X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=b87cd2b06a95f10bd02cd94b22a0d4095d5cd5c7;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=546ba1a7dbe4443e0e40da5929f4d07585b6dea5;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 546ba1a..b87cd2b 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,1114 +1,1259 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * 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/>.
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-import jalview.util.*;
-
-/**
- * NOTE: Columns are zero based.
- */
-public class ColumnSelection
-{
-  Vector selected = new Vector();
-
-  // Vector of int [] {startCol, endCol}
-  Vector hiddenColumns;
-
-  /**
-   * Add a column to the selection
-   * 
-   * @param col
-   *          index of column
-   */
-  public void addElement(int col)
-  {
-    Integer column = new Integer(col);
-    if (!selected.contains(column))
-    {
-      selected.addElement(column);
-    }
-  }
-
-  /**
-   * clears column selection
-   */
-  public void clear()
-  {
-    selected.removeAllElements();
-  }
-
-  /**
-   * removes col from selection
-   * 
-   * @param col
-   *          index of column to be removed
-   */
-  public void removeElement(int col)
-  {
-    Integer colInt = new Integer(col);
-
-    if (selected.contains(colInt))
-    {
-      selected.removeElement(colInt);
-    }
-  }
-
-  /**
-   * removes a range of columns from the selection
-   * 
-   * @param start
-   *          int - first column in range to be removed
-   * @param end
-   *          int - last col
-   */
-  public void removeElements(int start, int end)
-  {
-    Integer colInt;
-    for (int i = start; i < end; i++)
-    {
-      colInt = new Integer(i);
-      if (selected.contains(colInt))
-      {
-        selected.removeElement(colInt);
-      }
-    }
-  }
-
-  /**
-   * 
-   * @return Vector containing selected columns as Integers
-   */
-  public Vector getSelected()
-  {
-    return selected;
-  }
-
-  /**
-   * 
-   * @param col
-   *          index to search for in column selection
-   * 
-   * @return true if Integer(col) is in selection.
-   */
-  public boolean contains(int col)
-  {
-    return selected.contains(new Integer(col));
-  }
-
-  /**
-   * Column number at position i in selection
-   * 
-   * @param i
-   *          index into selected columns
-   * 
-   * @return column number in alignment
-   */
-  public int columnAt(int i)
-  {
-    return ((Integer) selected.elementAt(i)).intValue();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int size()
-  {
-    return selected.size();
-  }
-
-  /**
-   * rightmost selected column
-   * 
-   * @return rightmost column in alignment that is selected
-   */
-  public int getMax()
-  {
-    int max = -1;
-
-    for (int i = 0; i < selected.size(); i++)
-    {
-      if (columnAt(i) > max)
-      {
-        max = columnAt(i);
-      }
-    }
-
-    return max;
-  }
-
-  /**
-   * Leftmost column in selection
-   * 
-   * @return column index of leftmost column in selection
-   */
-  public int getMin()
-  {
-    int min = 1000000000;
-
-    for (int i = 0; i < selected.size(); i++)
-    {
-      if (columnAt(i) < min)
-      {
-        min = columnAt(i);
-      }
-    }
-
-    return min;
-  }
-
-  /**
-   * 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 Vector compensateForEdit(int start, int change)
-  {
-    Vector deletedHiddenColumns = null;
-    for (int i = 0; i < size(); i++)
-    {
-      int temp = columnAt(i);
-
-      if (temp >= start)
-      {
-        selected.setElementAt(new Integer(temp - change), i);
-      }
-    }
-
-    if (hiddenColumns != null)
-    {
-      deletedHiddenColumns = new Vector();
-      int hSize = hiddenColumns.size();
-      for (int i = 0; i < hSize; i++)
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
-        if (region[0] > start && start + change > region[1])
-        {
-          deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
-
-          hiddenColumns.removeElementAt(i);
-          i--;
-          hSize--;
-          continue;
-        }
-
-        if (region[0] > start)
-        {
-          region[0] -= change;
-          region[1] -= change;
-        }
-
-        if (region[0] < 0)
-        {
-          region[0] = 0;
-        }
-
-      }
-
-      this.revealHiddenColumns(0);
-    }
-
-    return deletedHiddenColumns;
-  }
-
-  /**
-   * 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)
-   */
-  private void compensateForDelEdits(int start, int change)
-  {
-    for (int i = 0; i < size(); i++)
-    {
-      int temp = columnAt(i);
-
-      if (temp >= start)
-      {
-        selected.setElementAt(new Integer(temp - change), i);
-      }
-    }
-
-    if (hiddenColumns != null)
-    {
-      for (int i = 0; i < hiddenColumns.size(); i++)
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
-        if (region[0] >= start)
-        {
-          region[0] -= change;
-        }
-        if (region[1] >= start)
-        {
-          region[1] -= change;
-        }
-        if (region[1] < region[0])
-        {
-          hiddenColumns.removeElementAt(i--);
-        }
-
-        if (region[0] < 0)
-        {
-          region[0] = 0;
-        }
-        if (region[1] < 0)
-        {
-          region[1] = 0;
-        }
-      }
-    }
-  }
-
-  /**
-   * Adjust hidden column boundaries based on a series of column additions or
-   * deletions in visible regions.
