From 5655997c202bfcb4ab2778999d785490d3a7dbae Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 6 Oct 2006 16:15:29 +0000
Subject: [PATCH] new getVisibleContigs method mirrors the getVisibleContigs
 method in AlignmentView

---
 src/jalview/datamodel/ColumnSelection.java | 1112 +++++++++++++++-------------
 1 file changed, 580 insertions(+), 532 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 2d22231..c895b2f 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -27,641 +27,640 @@ import java.util.*;
  */
 public class ColumnSelection
 {
-    Vector selected = new Vector();
+  Vector selected = new Vector();
 
-    //Vector of int [] {startCol, endCol}
-    Vector hiddenColumns;
+  //Vector of int [] {startCol, endCol}
+  Vector hiddenColumns;
 
-    /**
-     * Add a column to the selection
-     *
-     * @param col index of column
-     */
-    public void addElement(int col)
+  /**
+   * 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))
     {
-        Integer column = new Integer(col);
-        if (!selected.contains(column))
-        {
-            selected.addElement(column);
-        }
+      selected.addElement(column);
     }
+  }
 
-    /**
-     * clears column selection
-     */
-    public void clear()
-    {
-        selected.removeAllElements();
-    }
+  /**
+   * 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);
+  /**
+   * 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);
-        }
+    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)
+  /**
+   * 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;
-      for(int i=start; i<end; i++)
+      colInt = new Integer(i);
+      if (selected.contains(colInt))
       {
-        colInt = new Integer(i);
-        if (selected.contains(colInt))
-        {
-            selected.removeElement(colInt);
-        }
+        selected.removeElement(colInt);
       }
     }
-    /**
-     *
-     * @return Vector containing selected columns as Integers
-     */
-    public Vector getSelected()
-    {
-      return selected;
-    }
+  }
+  /**
+   *
+   * @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));
-    }
+  /**
+   *
+   * @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;
 
-    /**
-     * 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) > max)
+      {
+        max = columnAt(i);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int size()
+    return max;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getMin()
+  {
+    int min = 1000000000;
+
+    for (int i = 0; i < selected.size(); i++)
     {
-        return selected.size();
+      if (columnAt(i) < min)
+      {
+        min = columnAt(i);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMax()
-    {
-        int max = -1;
+    return min;
+  }
 
-        for (int i = 0; i < selected.size(); i++)
-        {
-            if (columnAt(i) > max)
-            {
-                max = columnAt(i);
-            }
-        }
 
-        return max;
+  /**
+   * 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);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMin()
+    if(hiddenColumns!=null)
     {
-        int min = 1000000000;
-
-        for (int i = 0; i < selected.size(); i++)
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if(region[0] > start)
         {
-            if (columnAt(i) < min)
-            {
-                min = columnAt(i);
-            }
+          region[0] -= change;
+          region[1] -= change;
         }
-
-        return min;
+        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);
+      }
+    }
 
-    /**
-     * 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)
+    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(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;
-          }
+        if (region[1]>= start) {
+          region[1] -=change;
         }
-    }
-    /**
-     * 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 (region[1]<region[0]) {
+          hiddenColumns.removeElementAt(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;
-          }
-        }
+        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) {
+      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;
+      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 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;
         }
-        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 (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;
         }
-        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; // 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;
+    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;
           }
-          // and shift the rest.
-          this.compensateForEdits(deletions);
         }
+        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)
+  }
+  /**
+   * 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)
     {
-      int result = column;
-      if (hiddenColumns != null)
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if (result >= region[0])
         {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          if (result >= region[0])
-          {
-            result += region[1] - region[0] + 1;
-          }
+          result += region[1] - region[0] + 1;
         }
       }
-      return result;
     }
+    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)
+  /**
+   * 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 result = hiddenColumn;
-      if (hiddenColumns != null)
+      int index = 0;
+      int gaps = 0;
+      do
       {
-        int index = 0;
-        int gaps = 0;
-        do
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if (hiddenColumn > region[1])
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if (hiddenColumn > region[1])
-          {
-            result -= region[1]+1-region[0];
-          }
-          index++;
+          result -= region[1]+1-region[0];
         }
-        while (index < hiddenColumns.size());
-
-        result -= gaps;
+        index++;
       }
+      while (index < hiddenColumns.size());
 
-      return result;
+      result -= gaps;
     }
 
-    /**
-     * Use this method to determine where the next hiddenRegion starts
-    */
-    public int findHiddenRegionPosition(int hiddenRegion)
+    return result;
+  }
+
+  /**
+   * Use this method to determine where the next hiddenRegion starts
+   */
+  public int findHiddenRegionPosition(int hiddenRegion)
+  {
+    int result = 0;
+    if (hiddenColumns != null)
     {
-      int result = 0;
-      if (hiddenColumns != null)
+      int index = 0;
+      int gaps = 0;
+      do
       {
-        int index = 0;
-        int gaps = 0;
-        do
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if(hiddenRegion==0)
         {
-          int[] region = (int[]) hiddenColumns.elementAt(index);
-          if(hiddenRegion==0)
-          {
-            return region[0];
-          }
-
-            gaps +=  region[1] +1 - region[0];
-            result = region[1] +1;
-            index++;
+          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])
-            return region[0];
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if(alPos < region[0])
+          return region[0];
 
