X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=624e083eabb2d969f8a1211e120c1f09b302a779;hb=a97249105994383dca7ea64259b17ba8ddce31be;hp=2d2223111c2bb0c75b1aa104ab76ba9e98059ebf;hpb=d545553b53ac1bd1e29eb72250cdb29745f7292f;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 2d22231..624e083 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,728 +1,1607 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * NOTE: Columns are zero based.
  */
 public class ColumnSelection
 {
-    Vector selected = new Vector();
+  private class IntList
+  {
+    /*
+     * list of selected columns (ordered by selection order, not column order)
+     */
+    private List<Integer> order = new ArrayList<Integer>();
 
-    //Vector of int [] {startCol, endCol}
-    Vector hiddenColumns;
+    /**
+     * bitfield for column selection - allows quick lookup
+     */
+    private BitSet selected = new BitSet();
 
     /**
-     * Add a column to the selection
-     *
-     * @param col index of column
+     * adds a new column i to the selection - only if i is not already selected
+     * 
+     * @param i
      */
-    public void addElement(int col)
+    public void add(int i)
     {
-        Integer column = new Integer(col);
-        if (!selected.contains(column))
-        {
-            selected.addElement(column);
-        }
+      if (!selected.get(i))
+      {
+        order.add(Integer.valueOf(i));
+        selected.set(i);
+      }
     }
 
-    /**
-     * clears column selection
-     */
     public void clear()
     {
-        selected.removeAllElements();
+      order.clear();
+      selected.clear();
     }
 
-    /**
-     * removes col from selection
-     *
-     * @param col index of column to be removed
-     */
-    public void removeElement(int col)
+    public void remove(int col)
     {
-        Integer colInt = new Integer(col);
 
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
-    }
+      Integer colInt = new Integer(col);
 
-    /**
-     * 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++)
+      if (selected.get(col))
       {
-        colInt = new Integer(i);
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
+        // if this ever changes to List.remove(), ensure Integer not int
+        // argument
+        // as List.remove(int i) removes the i'th item which is wrong
+        order.remove(colInt);
+        selected.clear(col);
       }
     }
-    /**
-     *
-     * @return Vector containing selected columns as Integers
-     */
-    public Vector getSelected()
+
+    public boolean contains(Integer colInt)
     {
-      return selected;
+      return selected.get(colInt);
     }
 
-    /**
-     *
-     * @param col index to search for in column selection
-     *
-     * @return true if Integer(col) is in selection.
-     */
-    public boolean contains(int col)
+    public boolean isEmpty()
     {
-        return selected.contains(new Integer(col));
+      return order.isEmpty();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int columnAt(int i)
+    public List<Integer> getList()
     {
-        return ((Integer) selected.elementAt(i)).intValue();
+      return order;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
     public int size()
     {
-        return selected.size();
+      return order.size();
     }
 
     /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+     * gets the column that was selected first, second or i'th
+     * 
+     * @param i
+     * @return
      */
-    public int getMax()
+    public int elementAt(int i)
     {
-        int max = -1;
+      return order.get(i);
+    }
 
-        for (int i = 0; i < selected.size(); i++)
+    protected boolean pruneColumnList(final List<int[]> shifts)
+    {
+      int s = 0, t = shifts.size();
+      int[] sr = shifts.get(s++);
+      boolean pruned = false;
+      int i = 0, j = order.size();
+      while (i < j && s <= t)
+      {
+        int c = order.get(i++).intValue();
+        if (sr[0] <= c)
         {
-            if (columnAt(i) > max)
+          if (sr[1] + sr[0] >= c)
+          { // sr[1] -ve means inseriton.
+            order.remove(--i);
+            selected.clear(c);
+            j--;
+          }
+          else
+          {
+            if (s < t)
             {
-                max = columnAt(i);
+              sr = shifts.get(s);
             }
+            s++;
+          }
         }
-
-        return max;
+      }
+      return pruned;
     }
 
     /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+     * shift every selected column at or above start by change
+     * 
+     * @param start
+     *          - leftmost column to be shifted
+     * @param change
+     *          - delta for shift
      */
-    public int getMin()
+    public void compensateForEdits(int start, int change)
     {
-        int min = 1000000000;
+      BitSet mask = new BitSet();
+      for (int i = 0; i < order.size(); i++)
+      {
+        int temp = order.get(i);
 