-   * 
-   * @param shiftrecord
-   * @return
-   */
-  public ShiftList compensateForEdits(ShiftList shiftrecord)
-  {
-    if (shiftrecord != null)
-    {
-      Vector shifts = shiftrecord.shifts;
-      if (shifts != null && shifts.size() > 0)
-      {
-        int shifted = 0;
-        for (int i = 0, j = shifts.size(); i < j; i++)
-        {
-          int[] sh = (int[]) shifts.elementAt(i);
-          // compensateForEdit(shifted+sh[0], sh[1]);
-          compensateForDelEdits(shifted + sh[0], sh[1]);
-          shifted -= sh[1];
-        }
-      }
-      return shiftrecord.getInverse();
-    }
-    return null;
-  }
-
-  /**
-   * removes intersection of position,length ranges in deletions from the
-   * start,end regions marked in intervals.
-   * 
-   * @param deletions
-   * @param intervals
-   * @return
-   */
-  private boolean pruneIntervalVector(Vector deletions, Vector intervals)
-  {
-    boolean pruned = false;
-    int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
-    int hr[] = (int[]) intervals.elementAt(i);
-    int sr[] = (int[]) deletions.elementAt(s);
-    while (i <= j && s <= t)
-    {
-      boolean trailinghn = hr[1] >= sr[0];
-      if (!trailinghn)
-      {
-        if (i < j)
-        {
-          hr = (int[]) intervals.elementAt(++i);
-        }
-        else
-        {
-          i++;
-        }
-        continue;
-      }
-      int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
-      if (endshift < hr[0] || endshift < sr[0])
-      { // leadinghc disjoint or not a deletion
-        if (s < t)
-        {
-          sr = (int[]) deletions.elementAt(++s);
-        }
-        else
-        {
-          s++;
-        }
-        continue;
-      }
-      boolean leadinghn = hr[0] >= sr[0];
-      boolean leadinghc = hr[0] < endshift;
-      boolean trailinghc = hr[1] < endshift;
-      if (leadinghn)
-      {
-        if (trailinghc)
-        { // deleted hidden region.
-          intervals.removeElementAt(i);
-          pruned = true;
-          j--;
-          if (i <= j)
-          {
-            hr = (int[]) intervals.elementAt(i);
-          }
-          continue;
-        }
-        if (leadinghc)
-        {
-          hr[0] = endshift; // clip c terminal region
-          leadinghn = !leadinghn;
-          pruned = true;
-        }
-      }
-      if (!leadinghn)
-      {
-        if (trailinghc)
-        {
-          if (trailinghn)
-          {
-            hr[1] = sr[0] - 1;
-            pruned = true;
-          }
-        }
-        else
-        {
-          // sr contained in hr
-          if (s < t)
-          {
-            sr = (int[]) deletions.elementAt(++s);
-          }
-          else
-          {
-            s++;
-          }
-          continue;
-        }
-      }
-    }
-    return pruned; // true if any interval was removed or modified by
-    // operations.
-  }
-
-  private boolean pruneColumnList(Vector deletion, Vector list)
-  {
-    int s = 0, t = deletion.size();
-    int[] sr = (int[]) list.elementAt(s++);
-    boolean pruned = false;
-    int i = 0, j = list.size();
-    while (i < j && s <= t)
-    {
-      int c = ((Integer) list.elementAt(i++)).intValue();
-      if (sr[0] <= c)
-      {
-        if (sr[1] + sr[0] >= c)
-        { // sr[1] -ve means inseriton.
-          list.removeElementAt(--i);
-          j--;
-        }
-        else
-        {
-          if (s < t)
-          {
-            sr = (int[]) deletion.elementAt(s);
-          }
-          s++;
-        }
-      }
-    }
-    return pruned;
-  }
-
-  /**
-   * remove any hiddenColumns or selected columns and shift remaining based on a
-   * series of position, range deletions.
-   * 
-   * @param deletions
-   */
-  public void pruneDeletions(ShiftList deletions)
-  {
-    if (deletions != null)
-    {
-      Vector shifts = deletions.shifts;
-      if (shifts != null && shifts.size() > 0)
-      {
-        // delete any intervals intersecting.
-        if (hiddenColumns != null)
-        {
-          pruneIntervalVector(shifts, hiddenColumns);
-          if (hiddenColumns != null && hiddenColumns.size() == 0)
-          {
-            hiddenColumns = null;
-          }
-        }
-        if (selected != null && selected.size() > 0)
-        {
-          pruneColumnList(shifts, selected);
-          if (selected != null && selected.size() == 0)
-          {
-            selected = null;
-          }
-        }
-        // and shift the rest.
-        this.compensateForEdits(deletions);
-      }
-    }
-  }
-
-  /**
-   * This Method is used to return all the HiddenColumn regions less than the
-   * given index.
-   * 
-   * @param end
-   *          int
-   * @return Vector
-   */
-  public Vector getHiddenColumns()
-  {
-    return hiddenColumns;
-  }
-
-  /**
-   * Return absolute column index for a visible column index
-   * 
-   * @param column
-   *          int column index in alignment view
-   * @return alignment column index for column
-   */
-  public int adjustForHiddenColumns(int column)
-  {
-    int result = column;
-    if (hiddenColumns != null)
-    {
-      for (int i = 0; i < hiddenColumns.size(); i++)
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
-        if (result >= region[0])
-        {
-          result += region[1] - region[0] + 1;
-        }
-      }
-    }
-    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.