-          index++;
-        }
-        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 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)
     {
-      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])
-            return region[1];
+        int[] region = (int[]) hiddenColumns.elementAt(index);
+        if(alPos > region[1])
+          return region[1];
 
-          index--;
-        }
-        while(index >-1);
+        index--;
       }
+      while(index >-1);
+    }
 
-      return alPos;
+    return alPos;
 
-    }
+  }
 
-    public void hideSelectedColumns()
+  public void hideSelectedColumns()
+  {
+    while (size() > 0)
     {
-      while (size() > 0)
-      {
-        int column = ( (Integer) getSelected().firstElement()).intValue();
-        hideColumns(column);
-      }
-
+      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;
+  public void hideColumns(int start, int end)
+  {
+    if(hiddenColumns==null)
+      hiddenColumns = new Vector();
 
-      for (int i = 0; i < hiddenColumns.size(); i++)
+    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])
       {
-        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;
-        }
+        hiddenColumns.removeElementAt(i);
+        overlap = true;
+        break;
       }
-
-      if(overlap)
+      else if (end < region[0] && start < region[0])
       {
-         hideColumns(start, end);
+        hiddenColumns.insertElementAt(new int[]
+                                              {start, end}, i);
+        added = true;
+        break;
       }
-      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)
+    if(overlap)
     {
-      // First find out range of columns to hide
-      int min = col, max = col+1;
-      while( contains(min) )
-      {  removeElement(min); min --;  }
+      hideColumns(start, end);
+    }
+    else if (!added)
+      hiddenColumns.addElement(new int[] {start, end});
 
-      while( contains(max) )
-      { removeElement(max);  max ++;  }
+  }
 
-      min++; max--;
+  /**
+   * 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 --;  }
 
-      hideColumns(min, max);
-    }
+    while( contains(max) )
+    { removeElement(max);  max ++;  }
+
+    min++; max--;
+
+    hideColumns(min, max);
+  }
 
-    public void revealAllHiddenColumns()
+  public void revealAllHiddenColumns()
+  {
+    if(hiddenColumns!=null)
     {
-      if(hiddenColumns!=null)
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        for (int j = region[0]; j < region[1]+1; j++)
         {
-          int[] region = (int[]) hiddenColumns.elementAt(i);
-          for (int j = region[0]; j < region[1]+1; j++)
-          {
-            addElement(j);
-          }
+          addElement(j);
         }
       }
-
-      hiddenColumns = null;
     }
 
-    public void revealHiddenColumns(int res)
+    hiddenColumns = null;
+  }
+
+  public void revealHiddenColumns(int res)
+  {
+    for(int i=0; i<hiddenColumns.size(); i++)
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      int [] region = (int[])hiddenColumns.elementAt(i);
+      if( res == region[0])
       {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( res == region[0])
+        for (int j = region[0]; j < region[1]+1; j++)
         {
-          for (int j = region[0]; j < region[1]+1; j++)
-          {
-            addElement(j);
-          }
-
-          hiddenColumns.removeElement(region);
-          break;
+          addElement(j);
         }
+
+        hiddenColumns.removeElement(region);
+        break;
       }
-      if(hiddenColumns.size()==0)
-        hiddenColumns = null;
     }
+    if(hiddenColumns.size()==0)
+      hiddenColumns = null;
+  }
 
-    public boolean isVisible(int column)
+  public boolean isVisible(int column)
+  {
+    for(int i=0; i<hiddenColumns.size(); i++)
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      int [] region = (int[])hiddenColumns.elementAt(i);
+      if( column >= region[0] && column <= region[1])
       {
-        int [] region = (int[])hiddenColumns.elementAt(i);
-        if( column >= region[0] && column <= region[1])
-        {
-          return false;
-        }
+        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);
-          }
+    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);
-            }
+      }
+      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
    */
@@ -673,56 +672,105 @@ public class ColumnSelection
     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;
+        int hideStart, hideEnd;
 
-           for (int j = 0; j < regions.size(); j++)
-           {
-             region = (int[]) regions.elementAt(j);
-             hideStart = region[0];
-             hideEnd = region[1];
+        for (int j = 0; j < regions.size(); j++)
+        {
+          region = (int[]) regions.elementAt(j);
+          hideStart = region[0];
+          hideEnd = region[1];
 
-             if(hideStart < start)
-             {
-               continue;
-             }
+          if(hideStart < start)
+          {
+            continue;
+          }
 
-             blockStart = Math.min(blockStart, hideEnd+1);
-             blockEnd = Math.min(blockEnd, hideStart);
+          blockStart = Math.min(blockStart, hideEnd+1);
+          blockEnd = Math.min(blockEnd, hideStart);
 
-             if(blockStart>blockEnd)
-             {
-                break;
-             }
+          if(blockStart>blockEnd)
+          {
+            break;
+          }
 
 
-             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
 
-             blockStart = hideEnd+1;
-             blockEnd = end;
-           }
+          blockStart = hideEnd+1;
+          blockEnd = end;
+        }
 
-           if(end>blockStart)
-             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        if(end>blockStart)
+          visibleSeq.append(seqs[i].getSequence(blockStart, end));
 
-           selection[i] = visibleSeq.toString();
-        }
+        selection[i] = visibleSeq.toString();
       }
-      else
+    }
+    else
+    {
+      for(i=0; i<iSize; i++)
       {
-        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 };
     }
-  
+  }
 }
-- 
1.7.10.2