X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=4904495ee9ad8b919fecee944b3a8668900b6148;hb=0f3ec4858fa41dcc8b815402ba971fb2184ae27b;hp=ad6689488792191e953f429f752a7c1ca742912c;hpb=af8696684758d73680cb775f35b05c5eda879353;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index ad66894..4904495 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -20,432 +20,884 @@ 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;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     */
-    public void addElement(int col)
+  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))
     {
-        if (!selected.contains(new Integer(col)))
-        {
-            selected.addElement(new Integer(col));
-        }
+      selected.addElement(column);
     }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void clear()
+  }
+
+  /**
+   * 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.removeAllElements();
+      selected.removeElement(colInt);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     */
-    public void removeElement(int 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++)
     {
-        Integer colInt = new Integer(col);
-
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
+      colInt = new Integer(i);
+      if (selected.contains(colInt))
+      {
+        selected.removeElement(colInt);
+      }
     }
-
-    public void removeElements(int start, int end)
+  }
+
+  /**
+   *
+   * @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));
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int columnAt(int i)
+  {
+    return ( (Integer) selected.elementAt(i)).intValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int size()
+  {
+    return selected.size();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getMax()
+  {
+    int max = -1;
+
+    for (int i = 0; i < selected.size(); i++)
     {
-      Integer colInt;
-      for(int i=start; i<end; i++)
+      if (columnAt(i) > max)
       {
-        colInt = new Integer(i);
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
+        max = columnAt(i);
       }
     }
 
-    public Vector getSelected()
-    {
-      return selected;
-    }
+    return max;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean contains(int col)
-    {
-        return selected.contains(new Integer(col));
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getMin()
+  {
+    int min = 1000000000;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int columnAt(int i)
+    for (int i = 0; i < selected.size(); i++)
     {
-        return ((Integer) selected.elementAt(i)).intValue();
+      if (columnAt(i) < min)
+      {
+        min = columnAt(i);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int size()
+    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++)
     {
-        return selected.size();
+      int temp = columnAt(i);
+
+      if (temp >= start)
+      {
+        selected.setElementAt(new Integer(temp - change), i);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMax()
+    if (hiddenColumns != null)
     {
-        int max = -1;
-
-        for (int i = 0; i < selected.size(); i++)
+      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])
         {
-            if (columnAt(i) > max)
-            {
-                max = columnAt(i);
-            }
-        }
+          deletedHiddenColumns.addElement(
+              hiddenColumns.elementAt(i));
 
-        return max;
-    }
+          hiddenColumns.removeElementAt(i);
+          i--;
+          hSize--;
+          continue;
+        }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMin()
-    {
-        int min = 1000000000;
+        if (region[0] > start)
+        {
+          region[0] -= change;
+          region[1] -= change;
+        }
 
-        for (int i = 0; i < selected.size(); i++)
+        if (region[0] < 0)
         {
-            if (columnAt(i) < min)
-            {
-                min = columnAt(i);
-            }
+          region[0] = 0;
         }
 
-        return min;
+      }
+
+      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);
+      }
+    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     * @param change DOCUMENT ME!
-     */
-    public void compensateForEdit(int start, int change)
+    if (hiddenColumns != null)
     {
-        for (int i = 0; i < size(); i++)
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) 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 (region[1] >= start)
+        {
+          region[1] -= change;
+        }
+        if (region[1] < region[0])
+        {
+          hiddenColumns.removeElementAt(i--);
         }
 