-   * 
-   * @param hiddenColumn
-   *          int
-   * @return int
-   */
-  public int findColumnPosition(int hiddenColumn)
-  {
-    int result = hiddenColumn;
-    if (hiddenColumns != null)
-    {
-      int index = 0;
-      int[] region;
-      do
-      {
-        region = (int[]) hiddenColumns.elementAt(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])
-      {
-        return region[0]+hiddenColumn-result;
-      }
-    }
-    return result; // return the shifted position after removing hidden columns.
-  }
-
-  /**
-   * Use this method to determine where the next hiddenRegion starts
-   */
-  public int findHiddenRegionPosition(int hiddenRegion)
-  {
-    int result = 0;
-    if (hiddenColumns != null)
-    {
-      int index = 0;
-      int gaps = 0;
-      do
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
-        if (hiddenRegion == 0)
-        {
-          return region[0];
-        }
-
-        gaps += region[1] + 1 - region[0];
-        result = region[1] + 1;
-        index++;
-      } while (index < hiddenRegion + 1);
-
-      result -= gaps;
-    }
-
-    return result;
-  }
-
-  /**
-   * 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)
-  {
-    if (hiddenColumns != null)
-    {
-      int index = 0;
-      do
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
-        if (alPos < region[0])
-        {
-          return region[0];
-        }
-
-        index++;
-      } while (index < hiddenColumns.size());
-    }
-
-    return alPos;
-
-  }
-
-  /**
-   * 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)
-  {
-    if (hiddenColumns != null)
-    {
-      int index = hiddenColumns.size() - 1;
-      do
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
-        if (alPos > region[1])
-        {
-          return region[1];
-        }
-
-        index--;
-      } while (index > -1);
-    }
-
-    return alPos;
-
-  }
-
-  public void hideSelectedColumns()
-  {
-    while (size() > 0)
-    {
-      int column = ((Integer) getSelected().firstElement()).intValue();
-      hideColumns(column);
-    }
-
-  }
-
-  public void hideColumns(int start, int end)
-  {
-    if (hiddenColumns == null)
-    {
-      hiddenColumns = new Vector();
-    }
-
-    boolean added = false;
-    boolean overlap = false;
-
-    for (int i = 0; i < hiddenColumns.size(); i++)
-    {
-      int[] region = (int[]) hiddenColumns.elementAt(i);
-      if (start <= region[1] && end >= region[0])
-      {
-        hiddenColumns.removeElementAt(i);
-        overlap = true;
-        break;
-      }
-      else if (end < region[0] && start < region[0])
-      {
-        hiddenColumns.insertElementAt(new int[]
-        { start, end }, i);
-        added = true;
-        break;
-      }
-    }
-
-    if (overlap)
-    {
-      hideColumns(start, end);
-    }
-    else if (!added)
-    {
-      hiddenColumns.addElement(new int[]
-      { start, end });
-    }
-
-  }
-
-  /**
-   * This method will find a range of selected columns around the column
-   * specified
-   * 
-   * @param res
-   *          int
-   */
-  public void hideColumns(int col)
-  {
-    // First find out range of columns to hide
-    int min = col, max = col + 1;
-    while (contains(min))
-    {
-      removeElement(min);
-      min--;
-    }
-
-    while (contains(max))
-    {
-      removeElement(max);
-      max++;
-    }
-
-    min++;
-    max--;
-    if (min > max)
-    {
-      min = max;
-    }
-
-    hideColumns(min, max);
-  }
-
-  public void revealAllHiddenColumns()
-  {
-    if (hiddenColumns != null)
-    {
-      for (int i = 0; i < hiddenColumns.size(); i++)
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
-        for (int j = region[0]; j < region[1] + 1; j++)
-        {
-          addElement(j);
-        }
-      }
-    }
-
-    hiddenColumns = null;
-  }
-
-  public void revealHiddenColumns(int res)
-  {
-    for (int i = 0; i < hiddenColumns.size(); i++)
-    {
-      int[] region = (int[]) hiddenColumns.elementAt(i);
-      if (res == region[0])
-      {
-        for (int j = region[0]; j < region[1] + 1; j++)
-        {
-          addElement(j);
-        }
-
-        hiddenColumns.removeElement(region);
-        break;
-      }
-    }
-    if (hiddenColumns.size() == 0)
-    {
-      hiddenColumns = null;
-    }
-  }
-
-  public boolean isVisible(int column)
-  {
-    if (hiddenColumns != null)
-      for (int i = 0; i < hiddenColumns.size(); i++)
-      {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
-        if (column >= region[0] && column <= region[1])
-        {
-          return false;
-        }
-      }
-
-    return true;
-  }
-
-  /**
-   * Copy constructor
-   * 
-   * @param copy
-   */
-  public ColumnSelection(ColumnSelection copy)
-  {
-    if (copy != null)
-    {
-      if (copy.selected != null)
-      {
-        selected = new Vector();
-        for (int i = 0, j = copy.selected.size(); i < j; i++)
-        {
-          selected.addElement(copy.selected.elementAt(i));
-        }
-      }