-        for (int i = 0; i < selected.size(); i++)
+        if (temp >= start)
         {
-            if (columnAt(i) < min)
-            {
-                min = columnAt(i);
-            }
+          // clear shifted bits and update List of selected columns
+          selected.clear(temp);
+          mask.set(temp - change);
+          order.set(i, new Integer(temp - change));
         }
+      }
+      // lastly update the bitfield all at once
+      selected.or(mask);
+    }
 
-        return min;
+    public boolean isSelected(int column)
+    {
+      return selected.get(column);
+    }
+
+    public int getMaxColumn()
+    {
+      return selected.length() - 1;
     }
 
+    public int getMinColumn()
+    {
+      return selected.get(0) ? 0 : selected.nextSetBit(0);
+    }
 
     /**
-     * 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)
+     * @return a series of selection intervals along the range
      */
-    public void compensateForEdit(int start, int change)
+    public List<int[]> getRanges()
+    {
+      List<int[]> rlist = new ArrayList<int[]>();
+      if (selected.isEmpty())
+      {
+        return rlist;
+      }
+      int next = selected.nextSetBit(0), clear = -1;
+      while (next != -1)
+      {
+        clear = selected.nextClearBit(next);
+        rlist.add(new int[] { next, clear - 1 });
+        next = selected.nextSetBit(clear);
+      }
+      return rlist;
+    }
+  }
+
+  IntList selected = new IntList();
+
+  /*
+   * list of hidden column [start, end] ranges; the list is maintained in
+   * ascending start column order
+   */
+  Vector<int[]> hiddenColumns;
+
+  /**
+   * Add a column to the selection
+   * 
+   * @param col
+   *          index of column
+   */
+  public void addElement(int col)
+  {
+    selected.add(col);
+  }
+
+  /**
+   * clears column selection
+   */
+  public void clear()
+  {
+    selected.clear();
+  }
+
+  /**
+   * Removes value 'col' from the selection (not the col'th item)
+   * 
+   * @param col
+   *          index of column to be removed
+   */
+  public void removeElement(int col)
+  {
+    selected.remove(col);
+  }
+
+  /**
+   * 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.remove(colInt);
+      }
+    }
+  }
+
+  /**
+   * Returns a list of selected columns. The list contains no duplicates but is
+   * not necessarily ordered. It also may include columns hidden from the
+   * current view
+   */
+  public List<Integer> getSelected()
+  {
+    return selected.getList();
+  }
+
+  /**
+   * @return list of int arrays containing start and end column position for
+   *         runs of selected columns ordered from right to left.
+   */
+  public List<int[]> getSelectedRanges()
+  {
+    return selected.getRanges();
+  }
+
+  /**
+   * 
+   * @param col
+   *          index to search for in column selection
+   * 
+   * @return true if col is selected
+   */
+  public boolean contains(int col)
+  {
+    return (col > -1) ? selected.isSelected(col) : false;
+  }
+
+  /**
+   * Answers true if no columns are selected, else false
+   */
+  public boolean isEmpty()
+  {
+    return selected == null || selected.isEmpty();
+  }
+
+  /**
+   * rightmost selected column
+   * 
+   * @return rightmost column in alignment that is selected
+   */
+  public int getMax()
+  {
+    if (selected.isEmpty())
     {
-        for (int i = 0; i < size(); i++)
+      return -1;
+    }
+    return selected.getMaxColumn();
+  }
+
+  /**
+   * Leftmost column in selection
+   * 
+   * @return column index of leftmost column in selection
+   */
+  public int getMin()
+  {
+    if (selected.isEmpty())
+    {
+      return 1000000000;
+    }
+    return selected.getMinColumn();
+  }
+
+  /**
+   * 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)
+  {
+    List<int[]> deletedHiddenColumns = null;
+    selected.compensateForEdits(start, change);
+
+    if (hiddenColumns != null)
+    {
+      deletedHiddenColumns = new ArrayList<int[]>();
+      int hSize = hiddenColumns.size();
+      for (int i = 0; i < hSize; i++)
+      {
+        int[] region = hiddenColumns.elementAt(i);
+        if (region[0] > start && start + change > region[1])
         {
-            int temp = columnAt(i);
+          deletedHiddenColumns.add(region);
 
-            if (temp >= start)
-            {
-                selected.setElementAt(new Integer(temp - change), i);
-            }
+          hiddenColumns.removeElementAt(i);
+          i--;
+          hSize--;
+          continue;
         }
 
