From 8b08ad675b71e43e127d7be3b65c6d2f9d9094db Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 10 Oct 2006 10:44:03 +0000
Subject: [PATCH] 1.1 compatible

---
 src/jalview/datamodel/ColumnSelection.java | 1552 ++++++++++++++--------------
 1 file changed, 776 insertions(+), 776 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index c895b2f..c35ff46 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,776 +1,776 @@
-/*
- * 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
- * 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.
- *
- * 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
- */
-package jalview.datamodel;
-
-import jalview.util.ShiftList;
-
-import java.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));
-  }
-
-  /**
-   * 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++)
-    {
-      if (columnAt(i) > max)
-      {
-        max = columnAt(i);
-      }
-    }
-
-    return max;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  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 void compensateForEdit(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;
-          region[1] -= change;
-        }
-        if(region[0]<0)
-          region[0] = 0;
-        if(region[1] <0)
-          region[1] = 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)
-  {
-    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 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());
-
-      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];
-        }
-
-        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 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)
-  {
-    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--;
-
-    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)
-  {
-    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.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
-        }
-      }
-      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);
-          }
-        }
-      }
-    }
-  }
-  /**
-   * 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].getSequence(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.get(i);
-        visiblecontigs.setElementAt(null, i);
-        vcontigs[i*2] = vc[0];
-        vcontigs[i*2+1] = vc[1];
-      }
-      visiblecontigs.clear();
-      return vcontigs;
-    }     
-    else
-    {
-      return new int[] { start, end-1 };
-    }
-  }
-}
+/*
+ * 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
+ * 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.
+ *
+ * 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
+ */
+package jalview.datamodel;
+
+import jalview.util.ShiftList;
+
+import java.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));
+  }
+
+  /**
+   * 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++)
+    {
+      if (columnAt(i) > max)
+      {
+        max = columnAt(i);
+      }
+    }
+
+    return max;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  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 void compensateForEdit(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;
+          region[1] -= change;
+        }
+        if(region[0]<0)
+          region[0] = 0;
+        if(region[1] <0)
+          region[1] = 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)
+  {
+    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 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());
+
+      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];
+        }
+
+        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 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)
+  {
+    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--;
+
+    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)
+  {
+    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.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
+        }
+      }
+      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);
+          }
+        }
+      }
+    }
+  }
+  /**
+   * 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].getSequence(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 };
+    }
+  }
+}
-- 
1.7.10.2