-      if (copy.hiddenColumns != null)
-      {
-        hiddenColumns = new Vector(copy.hiddenColumns.size());
-        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
-        {
-          int[] rh, cp;
-          rh = (int[]) copy.hiddenColumns.elementAt(i);
-          if (rh != null)
-          {
-            cp = new int[rh.length];
-            System.arraycopy(rh, 0, cp, 0, rh.length);
-            hiddenColumns.addElement(cp);
-          }
-        }
-      }
-    }
-  }
-
-  /**
-   * ColumnSelection
-   */
-  public ColumnSelection()
-  {
-  }
-
-  public String[] getVisibleSequenceStrings(int start, int end,
-          SequenceI[] seqs)
-  {
-    int i, iSize = seqs.length;
-    String selection[] = new String[iSize];
-    if (hiddenColumns != null && hiddenColumns.size() > 0)
-    {
-      for (i = 0; i < iSize; i++)
-      {
-        StringBuffer visibleSeq = new StringBuffer();
-        Vector regions = getHiddenColumns();
-
-        int blockStart = start, blockEnd = end;
-        int[] region;
-        int hideStart, hideEnd;
-
-        for (int j = 0; j < regions.size(); j++)
-        {
-          region = (int[]) regions.elementAt(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));
-        }
-
-        selection[i] = visibleSeq.toString();
-      }
-    }
-    else
-    {
-      for (i = 0; i < iSize; i++)
-      {
-        selection[i] = seqs[i].getSequenceAsString(start, end);
-      }
-    }
-
-    return selection;
-  }
-
-  /**
-   * 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)
-  {
-    if (hiddenColumns != null && hiddenColumns.size() > 0)
-    {
-      Vector visiblecontigs = new Vector();
-      Vector regions = getHiddenColumns();
-
-      int vstart = start;
-      int[] region;
-      int hideStart, hideEnd;
-
-      for (int j = 0; vstart < end && j < regions.size(); j++)
-      {
-        region = (int[]) regions.elementAt(j);
-        hideStart = region[0];
-        hideEnd = region[1];
-
-        if (hideEnd < vstart)
-        {
-          continue;
-        }
-        if (hideStart > vstart)
-        {
-          visiblecontigs.addElement(new int[]
-          { vstart, hideStart - 1 });
-        }
-        vstart = hideEnd + 1;
-      }
-
-      if (vstart < end)
-      {
-        visiblecontigs.addElement(new int[]
-        { vstart, end - 1 });
-      }
-      int[] vcontigs = new int[visiblecontigs.size() * 2];
-      for (int i = 0, j = visiblecontigs.size(); i < j; i++)
-      {
-        int[] vc = (int[]) visiblecontigs.elementAt(i);
-        visiblecontigs.setElementAt(null, i);
-        vcontigs[i * 2] = vc[0];
-        vcontigs[i * 2 + 1] = vc[1];
-      }
-      visiblecontigs.removeAllElements();
-      return vcontigs;
-    }
-    else
-    {
-      return new int[]
-      { start, end - 1 };
-    }
-  }
-
-  /**
-   * 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)
-  {
-    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 annels = new Vector();
-      Annotation[] els = null;
-      Vector regions = getHiddenColumns();
-      int blockStart = start, blockEnd = end;
-      int[] region;
-      int hideStart, hideEnd, w = 0;
-
-      for (int j = 0; j < regions.size(); j++)
-      {
-        region = (int[]) regions.elementAt(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;
-      Enumeration e = annels.elements();
-      alignmentAnnotation.annotations = new Annotation[w];
-      w = 0;
-      while (e.hasMoreElements())
-      {
-        Annotation[] chnk = (Annotation[]) e.nextElement();
-        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
-                chnk.length);
-        w += chnk.length;
-      }
-    }
-    else
-    {
-      alignmentAnnotation.restrict(start, end);
-    }
-  }
-
-  /**
-   * Invert the column selection from first to end-1. leaves hiddenColumns
-   * untouched (and unselected)
-   * 
-   * @param first
-   * @param end
-   */
-  public void invertColumnSelection(int first, int width)
-  {
-    boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
-    for (int i = first; i < width; i++)
-    {
-      if (contains(i))
-      {
-        removeElement(i);
-      }
-      else
-      {
-        if (!hasHidden || isVisible(i))
-        {
-          addElement(i);
-        }
-      }
-    }
-  }
-
-  /**
-   * add in any unselected columns from the given column selection, excluding
-   * any that are hidden.
-   * 
-   * @param colsel
-   */
-  public void addElementsFrom(ColumnSelection colsel)
-  {
-    if (colsel != null && colsel.size() > 0)
-    {
-      Enumeration e = colsel.getSelected().elements();
-      while (e.hasMoreElements())
-      {
-        Object eo = e.nextElement();
-        if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
-        {
-          if (!selected.contains(eo))
-          {
-            selected.addElement(eo);
-          }
-        }
-      }
-    }
-  }
-
-  /**
-   * set the selected columns the given column selection, excluding any columns
-   * that are hidden.