-        if(hiddenColumns!=null)
+        if (region[0] > start)
         {
-          for(int i=0; i<hiddenColumns.size(); i++)
-          {
-            int[] region = (int[]) hiddenColumns.elementAt(i);
-            if(region[0] > start)
-            {
-              region[0] -= change;
-              region[1] -= change;
-            }
-            if(region[0]<0)
-              region[0] = 0;
-            if(region[1] <0)
-             region[1] = 0;
-          }
+          region[0] -= change;
+          region[1] -= change;
         }
+
+        if (region[0] < 0)
+        {
+          region[0] = 0;
+        }
+
+      }
+
+      this.revealHiddenColumns(0);
     }
-    /**
-     * 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)
+
+    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)
+  {
+
+    selected.compensateForEdits(start, change);
+
+    if (hiddenColumns != null)
     {
-        for (int i = 0; i < size(); i++)
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = hiddenColumns.elementAt(i);
+        if (region[0] >= start)
         {
-            int temp = columnAt(i);
-
-            if (temp >= start)
-            {
-                selected.setElementAt(new Integer(temp - change), i);
-            }
+          region[0] -= change;
         }
-
-        if(hiddenColumns!=null)
+        if (region[1] >= start)
         {
-          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--);
-            }
+          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;
-          }
+        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];
-          }
+  }
+
+  /**
+   * 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)
+    {
+      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);
+          // compensateForEdit(shifted+sh[0], sh[1]);
+          compensateForDelEdits(shifted + sh[0], sh[1]);
+          shifted -= sh[1];
         }
-        return shiftrecord.getInverse();
       }
-      return null;
+      return shiftrecord.getInverse();
     }
-    /**
-     * 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++;
+    return null;
+  }
+
+  /**
+   * removes intersection of position,length ranges in deletions from the
+   * start,end regions marked in intervals.
+   * 
+   * @param shifts
+   * @param intervals
+   * @return
+   */
+  private boolean pruneIntervalVector(final List<int[]> shifts,
+          Vector<int[]> intervals)
+  {
+    boolean pruned = false;
+    int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+    int hr[] = intervals.elementAt(i);
+    int sr[] = shifts.get(s);
+    while (i <= j && s <= t)
+    {
+      boolean trailinghn = hr[1] >= sr[0];
+      if (!trailinghn)
+      {
+        if (i < j)
+        {
+          hr = intervals.elementAt(++i);
+        }
+        else
+        {
+          i++;
+        }
+        continue;
+      }
+      int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
+      if (endshift < hr[0] || endshift < sr[0])
+      { // leadinghc disjoint or not a deletion
+        if (s < t)
+        {
+          sr = shifts.get(++s);
+        }
+        else
+        {
+          s++;
+        }
+        continue;
+      }
+      boolean leadinghn = hr[0] >= sr[0];
+      boolean leadinghc = hr[0] < endshift;
+      boolean trailinghc = hr[1] < endshift;
+      if (leadinghn)
+      {
+        if (trailinghc)
+        { // deleted hidden region.
+          intervals.removeElementAt(i);
+          pruned = true;
+          j--;
+          if (i <= j)
+          {
+            hr = intervals.elementAt(i);
+          }
           continue;
         }
-        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);
+        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;
         }
-        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;
+      }
+    }
+    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(ShiftList deletions)
+  {
+    if (deletions != null)
+    {
+      final List<int[]> shifts = deletions.getShifts();
+      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 (!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;
+        if (selected != null && selected.size() > 0)
+        {
+          selected.pruneColumnList(shifts);
+          if (selected != null && selected.size() == 0)
+          {
+            selected = null;
           }
         }
+        // and shift the rest.
+        this.compensateForEdits(deletions);
       }
-      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++;
-          }
+  }
+
+  /**
+   * This Method is used to return all the HiddenColumn regions
+   * 
+   * @return empty list or List of hidden column intervals
+   */
+  public List<int[]> getHiddenColumns()
+  {
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : 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 = hiddenColumns.elementAt(i);
+        if (result >= region[0])
+        {
+          result += region[1] - region[0] + 1;
         }
       }
-      return pruned;
     }
-    /**
-     * remove any hiddenColumns or selected columns and shift remaining
-     * based on a series of position, range deletions.
-     * @param deletions
+    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 = 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
+   * 
+   * @param hiddenRegion
+   *          index of hidden region (counts from 0)
+   * @return column number in visible view
+   */
+  public int findHiddenRegionPosition(int hiddenRegion)
+  {
+    int result = 0;
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      int gaps = 0;
+      do
+      {
+        int[] region = hiddenColumns.elementAt(index);
+        if (hiddenRegion == 0)
+        {
+          return region[0];
+        }
+
+        gaps += region[1] + 1 - region[0];
+        result = region[1] + 1;
+        index++;
+      } while (index <= hiddenRegion);
+
+      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 = 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 = hiddenColumns.elementAt(index);
+        if (alPos > region[1])
+        {
+          return region[1];
+        }
+
+        index--;
+      } while (index > -1);
+    }
+
+    return alPos;
+
+  }
+
+  public void hideSelectedColumns()
+  {
+    synchronized (selected)
+    {
+      for (int[] selregions : selected.getRanges())
+      {
+        hideColumns(selregions[0], selregions[1]);
+      }
+      selected.clear();
+    }
+
+  }
+
+  /**
+   * Adds the specified column range to the hidden columns
+   * 
+   * @param start
+   * @param end
+   */
+  public void hideColumns(int start, int end)
+  {
+    if (hiddenColumns == null)
+    {
+      hiddenColumns = new Vector<int[]>();
+    }
+
+    /*
+     * traverse existing hidden ranges and insert / amend / append as
+     * appropriate
      */
-    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);
+    for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      int[] region = hiddenColumns.elementAt(i);
+
+      if (end < region[0] - 1)
+      {
+        /*
+         * insert discontiguous preceding range
+         */
+        hiddenColumns.insertElementAt(new int[] { start, end }, i);
+        return;
+      }
+
+      if (end <= region[1])
+      {
+        /*
+         * new range overlaps existing, or is contiguous preceding it - adjust
+         * start column
+         */
+        region[0] = Math.min(region[0], start);
+        return;
+      }
+
+      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);
+        return;
+      }
+    }
+
+    /*
+     * remaining case is that the new range follows everything else
+     */
+    hiddenColumns.addElement(new int[] { start, end });
+  }
+
+  /**
+   * Hides the specified column and any adjacent selected columns
+   * 
+   * @param res
+   *          int
+   */
+  public void hideColumns(int col)
+  {
+    /*
+     * deselect column (whether selected or not!)
+     */
+    removeElement(col);
+
+    /*
+     * find adjacent selected columns
+     */
+    int min = col - 1, max = col + 1;
+    while (contains(min))
+    {
+      removeElement(min);
+      min--;
+    }
+
+    while (contains(max))
+    {
+      removeElement(max);
+      max++;
+    }
+
+    /*
+     * min, max are now the closest unselected columns
+     */
+    min++;
+    max--;
+    if (min > max)
+    {
+      min = max;
+    }
+
+    hideColumns(min, max);
+  }
+
+  /**
+   * Unhides, and adds to the selection list, all hidden columns
+   */
+  public void revealAllHiddenColumns()
+  {
+    if (hiddenColumns != null)
+    {
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = hiddenColumns.elementAt(i);
+        for (int j = region[0]; j < region[1] + 1; j++)
+        {
+          addElement(j);
+        }
+      }
+    }
+
+    hiddenColumns = null;
+  }
+
+  /**
+   * Reveals, and marks as selected, the hidden column range with the given
+   * start column
+   * 
+   * @param start
+   */
+  public void revealHiddenColumns(int start)
+  {
+    for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      int[] region = hiddenColumns.elementAt(i);
+      if (start == region[0])
+      {
+        for (int j = region[0]; j < region[1] + 1; j++)
+        {
+          addElement(j);
         }
+
+        hiddenColumns.removeElement(region);
+        break;
       }
     }
-    /**
-     * This Method is used to return all the HiddenColumn regions
-     * less than the given index.
-     * @param end int
-     * @return Vector
-     */
-    public Vector getHiddenColumns()
+    if (hiddenColumns.size() == 0)
     {
-      return hiddenColumns;
+      hiddenColumns = null;
     }
-    /**
-     * 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)
+  }
+
+  public boolean isVisible(int column)
+  {
+    if (hiddenColumns != null)
     {
-      int result = column;
-      if (hiddenColumns != null)
+      for (int[] region : hiddenColumns)
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
+        if (column >= region[0] && column <= region[1])
         {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          if (result >= region[0])
-          {
-            result += region[1] - region[0] + 1;
-          }
+          return false;
         }
       }
-      return result;
     }
 
