region[0] > start && start + change > region[1])
+          {
+            deletedHiddenColumns.add(region);
+
+            hiddenColumns.remove(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.get(i);
+          if (region[0] >= start)
+          {
+            region[0] -= change;
+          }
+          if (region[1] >= start)
+          {
+            region[1] -= change;
+          }
+          if (region[1] < region[0])
+          {
+            hiddenColumns.remove(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;
+        int hideEnd;
+
+        for (int j = 0; vstart < end && j < regions.size(); j++)
+        {
+          region = regions.get(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+
+          if (hideEnd < vstart)
+          {
+            continue;
+          }
+          if (hideStart > vstart)
+          {
+            visiblecontigs.add(new int[] { vstart, hideStart - 1 });
+          }
+          vstart = hideEnd + 1;
+        }
+
+        if (vstart < end)
+        {
+          visiblecontigs.add(new int[] { vstart, end - 1 });
+        }
+        int[] 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 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();
+          List<int[]> regions = getHiddenRegions();
+
+          int blockStart = start;
+          int blockEnd = end;
+          int[] region;
+          int hideStart;
+          int 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();
+        }
+      }
+      else
+      {
+        for (int i = 0; i < iSize; i++)
+        {
+          selections[i] = seqs[i].getSequenceAsString(start, end);
+        }
+      }
+
+      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();
+      int lpos = seq.getEnd();
+      int start = 0;
+
+      if (hiddenColumns == null || hiddenColumns.size() == 0)
+      {
+        int ifpos = seq.findIndex(fpos) - 1;
+        int 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;
+      int lastvispos = -1;
+      int rcount = 0;
+      int hideStart = seq.getLength();
+      int hideEnd = -1;
+      int visPrev = 0;
+      int visNext = 0;
+      int firstP = -1;
+      int lastP = -1;
+      boolean foundStart = false;
+      for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+              && p < pLen; p++)
+      {
+        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 };
+      }
+      // otherwise, sequence was completely hidden
+      return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param alignmentAnnotation
+   */
+  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param alignmentAnnotation
+   *          the annotation to operate on
+   */
+  public void makeVisibleAnnotation(int start, int end,
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    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;
+        int blockEnd = end;
+        int[] region;
+        int hideStart;
+        int hideEnd;
+        int 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;
+          }
+
+          annels.addElement(els = new Annotation[blockEnd - blockStart]);
+          System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+                  0, els.length);
+          w += els.length;
+          blockStart = hideEnd + 1;
+          blockEnd = end;
+        }
+
+        if (end > blockStart)
+        {
+          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;
+        }
+        if (w == 0)
+        {
+          return;
+        }
+
+        alignmentAnnotation.annotations = new Annotation[w];
+        w = 0;
+
+        for (Annotation[] chnk : annels)
+        {
+          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                  chnk.length);
+          w += chnk.length;
+        }
+      }
+      else
+      {
+        alignmentAnnotation.restrict(start, end);
+      }
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * 
+   * @return true if there are columns hidden
+   */
+  public boolean hasHiddenColumns()
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      return hiddenColumns != null && hiddenColumns.size() > 0;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * 
+   * @return true if there are more than one set of columns hidden
+   */
+  public boolean hasManyHiddenColumns()
+  {
+    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
+   */
+  public void hideInsertionsFor(SequenceI sr)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      List<int[]> inserts = sr.getInsertions();
+      for (int[] r : inserts)
+      {
+        hideColumns(r[0], r[1]);
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * Unhides, and adds to the selection list, all hidden columns
+   */
+  public void revealAllHiddenColumns(ColumnSelection sel)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      if (hiddenColumns != null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = hiddenColumns.get(i);
+          for (int j = region[0]; j < region[1] + 1; j++)
+          {
+            sel.addElement(j);
+          }
+        }
+      }
+
+      hiddenColumns = null;
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * Reveals, and marks as selected, the hidden column range with the given
+   * start column
+   * 
+   * @param start
+   */
+  public void revealHiddenColumns(int start, ColumnSelection sel)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = hiddenColumns.get(i);
+        if (start == region[0])
+        {
+          for (int j = region[0]; j < region[1] + 1; j++)
+          {
+            sel.addElement(j);
+          }
+
+          hiddenColumns.remove(region);
+          break;
+        }
+      }
+      if (hiddenColumns.size() == 0)
+      {
+        hiddenColumns = null;
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * removes intersection of position,length ranges in deletions from the
+   * start,end regions marked in intervals.