-   * 
-   * @param colsel
-   */
-  public void setElementsFrom(ColumnSelection colsel)
-  {
-    selected = new Vector();
-    if (colsel.selected != null && colsel.selected.size() > 0)
-    {
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
-      {
-        // only select visible columns in this columns selection
-        selected = new Vector();
-        addElementsFrom(colsel);
-      }
-      else
-      {
-        // add everything regardless
-        Enumeration en = colsel.selected.elements();
-        while (en.hasMoreElements())
-        {
-          selected.addElement(en.nextElement());
-        }
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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 java.util.*;
+
+import jalview.util.*;
+
+/**
+ * NOTE: Columns are zero based.
+ */
+public class ColumnSelection
+{
+  Vector selected = new Vector();
+
+  // Vector of int [] {startCol, endCol}
+  Vector hiddenColumns;
+
+  /**
+   * Add a column to the selection
+   * 
+   * @param col
+   *          index of column
+   */
+  public void addElement(int col)
+  {
+    Integer column = new Integer(col);
+    if (!selected.contains(column))
+    {
+      selected.addElement(column);
+    }
+  }
+
+  /**
+   * clears column selection
+   */
+  public void clear()
+  {
+    selected.removeAllElements();
+  }
+
+  /**
+   * removes col from selection
+   * 
+   * @param col
+   *          index of column to be removed
+   */
+  public void removeElement(int col)
+  {
+    Integer colInt = new Integer(col);
+
+    if (selected.contains(colInt))
+    {
+      selected.removeElement(colInt);
+    }
+  }
+
+  /**
+   * removes a range of columns from the selection
+   * 
+   * @param start
+   *          int - first column in range to be removed
+   * @param end
+   *          int - last col
+   */
+  public void removeElements(int start, int end)
+  {
+    Integer colInt;
+    for (int i = start; i < end; i++)
+    {
+      colInt = new Integer(i);
+      if (selected.contains(colInt))
+      {
+        selected.removeElement(colInt);
+      }
+    }
+  }
+
+  /**
+   * 
+   * @return Vector containing selected columns as Integers
+   */
+  public Vector getSelected()
+  {
+    return selected;
+  }
+
+  /**
+   * 
+   * @param col
+   *          index to search for in column selection
+   * 
+   * @return true if Integer(col) is in selection.
+   */
+  public boolean contains(int col)
+  {
+    return selected.contains(new Integer(col));
+  }
+
+  /**
+   * Column number at position i in selection
+   * 
+   * @param i
+   *          index into selected columns
+   * 
+   * @return column number in alignment
+   */
+  public int columnAt(int i)
+  {
+    return ((Integer) selected.elementAt(i)).intValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int size()
+  {
+    return selected.size();
+  }
+
+  /**
+   * rightmost selected column
+   * 
+   * @return rightmost column in alignment that is selected
+   */
+  public int getMax()
+  {
+    int max = -1;
+
+    for (int i = 0; i < selected.size(); i++)
+    {
+      if (columnAt(i) > max)
+      {
+        max = columnAt(i);
+      }
+    }
+
+    return max;
+  }
+
+  /**
+   * Leftmost column in selection
+   * 
+   * @return column index of leftmost column in selection
+   */
+  public int getMin()
+  {
+    int min = 1000000000;
+
+    for (int i = 0; i < selected.size(); i++)
+    {
+      if (columnAt(i) < min)
+      {
+        min = columnAt(i);
+      }
+    }
+
+    return min;
+  }
+
+  /**
+   * 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 Vector compensateForEdit(int start, int change)
+  {
+    Vector deletedHiddenColumns = null;
+    for (int i = 0; i < size(); i++)
+    {
+      int temp = columnAt(i);
+
+      if (temp >= start)
+      {
+        selected.setElementAt(new Integer(temp - change), i);
+      }
+    }
+
+    if (hiddenColumns != null)
+    {
+      deletedHiddenColumns = new Vector();
+      int hSize = hiddenColumns.size();
+      for (int i = 0; i < hSize; i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if (region[0] > start && start + change > region[1])
+        {
+          deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
+
+          hiddenColumns.removeElementAt(i);
+          i--;
+          hSize--;
+          continue;
+        }
+
+        if (region[0] > start)
+        {
+          region[0] -= change;
+          region[1] -= change;
+        }
+
+        if (region[0] < 0)
+        {
+          region[0] = 0;
+        }
+
+      }
+
+      this.revealHiddenColumns(0);
+    }
+
+    return deletedHiddenColumns;
+  }
+
+  /**
+   * 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)
+   */
+  private void compensateForDelEdits(int start, int change)
+  {
+    for (int i = 0; i < size(); i++)
+    {
+      int temp = columnAt(i);
+
+      if (temp >= start)
+      {
+        selected.setElementAt(new Integer(temp - change), i);
+      }
+    }
+
+    if (hiddenColumns != null)
+    {
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if (region[0] >= start)
+        {
+          region[0] -= change;
+        }
+        if (region[1] >= start)
+        {
+          region[1] -= change;
+        }
+        if (region[1] < region[0])
+        {
+          hiddenColumns.removeElementAt(i--);
+        }
+
+        if (region[0] < 0)
+        {
+          region[0] = 0;
+        }
+        if (region[1] < 0)
+        {
+          region[1] = 0;
+        }
+      }
+    }
+  }
+
+  /**
+   * Adjust hidden column boundaries based on a series of column additions or
+   * deletions in visible regions.