-    /**
-     * Use this method to find out where a visible column is in the alignment
-     * when hidden columns exist
-     * @param hiddenColumn int
-     * @return int
-     */
-    public int findColumnPosition(int hiddenColumn)
+    return true;
+  }
+
+  /**
+   * Copy constructor
+   * 
+   * @param copy
+   */
+  public ColumnSelection(ColumnSelection copy)
+  {
+    if (copy != null)
     {
-      int result = hiddenColumn;
-      if (hiddenColumns != null)
+      if (copy.selected != null)
+      {
+        selected = new IntList();
+        for (int i = 0, j = copy.selected.size(); i < j; i++)
+        {
+          selected.add(copy.selected.elementAt(i));
+        }
+      }
+      if (copy.hiddenColumns != null)
       {
-        int index = 0;
-        int gaps = 0;
-        do
+        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
+        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if (hiddenColumn > region[1])
+          int[] rh, cp;
+          rh = copy.hiddenColumns.elementAt(i);
+          if (rh != null)
           {
-            result -= region[1]+1-region[0];
+            cp = new int[rh.length];
+            System.arraycopy(rh, 0, cp, 0, rh.length);
+            hiddenColumns.addElement(cp);
           }
-          index++;
         }
-        while (index < hiddenColumns.size());
-
-        result -= gaps;
       }
-
-      return result;
     }
+  }
 