-        if(hiddenColumns!=null)
+        if (region[0] < 0)
         {
-          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] = 0;
         }
+        if (region[1] < 0)
+        {
+          region[1] = 0;
+        }
+      }
     }
-
-    /**
-     * This Method is used to return all the HiddenColumn regions
-     * less than the given index.
-     * @param end int
-     * @return Vector
-     */
-    public Vector getHiddenColumns()
+  }
+
+  /**
+   * 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)
     {
-      return hiddenColumns;
+      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();
     }
-
-    public int adjustForHiddenColumns(int column)
+    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)
     {
-      int result = column;
-      if (hiddenColumns != null)
+      boolean trailinghn = hr[1] >= sr[0];
+      if (!trailinghn)
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
+        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)
         {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          if (result >= region[0])
+          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)
           {
-            result += region[1] - region[0] + 1;
+            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 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 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 result = hiddenColumn;
-      if (hiddenColumns != null)
+      int c = ( (Integer) list.elementAt(i++)).intValue();
+      if (sr[0] <= c)
       {
-        int index = 0;
-        int gaps = 0;
-        do
+        if (sr[1] + sr[0] >= c)
+        { // sr[1] -ve means inseriton.
+          list.removeElementAt(--i);
+          j--;
+        }
+        else
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if (hiddenColumn > region[1])
+          if (s < t)
           {
-            result -= region[1]+1-region[0];
+            sr = (int[]) deletion.elementAt(s);
           }
-          index++;
+          s++;
         }
-        while (index < hiddenColumns.size());
-
-        result -= gaps;
       }
-
-      return result;
     }
-
-    /**
-     * Use this method to determine where the next hiddenRegion starts
-    */
-    public int findHiddenRegionPosition(int hiddenRegion)
+    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)
     {
-      int result = 0;
-      if (hiddenColumns != null)
+      Vector shifts = deletions.shifts;
+      if (shifts != null && shifts.size() > 0)
       {
-        int index = 0;
-        int gaps = 0;
-        do
+        // delete any intervals intersecting.
+        if (hiddenColumns != null)
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(hiddenRegion==0)
+          pruneIntervalVector(shifts, hiddenColumns);
+          if (hiddenColumns != null && hiddenColumns.size() == 0)
           {
-            return region[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 visible column is in the alignment
+   * when hidden columns exist
+   * @param hiddenColumn int
+   * @return int
+   */
+  public int findColumnPosition(int hiddenColumn)
+  {
+    int result = hiddenColumn;
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      int gaps = 0;
+      do
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if (hiddenColumn > region[1])
+        {
+          result -= region[1] + 1 - region[0];
+        }
+        index++;
+      }
+      while (index < hiddenColumns.size());
 
-            gaps +=  region[1] +1 - region[0];
-            result = region[1] +1;
-            index++;
+      result -= gaps;
+    }
+
+    return result;
+  }
+
+  /**
+   * 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];
         }
-        while(index < hiddenRegion+1);
 
-        result -= gaps;
+        gaps += region[1] + 1 - region[0];
+        result = region[1] + 1;
+        index++;
       }
+      while (index < hiddenRegion + 1);
 
-      return result;
+      result -= gaps;
     }
 
-    /**
-     * 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)
+    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)
     {
-      if (hiddenColumns != null)
+      int index = 0;
+      do
       {
-        int index = 0;
-        do
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if (alPos < region[0])
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(alPos < region[0])
-            return region[0];
-
-          index++;
+          return region[0];
         }
-        while(index < hiddenColumns.size());
+
+        index++;
       }
+      while (index < hiddenColumns.size());
+    }
 
-      return alPos;
+    return alPos;
 
-    }
-    /**
-     * 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)
+  }
+
+  /**
+   * 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)
     {
-      if (hiddenColumns != null)
+      int index = hiddenColumns.size() - 1;
+      do
       {
-        int index = hiddenColumns.size()-1;
-        do
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if (alPos > region[1])
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(alPos > region[1])
-            return region[1];
-
-          index--;
+          return region[1];
         }
-        while(index >-1);
+
+        index--;
       }
+      while (index > -1);
+    }
 
-      return alPos;
+    return alPos;
+
+  }
+
+  public void hideSelectedColumns()
+  {
+    while (size() > 0)
+    {
+      int column = ( (Integer) getSelected().firstElement()).intValue();
+      hideColumns(column);
     }
 