+   * 
+   * @param shiftrecord
+   * @return
+   */
+  public ShiftList compensateForEdits(ShiftList shiftrecord)
+  {
+    if (shiftrecord != null)
+    {
+      Vector shifts = shiftrecord.shifts;
+      if (shifts != null && shifts.size() > 0)
+      {
+        int shifted = 0;
+        for (int i = 0, j = shifts.size(); i < j; i++)
+        {
+          int[] sh = (int[]) shifts.elementAt(i);
+          // compensateForEdit(shifted+sh[0], sh[1]);
+          compensateForDelEdits(shifted + sh[0], sh[1]);
+          shifted -= sh[1];
+        }
+      }
+      return shiftrecord.getInverse();
+    }
+    return null;
+  }
+
+  /**
+   * removes intersection of position,length ranges in deletions from the
+   * start,end regions marked in intervals.
+   * 
+   * @param deletions
+   * @param intervals
+   * @return
+   */
+  private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+  {
+    boolean pruned = false;
+    int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
+    int hr[] = (int[]) intervals.elementAt(i);
+    int sr[] = (int[]) deletions.elementAt(s);
+    while (i <= j && s <= t)
+    {
+      boolean trailinghn = hr[1] >= sr[0];
+      if (!trailinghn)
+      {
+        if (i < j)
+        {
+          hr = (int[]) intervals.elementAt(++i);
+        }
+        else
+        {
+          i++;
+        }
+        continue;
+      }
+      int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
+      if (endshift < hr[0] || endshift < sr[0])
+      { // leadinghc disjoint or not a deletion
+        if (s < t)
+        {
+          sr = (int[]) deletions.elementAt(++s);
+        }
+        else
+        {
+          s++;
+        }
+        continue;
+      }
+      boolean leadinghn = hr[0] >= sr[0];
+      boolean leadinghc = hr[0] < endshift;
+      boolean trailinghc = hr[1] < endshift;
+      if (leadinghn)
+      {
+        if (trailinghc)
+        { // deleted hidden region.
+          intervals.removeElementAt(i);
+          pruned = true;
+          j--;
+          if (i <= j)
+          {
+            hr = (int[]) intervals.elementAt(i);
+          }
+          continue;
+        }
+        if (leadinghc)
+        {
+          hr[0] = endshift; // clip c terminal region
+          leadinghn = !leadinghn;
+          pruned = true;
+        }
+      }
+      if (!leadinghn)
+      {
+        if (trailinghc)
+        {
+          if (trailinghn)
+          {
+            hr[1] = sr[0] - 1;
+            pruned = true;
+          }
+        }
+        else
+        {
+          // sr contained in hr
+          if (s < t)
+          {
+            sr = (int[]) deletions.elementAt(++s);
+          }
+          else
+          {
+            s++;
+          }
+          continue;
+        }
+      }
+    }
+    return pruned; // true if any interval was removed or modified by
+    // operations.
+  }
+
+  private boolean pruneColumnList(Vector deletion, Vector list)
+  {
+    int s = 0, t = deletion.size();
+    int[] sr = (int[]) list.elementAt(s++);
+    boolean pruned = false;
+    int i = 0, j = list.size();
+    while (i < j && s <= t)
+    {
+      int c = ((Integer) list.elementAt(i++)).intValue();
+      if (sr[0] <= c)
+      {
+        if (sr[1] + sr[0] >= c)
+        { // sr[1] -ve means inseriton.
+          list.removeElementAt(--i);
+          j--;
+        }
+        else
+        {
+          if (s < t)
+          {
+            sr = (int[]) deletion.elementAt(s);
+          }
+          s++;
+        }
+      }
+    }
+    return pruned;
+  }
+
+  /**
+   * remove any hiddenColumns or selected columns and shift remaining based on a
+   * series of position, range deletions.
+   * 
+   * @param deletions
+   */
+  public void pruneDeletions(ShiftList deletions)
+  {
+    if (deletions != null)
+    {
+      Vector shifts = deletions.shifts;
+      if (shifts != null && shifts.size() > 0)
+      {
+        // delete any intervals intersecting.
+        if (hiddenColumns != null)
+        {
+          pruneIntervalVector(shifts, hiddenColumns);
+          if (hiddenColumns != null && hiddenColumns.size() == 0)
+          {
+            hiddenColumns = null;
+          }
+        }
+        if (selected != null && selected.size() > 0)
+        {
+          pruneColumnList(shifts, selected);
+          if (selected != null && selected.size() == 0)
+          {
+            selected = null;
+          }
+        }
+        // and shift the rest.
+        this.compensateForEdits(deletions);
+      }
+    }
+  }
+
+  /**
+   * This Method is used to return all the HiddenColumn regions less than the
+   * given index.
+   * 
+   * @param end
+   *          int
+   * @return Vector
+   */
+  public Vector getHiddenColumns()
+  {
+    return hiddenColumns;
+  }
+
+  /**
+   * Return absolute column index for a visible column index
+   * 
+   * @param column
+   *          int column index in alignment view
+   * @return alignment column index for column
+   */
+  public int adjustForHiddenColumns(int column)
+  {
+    int result = column;
+    if (hiddenColumns != null)
+    {
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if (result >= region[0])
+        {
+          result += region[1] - region[0] + 1;
+        }
+      }
+    }
+    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.