-    /**
-     * Use this method to determine where the next hiddenRegion starts
-    */
-    public int findHiddenRegionPosition(int hiddenRegion)
+  /**
+   * 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)
     {
-      int result = 0;
-      if (hiddenColumns != null)
+      for (i = 0; i < iSize; i++)
       {
-        int index = 0;
-        int gaps = 0;
-        do
+        StringBuffer visibleSeq = new StringBuffer();
+        List<int[]> regions = getHiddenColumns();
+
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd;
+
+        for (int j = 0; j < regions.size(); j++)
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(hiddenRegion==0)
+          region = regions.get(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+
+          if (hideStart < start)
           {
-            return region[0];
+            continue;
+          }
+
+          blockStart = Math.min(blockStart, hideEnd + 1);
+          blockEnd = Math.min(blockEnd, hideStart);
+
+          if (blockStart > blockEnd)
+          {
+            break;
           }
 
-            gaps +=  region[1] +1 - region[0];
-            result = region[1] +1;
-            index++;
+          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+          blockStart = hideEnd + 1;
+          blockEnd = end;
         }
-        while(index < hiddenRegion+1);
 
-        result -= gaps;
-      }
+        if (end > blockStart)
+        {
+          visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        }
 
-      return result;
+        selection[i] = visibleSeq.toString();
+      }
     }
-
-    /**
-     * 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)
+    else
     {
-      if (hiddenColumns != null)
+      for (i = 0; i < iSize; i++)
       {
-        int index = 0;
-        do
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(alPos < region[0])
-            return region[0];
-
-          index++;
-        }
-        while(index < hiddenColumns.size());
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
+    }
 
-      return alPos;
+    return selection;
+  }
 
-    }
-    /**
-     * 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 getHiddenBoundaryLeft(int alPos)
+  /**
+   * 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)
     {
-      if (hiddenColumns != null)
+      List<int[]> visiblecontigs = new ArrayList<int[]>();
+      List<int[]> regions = getHiddenColumns();
+
+      int vstart = start;
+      int[] region;
+      int hideStart, hideEnd;
+
+      for (int j = 0; vstart < end && j < regions.size(); j++)
       {
-        int index = hiddenColumns.size()-1;
-        do
-        {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(alPos > region[1])
-            return region[1];
+        region = regions.get(j);
+        hideStart = region[0];
+        hideEnd = region[1];
 
-          index--;
+        if (hideEnd < vstart)
+        {
+          continue;
+        }
+        if (hideStart > vstart)
+        {
+          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
         }
-        while(index >-1);
+        vstart = hideEnd + 1;
       }
 
-      return alPos;
+      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 };
+    }
+  }
 