+   * 
+   * @param shifts
+   * @param intervals
+   * @return
+   */
+  private boolean pruneIntervalList(final List<int[]> shifts,
+          ArrayList<int[]> intervals)
+  {
+    boolean pruned = false;
+    int i = 0;
+    int j = intervals.size() - 1;
+    int s = 0;
+    int t = shifts.size() - 1;
+    int[] hr = intervals.get(i);
+    int[] sr = shifts.get(s);
+    while (i <= j && s <= t)
+    {
+      boolean trailinghn = hr[1] >= sr[0];
+      if (!trailinghn)
+      {
+        if (i < j)
+        {
+          hr = intervals.get(++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.remove(i);
+          pruned = true;
+          j--;
+          if (i <= j)
+          {
+            hr = intervals.get(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)
+      {
+        pruneIntervalList(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)
+  {
+    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;
+  }
+
+  /**
+   * 
+   * @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
+   */
+  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 = 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())
+    {
+      // 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();
+        }
+      }
+    }
+  }
+
+  /**
+   * remove any hiddenColumns or selected columns and shift remaining based on a
+   * series of position, range deletions.
+   * 
+   * @param deletions
+   */
+  private void pruneDeletions(ShiftList deletions)
+  {
+    if (deletions != null)
+    {
+      final List<int[]> shifts = deletions.getShifts();
+      if (shifts != null && shifts.size() > 0)
+      {
+        pruneDeletions(shifts);
+
+        // and shift the rest.
+        this.compensateForEdits(deletions);
+      }
+    }
+  }
+
+  /**
+   * Adjust hidden column boundaries based on a series of column additions or
+   * deletions in visible regions.
+   * 
+   * @param shiftrecord
+   * @return
+   */
+  private ShiftList compensateForEdits(ShiftList shiftrecord)
+  {
+    if (shiftrecord != null)
+    {
+      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();
+    }
+    return null;
+  }
+
+  /**
+   * Returns a hashCode built from hidden column ranges
+   */
+  @Override
+  public int hashCode()
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int hashCode = 1;
+      if (hiddenColumns != null)
+      {
+        for (int[] hidden : hiddenColumns)
+        {
+          hashCode = 31 * hashCode + hidden[0];
+          hashCode = 31 * hashCode + hidden[1];
+        }
+      }
+      return hashCode;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+  /**
+   * Hide columns corresponding to the marked bits
+   * 
+   * @param inserts
+   *          - columns map to bits starting from zero
+   */
+  public void hideMarkedBits(BitSet inserts)
+  {
+    try
+    {
+      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);
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * 
+   * @param inserts
+   *          BitSet where hidden columns will be marked
+   */
+  public void markHiddenRegions(BitSet inserts)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      if (hiddenColumns == null)
+      {
+        return;
+      }
+      for (int[] range : hiddenColumns)
+      {
+        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 };
+      }
+
+      for (int[] hiddenCol : hiddenColumns)
+      {
+        lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+        higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+      }
+
+      if (lowestRange[0] == -1 && lowestRange[1] == -1)
+      {
+        startPos = alignmentStartEnd[0];
+      }
+      else
+      {
+        startPos = lowestRange[1] + 1;
+      }
+
+      if (higestRange[0] == -1 && higestRange[1] == -1)
+      {
+        endPos = alignmentStartEnd[1];
+      }
+      else
+      {
+        endPos = higestRange[0] - 1;
+      }
+      return new int[] { startPos, endPos };
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+
+  }
+
+  /**
+   * Finds the hidden region (if any) which starts or ends at res
+   * 
+   * @param res
+   *          visible residue position, unadjusted for hidden columns
+   * @return region as [start,end] or null if no matching region is found
+   */
+  public int[] getRegionWithEdgeAtRes(int res)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int adjres = adjustForHiddenColumns(res);
+
+      int[] reveal = null;
+      if (hiddenColumns != null)
+      {
+        for (int[] region : hiddenColumns)
+        {
+          if (adjres + 1 == region[0] || adjres - 1 == region[1])
+          {
+            reveal = region;
+            break;
+          }
+        }
+      }
+      return reveal;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+  }
+
+}