-    public void hideSelectedColumns()
+  }
+
+  public void hideColumns(int start, int end)
+  {
+    if (hiddenColumns == null)
     {
-      while (size() > 0)
+      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])
       {
-        int column = ( (Integer) getSelected().firstElement()).intValue();
-        hideColumns(column);
+        hiddenColumns.insertElementAt(new int[]
+                                      {start, end}, i);
+        added = true;
+        break;
       }
+    }
 
+    if (overlap)
+    {
+      hideColumns(start, end);
+    }
+    else if (!added)
+    {
+      hiddenColumns.addElement(new int[]
+                               {start, end});
     }
 
-    public void hideColumns(int start, int 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))
     {
-      if(hiddenColumns==null)
-        hiddenColumns = new Vector();
+      removeElement(min);
+      min--;
+    }
 
-      boolean added = false;
-      boolean overlap = false;
+    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);
-        if ( start<=region[1] && end>=region[0])
-        {
-          hiddenColumns.removeElementAt(i);
-          overlap = true;
-          break;
-        }
-        else if (end < region[0] && start < region[0])
+        for (int j = region[0]; j < region[1] + 1; j++)
         {
-          hiddenColumns.insertElementAt(new int[]
-                                        {start, end}, i);
-          added = true;
-          break;
+          addElement(j);
         }
       }
+    }
+
+    hiddenColumns = null;
+  }
 
-      if(overlap)
+  public void revealHiddenColumns(int res)
+  {
+    for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      int[] region = (int[]) hiddenColumns.elementAt(i);
+      if (res == region[0])
       {
-         hideColumns(start, end);
-      }
-      else if (!added)
-        hiddenColumns.addElement(new int[] {start, end});
+        for (int j = region[0]; j < region[1] + 1; j++)
+        {
+          addElement(j);
+        }
 
+        hiddenColumns.removeElement(region);
+        break;
+      }
     }
-
-    /**
-     * This method will find a range of selected columns
-     * around the column specified
-     * @param res int
-     */
-    public void hideColumns(int col)
+    if (hiddenColumns.size() == 0)
     {
-      // 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 ++;  }
+      hiddenColumns = null;
+    }
+  }
 
-      min++; max--;
+  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;
+        }
+      }
 
-      hideColumns(min, max);
-    }
+    return true;
+  }
 
-    public void revealAllHiddenColumns()
+  /**
+   * Copy constructor
+   * @param copy
+   */
+  public ColumnSelection(ColumnSelection copy)
+  {
+    if (copy != null)
     {
-      if(hiddenColumns!=null)
+      if (copy.selected != null)
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
+        selected = new Vector();
+        for (int i = 0, j = copy.selected.size(); i < j; i++)
         {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          for (int j = region[0]; j < region[1]; j++)
+          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)
           {
-            addElement(j);
+            cp = new int[rh.length];
+            System.arraycopy(rh, 0, cp, 0, rh.length);
+            hiddenColumns.addElement(cp);
           }
         }
       }
-
-      hiddenColumns = null;
     }
-
-    public void revealHiddenColumns(int res)
+  }
+
+  /**
+   * 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(int i=0; i<hiddenColumns.size(); i++)
+      for (i = 0; i < iSize; i++)
       {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( res == region[0])
+        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++)
         {
-          for (int j = region[0]; j < region[1]; j++)
+          region = (int[]) regions.elementAt(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+
+          if (hideStart < start)
           {
-            addElement(j);
+            continue;
           }
 
-          hiddenColumns.removeElement(region);
-          break;
+          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);
       }
-      if(hiddenColumns.size()==0)
-        hiddenColumns = null;
     }
 
-    public boolean isVisible(int column)
+    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)
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      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++)
       {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( column >= region[0] && column <= region[1])
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        if (hideEnd < vstart)
         {
-          return false;
+          continue;
+        }
+        if (hideStart > vstart)
+        {
+          visiblecontigs.addElement(new int[]
+                                    {vstart, hideStart - 1});
         }
+        vstart = hideEnd + 1;
       }
-      return true;
-    }
 
+      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};
+    }
+  }
 }