+  /**
+   * 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
+   * 
+   * @param seq
+   * @return int[] { visible start, visible end, first seqpos, last seqpos }
+   */
+  public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+  {
+    int fpos=seq.getStart(),lpos= seq.getEnd();
+    int start = 0;
+    
+    if (hiddenColumns == null || hiddenColumns.size() == 0)
+    {
+      return new int[] { seq.findIndex(fpos) - 1, seq.findIndex(lpos) - 1,
+          fpos,
+          lpos };
     }
 
-    public void hideSelectedColumns()
+    // Simply walk along the sequence whilst watching for hidden column
+    // boundaries
+    List<int[]> regions = getHiddenColumns();
+    int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
+            .getLength(), hideEnd = -1;
+    int visPrev = 0, visNext = 0;
+    boolean foundStart = false;
+    for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+            && p < pLen; p++)
     {
-      while (size() > 0)
+      if (!Comparison.isGap(seq.getCharAt(p)))
       {
-        int column = ( (Integer) getSelected().firstElement()).intValue();
-        hideColumns(column);
+        // 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++;
       }
-
     }
-
-    public void hideColumns(int start, int end)
+    if (foundStart)
     {
-      if(hiddenColumns==null)
-        hiddenColumns = new Vector();
+      return new int[] { findColumnPosition(start),
+          findColumnPosition(lastvispos), fpos, lpos };
+    }
+    // otherwise, sequence was completely hidden
+    return new int[] { visPrev, visNext, 0, 0 };
+  }
 
-      boolean added = false;
-      boolean overlap = false;
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param alignmentAnnotation
+   */
+  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+  }
 
-      for (int i = 0; i < hiddenColumns.size(); i++)
+  /**
+   * 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<Annotation[]> annels = new Vector<Annotation[]>();
+      Annotation[] els = null;
+      List<int[]> regions = getHiddenColumns();
+      int blockStart = start, blockEnd = end;
+      int[] region;
+      int hideStart, hideEnd, w = 0;
+
+      for (int j = 0; j < regions.size(); j++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
-        if ( start<=region[1] && end>=region[0])
+        region = regions.get(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        if (hideStart < start)
         {
-          hiddenColumns.removeElementAt(i);
-          overlap = true;
-          break;
+          continue;
         }
-        else if (end < region[0] && start < region[0])
+
+        blockStart = Math.min(blockStart, hideEnd + 1);
+        blockEnd = Math.min(blockEnd, hideStart);
+
+        if (blockStart > blockEnd)
         {
-          hiddenColumns.insertElementAt(new int[]
-                                        {start, end}, i);
-          added = true;
           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(overlap)
+      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)
       {
-         hideColumns(start, end);
+        return;
       }
-      else if (!added)
-        hiddenColumns.addElement(new int[] {start, end});
 
-    }
+      alignmentAnnotation.annotations = new Annotation[w];
+      w = 0;
 
-    /**
-     * This method will find a range of selected columns
-     * around the column specified
-     * @param res int
-     */
-    public void hideColumns(int col)
+      for (Annotation[] chnk : annels)
+      {
+        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                chnk.length);
+        w += chnk.length;
+      }
+    }
+    else
     {
-      // 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--;
-
-      hideColumns(min, max);
+      alignmentAnnotation.restrict(start, end);
     }
+  }
 
-    public void revealAllHiddenColumns()
+  /**
+   * 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(hiddenColumns!=null)
+      if (contains(i))
+      {
+        removeElement(i);
+      }
+      else
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
+        if (!hasHidden || isVisible(i))
         {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          for (int j = region[0]; j < region[1]+1; j++)
-          {
-            addElement(j);
-          }
+          addElement(i);
         }
       }
-
-      hiddenColumns = null;
     }
+  }
 
-    public void revealHiddenColumns(int res)
+  /**
+   * 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.isEmpty())
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      for (Integer col : colsel.getSelected())
       {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( res == region[0])
+        if (hiddenColumns != null && isVisible(col.intValue()))
         {
-          for (int j = region[0]; j < region[1]+1; j++)
-          {
-            addElement(j);
-          }
-
-          hiddenColumns.removeElement(region);
-          break;
+          selected.add(col);
         }
       }
-      if(hiddenColumns.size()==0)
-        hiddenColumns = null;
     }
+  }
 