+   * 
+   * @param hiddenColumn
+   *          int
+   * @return int
+   */
+  public int findColumnPosition(int hiddenColumn)
+  {
+    int result = hiddenColumn;
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      int[] region;
+      do
+      {
+        region = (int[]) hiddenColumns.elementAt(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])
+      {
+        return region[0] + hiddenColumn - result;
+      }
+    }
+    return result; // return the shifted position after removing hidden columns.
+  }
+
+  /**
+   * Use this method to determine where the next hiddenRegion starts
+   */
+  public int findHiddenRegionPosition(int hiddenRegion)
+  {
+    int result = 0;
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      int gaps = 0;
+      do
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if (hiddenRegion == 0)
+        {
+          return region[0];
+        }
+
+        gaps += region[1] + 1 - region[0];
+        result = region[1] + 1;
+        index++;
+      } while (index < hiddenRegion + 1);
+
+      result -= gaps;
+    }
+
+    return result;
+  }
+
+  /**
+   * 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)
+  {
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      do
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if (alPos < region[0])
+        {
+          return region[0];
+        }
+
+        index++;
+      } while (index < hiddenColumns.size());
+    }
+
+    return alPos;
+
+  }
+
+  /**
+   * 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)
+  {
+    if (hiddenColumns != null)
+    {
+      int index = hiddenColumns.size() - 1;
+      do
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if (alPos > region[1])
+        {
+          return region[1];
+        }
+
+        index--;
+      } while (index > -1);
+    }
+
+    return alPos;
+
+  }
+
+  public void hideSelectedColumns()
+  {
+    while (size() > 0)
+    {
+      int column = ((Integer) getSelected().firstElement()).intValue();
+      hideColumns(column);
+    }
+
+  }
+
+  public void hideColumns(int start, int end)
+  {
+    if (hiddenColumns == null)
+    {
+      hiddenColumns = new Vector();
+    }
+
+    boolean added = false;
+    boolean overlap = false;
+
+    for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      int[] region = (int[]) hiddenColumns.elementAt(i);
+      if (start <= region[1] && end >= region[0])
+      {
+        hiddenColumns.removeElementAt(i);
+        overlap = true;
+        break;
+      }
+      else if (end < region[0] && start < region[0])
+      {
+        hiddenColumns.insertElementAt(new int[]
+        { start, end }, i);
+        added = true;
+        break;
+      }
+    }
+
+    if (overlap)
+    {
+      hideColumns(start, end);
+    }
+    else if (!added)
+    {
+      hiddenColumns.addElement(new int[]
+      { start, end });
+    }
+
+  }
+
+  /**
+   * This method will find a range of selected columns around the column
+   * specified
+   * 
+   * @param res
+   *          int
+   */
+  public void hideColumns(int col)
+  {
+    // First find out range of columns to hide
+    int min = col, max = col + 1;
+    while (contains(min))
+    {
+      removeElement(min);
+      min--;
+    }
+
+    while (contains(max))
+    {
+      removeElement(max);
+      max++;
+    }
+
+    min++;
+    max--;
+    if (min > max)
+    {
+      min = max;
+    }
+
+    hideColumns(min, max);
+  }
+
+  public void revealAllHiddenColumns()
+  {
+    if (hiddenColumns != null)
+    {
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        for (int j = region[0]; j < region[1] + 1; j++)
+        {
+          addElement(j);
+        }
+      }
+    }
+
+    hiddenColumns = null;
+  }
+
+  public void revealHiddenColumns(int res)
+  {
+    for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      int[] region = (int[]) hiddenColumns.elementAt(i);
+      if (res == region[0])
+      {
+        for (int j = region[0]; j < region[1] + 1; j++)
+        {
+          addElement(j);
+        }
+
+        hiddenColumns.removeElement(region);
+        break;
+      }
+    }
+    if (hiddenColumns.size() == 0)
+    {
+      hiddenColumns = null;
+    }
+  }
+
+  public boolean isVisible(int column)
+  {
+    if (hiddenColumns != null)
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if (column >= region[0] && column <= region[1])
+        {
+          return false;
+        }
+      }
+
+    return true;
+  }
+
+  /**
+   * Copy constructor
+   * 
+   * @param copy
+   */
+  public ColumnSelection(ColumnSelection copy)
+  {
+    if (copy != null)
+    {
+      if (copy.selected != null)
+      {
+        selected = new Vector();
+        for (int i = 0, j = copy.selected.size(); i < j; i++)
+        {
+          selected.addElement(copy.selected.elementAt(i));
+        }
+      }
+      if (copy.hiddenColumns != null)
+      {
+        hiddenColumns = new Vector(copy.hiddenColumns.size());
+        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+        {
+          int[] rh, cp;
+          rh = (int[]) copy.hiddenColumns.elementAt(i);
+          if (rh != null)
+          {
+            cp = new int[rh.length];
+            System.arraycopy(rh, 0, cp, 0, rh.length);
+            hiddenColumns.addElement(cp);
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * ColumnSelection
+   */
+  public ColumnSelection()
+  {
+  }
+
+  public String[] getVisibleSequenceStrings(int start, int end,
+          SequenceI[] seqs)
+  {
+    int i, iSize = seqs.length;
+    String selection[] = new String[iSize];
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      for (i = 0; i < iSize; i++)
+      {
+        StringBuffer visibleSeq = new StringBuffer();
+        Vector regions = getHiddenColumns();
+
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd;
+
+        for (int j = 0; j < regions.size(); j++)
+        {
+          region = (int[]) regions.elementAt(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));
+        }
+
+        selection[i] = visibleSeq.toString();
+      }
+    }
+    else
+    {
+      for (i = 0; i < iSize; i++)
+      {
+        selection[i] = seqs[i].getSequenceAsString(start, end);
+      }
+    }
+
+    return selection;
+  }
+
+  /**
+   * 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)
+  {
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      Vector visiblecontigs = new Vector();
+      Vector regions = getHiddenColumns();
+
+      int vstart = start;
+      int[] region;
+      int hideStart, hideEnd;
+
+      for (int j = 0; vstart < end && j < regions.size(); j++)
+      {
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        if (hideEnd < vstart)
+        {
+          continue;
+        }
+        if (hideStart > vstart)
+        {
+          visiblecontigs.addElement(new int[]
+          { vstart, hideStart - 1 });
+        }
+        vstart = hideEnd + 1;
+      }
+
+      if (vstart < end)
+      {
+        visiblecontigs.addElement(new int[]
+        { vstart, end - 1 });
+      }
+      int[] vcontigs = new int[visiblecontigs.size() * 2];
+      for (int i = 0, j = visiblecontigs.size(); i < j; i++)
+      {
+        int[] vc = (int[]) visiblecontigs.elementAt(i);
+        visiblecontigs.setElementAt(null, i);
+        vcontigs[i * 2] = vc[0];
+        vcontigs[i * 2 + 1] = vc[1];
+      }
+      visiblecontigs.removeAllElements();
+      return vcontigs;
+    }
+    else
+    {
+      return new int[]
+      { start, end - 1 };
+    }
+  }
+
+  /**
+   * 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)
+  {
+    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 annels = new Vector();
+      Annotation[] els = null;
+      Vector regions = getHiddenColumns();
+      int blockStart = start, blockEnd = end;
+      int[] region;
+      int hideStart, hideEnd, w = 0;
+
+      for (int j = 0; j < regions.size(); j++)
+      {
+        region = (int[]) regions.elementAt(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;
+      Enumeration e = annels.elements();
+      alignmentAnnotation.annotations = new Annotation[w];
+      w = 0;
+      while (e.hasMoreElements())
+      {
+        Annotation[] chnk = (Annotation[]) e.nextElement();
+        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                chnk.length);
+        w += chnk.length;
+      }
+    }
+    else
+    {
+      alignmentAnnotation.restrict(start, end);
+    }
+  }
+
+  /**
+   * Invert the column selection from first to end-1. leaves hiddenColumns
+   * untouched (and unselected)
+   * 
+   * @param first
+   * @param end
+   */
+  public void invertColumnSelection(int first, int width)
+  {
+    boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
+    for (int i = first; i < width; i++)
+    {
+      if (contains(i))
+      {
+        removeElement(i);
+      }
+      else
+      {
+        if (!hasHidden || isVisible(i))
+        {
+          addElement(i);
+        }
+      }
+    }
+  }
+
+  /**
+   * add in any unselected columns from the given column selection, excluding
+   * any that are hidden.
+   * 
+   * @param colsel
+   */
+  public void addElementsFrom(ColumnSelection colsel)
+  {
+    if (colsel != null && colsel.size() > 0)
+    {
+      Enumeration e = colsel.getSelected().elements();
+      while (e.hasMoreElements())
+      {
+        Object eo = e.nextElement();
+        if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+        {
+          if (!selected.contains(eo))
+          {
+            selected.addElement(eo);
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * set the selected columns the given column selection, excluding any columns
+   * that are hidden.
+   * 
+   * @param colsel
+   */
+  public void setElementsFrom(ColumnSelection colsel)
+  {
+    selected = new Vector();
+    if (colsel.selected != null && colsel.selected.size() > 0)
+    {
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
+      {
+        // only select visible columns in this columns selection
+        selected = new Vector();
+        addElementsFrom(colsel);
+      }
+      else
+      {
+        // add everything regardless
+        Enumeration en = colsel.selected.elements();
+        while (en.hasMoreElements())
+        {
+          selected.addElement(en.nextElement());
+        }
+      }
+    }
+  }
+
+  /**
+   * 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 Column selection for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public static ColumnSelection propagateInsertions(SequenceI profileseq,
+          Alignment al, AlignmentView input)
+  {
+    int profsqpos = 0;
+
+    // return propagateInsertions(profileseq, al, )
+    char gc = al.getGapCharacter();
+    Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+    ColumnSelection nview = (ColumnSelection) alandcolsel[1];
+    SequenceI origseq = ((SequenceI[]) alandcolsel[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
+   */
+  public 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;
+    // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+    // alandcolsel[0])[0].gapMap()))
+    // 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();
+        }
+      }
+    }
+  }
+}