-    public boolean isVisible(int column)
+  /**
+   * set the selected columns the given column selection, excluding any columns
+   * that are hidden.
+   * 
+   * @param colsel
+   */
+  public void setElementsFrom(ColumnSelection colsel)
+  {
+    selected = new IntList();
+    if (colsel.selected != null && colsel.selected.size() > 0)
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
+      {
+        // only select visible columns in this columns selection
+        addElementsFrom(colsel);
+      }
+      else
       {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( column >= region[0] && column <= region[1])
+        // add everything regardless
+        for (Integer col : colsel.getSelected())
         {
-          return false;
+          addElement(col);
         }
       }
-      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.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
-          }
+  }
+
+  /**
+   * 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,
+          AlignmentI 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);
         }
-        if (copy.hiddenColumns!=null) {
-          hiddenColumns=new Vector();
-          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.setElementAt(cp, i);
+        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();
+        }
       }
     }
+  }
 
   /**
-   * ColumnSelection
+   * 
+   * @return true if there are columns marked
    */
-  public ColumnSelection()
+  public boolean hasSelectedColumns()
   {
+    return (selected != null && selected.size() > 0);
   }
 
-  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;
+  /**
+   * 
+   * @return true if there are columns hidden
+   */
+  public boolean hasHiddenColumns()
+  {
+    return hiddenColumns != null && hiddenColumns.size() > 0;
+  }
 
-           for (int j = 0; j < regions.size(); j++)
-           {
-             region = (int[]) regions.elementAt(j);
-             hideStart = region[0];
-             hideEnd = region[1];
+  /**
+   * 
+   * @return true if there are more than one set of columns hidden
+   */
+  public boolean hasManyHiddenColumns()
+  {
+    return hiddenColumns != null && hiddenColumns.size() > 1;
+  }
 
-             if(hideStart < start)
-             {
-               continue;
-             }
+  /**
+   * mark the columns corresponding to gap characters as hidden in the column
+   * selection
+   * 
+   * @param sr
+   */
+  public void hideInsertionsFor(SequenceI sr)
+  {
+    List<int[]> inserts = sr.getInsertions();
+    for (int[] r : inserts)
+    {
+      hideColumns(r[0], r[1]);
+    }
+  }
 
-             blockStart = Math.min(blockStart, hideEnd+1);
-             blockEnd = Math.min(blockEnd, hideStart);
+  public boolean filterAnnotations(Annotation[] annotations,
+          AnnotationFilterParameter filterParams)
+  {
+    // JBPNote - this method needs to be refactored to become independent of
+    // viewmodel package
+    this.revealAllHiddenColumns();
+    this.clear();
+    int count = 0;
+    do
+    {
+      if (annotations[count] != null)
+      {
 
-             if(blockStart>blockEnd)
-             {
-                break;
-             }
+        boolean itemMatched = false;
 
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+                && annotations[count].value >= filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+                && annotations[count].value <= filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
 
-             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+        if (filterParams.isFilterAlphaHelix()
+                && annotations[count].secondaryStructure == 'H')
+        {
+          itemMatched = true;
+        }
 
-             blockStart = hideEnd+1;
-             blockEnd = end;
-           }
+        if (filterParams.isFilterBetaSheet()
+                && annotations[count].secondaryStructure == 'E')
+        {
+          itemMatched = true;
+        }
 
-           if(end>blockStart)
-             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        if (filterParams.isFilterTurn()
+                && annotations[count].secondaryStructure == 'S')
+        {
+          itemMatched = true;
+        }
 
-           selection[i] = visibleSeq.toString();
+        String regexSearchString = filterParams.getRegexString();
+        if (regexSearchString != null
+                && !filterParams.getRegexSearchFields().isEmpty())
+        {
+          List<SearchableAnnotationField> fields = filterParams
+                  .getRegexSearchFields();
+          try
+          {
+            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
+                    && annotations[count].displayCharacter
+                            .matches(regexSearchString))
+            {
+              itemMatched = true;
+            }
+          } catch (java.util.regex.PatternSyntaxException pse)
+          {
+            if (annotations[count].displayCharacter
+                    .equals(regexSearchString))
+            {
+              itemMatched = true;
+            }
+          }
+          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
+                  && annotations[count].description != null
+                  && annotations[count].description
+                          .matches(regexSearchString))
+          {
+            itemMatched = true;
+          }
         }
-      }
-      else
-      {
-        for(i=0; i<iSize; i++)
+
+        if (itemMatched)
         {
-        selection[i] = seqs[i].getSequence(start, end);
+          this.addElement(count);
         }
       }
-      
-    return selection;
-    }
-  
+      count++;
+    } while (count < annotations.length);
+    return false;
+  }
+
 }