X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=9ec4270c8830bba64486111cbca941963ab058d6;hb=49685e6426d5ac136dce4907196751680c667670;hp=6b448320f0aa225a53a266ab9f75bfec1203163c;hpb=d4f6172fff9d39d2cf3bd1a8d0260521615a5993;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6b44832..9ec4270 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,27 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
 
+import jalview.util.*;
+
 /**
  * NOTE: Columns are zero based.
  */
@@ -77,7 +77,7 @@ public class ColumnSelection
   public void removeElements(int start, int end)
   {
     Integer colInt;
-    for(int i=start; i<end; i++)
+    for (int i = start; i < end; i++)
     {
       colInt = new Integer(i);
       if (selected.contains(colInt))
@@ -86,6 +86,7 @@ public class ColumnSelection
       }
     }
   }
+
   /**
    *
    * @return Vector containing selected columns as Integers
@@ -107,15 +108,15 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
+   * Column number at position i in selection
    *
-   * @param i DOCUMENT ME!
+   * @param i index into selected columns
    *
-   * @return DOCUMENT ME!
+   * @return column number in alignment
    */
   public int columnAt(int i)
   {
-    return ((Integer) selected.elementAt(i)).intValue();
+    return ( (Integer) selected.elementAt(i)).intValue();
   }
 
   /**
@@ -129,9 +130,9 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
+   * rightmost selected column
    *
-   * @return DOCUMENT ME!
+   * @return rightmost column in alignment that is selected
    */
   public int getMax()
   {
@@ -149,9 +150,9 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
+   * Leftmost column in selection
    *
-   * @return DOCUMENT ME!
+   * @return column index of leftmost column in selection
    */
   public int getMin()
   {
@@ -168,7 +169,6 @@ public class ColumnSelection
     return min;
   }
 
-
   /**
    * propagate shift in alignment columns to column selection
    *
@@ -188,14 +188,14 @@ public class ColumnSelection
       }
     }
 
-    if(hiddenColumns!=null)
+    if (hiddenColumns != null)
     {
       deletedHiddenColumns = new Vector();
       int hSize = hiddenColumns.size();
-      for(int i=0; i<hSize; i++)
+      for (int i = 0; i < hSize; i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
-        if ( region[0]>start && start+change>region[1] )
+        if (region[0] > start && start + change > region[1])
         {
           deletedHiddenColumns.addElement(
               hiddenColumns.elementAt(i));
@@ -206,14 +206,16 @@ public class ColumnSelection
           continue;
         }
 
-        if(region[0]>start)
+        if (region[0] > start)
         {
           region[0] -= change;
           region[1] -= change;
         }
 
-        if(region[0]<0)
+        if (region[0] < 0)
+        {
           region[0] = 0;
+        }
 
       }
 
@@ -222,6 +224,7 @@ public class ColumnSelection
 
     return deletedHiddenColumns;
   }
+
   /**
    * propagate shift in alignment columns to column selection
    * special version of compensateForEdit - allowing for edits within hidden regions
@@ -240,51 +243,63 @@ public class ColumnSelection
       }
     }
 
-    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);
-        if(region[0] >= start)
+        if (region[0] >= start)
         {
           region[0] -= change;
         }
-        if (region[1]>= start) {
-          region[1] -=change;
+        if (region[1] >= start)
+        {
+          region[1] -= change;
         }
-        if (region[1]<region[0]) {
+        if (region[1] < region[0])
+        {
           hiddenColumns.removeElementAt(i--);
         }
 
-        if(region[0]<0)
+        if (region[0] < 0)
+        {
           region[0] = 0;
-        if(region[1] <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) {
+  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++) {
+      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];
+          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.
@@ -292,110 +307,155 @@ public class ColumnSelection
    * @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);
+  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);
+      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.
+      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;
+          pruned = true;
           j--;
-          if (i<=j)
-            hr=(int[]) intervals.elementAt(i);
+          if (i <= j)
+          {
+            hr = (int[]) intervals.elementAt(i);
+          }
           continue;
         }
-        if (leadinghc) {
-          hr[0]=endshift; // clip c terminal region
-          leadinghn=!leadinghn;
-          pruned=true;
+        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;
+      if (!leadinghn)
+      {
+        if (trailinghc)
+        {
+          if (trailinghn)
+          {
+            hr[1] = sr[0] - 1;
+            pruned = true;
           }
-        } else {
+        }
+        else
+        {
           // sr contained in hr
-          if (s<t)
-            sr=(int[]) deletions.elementAt(++s);
+          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.
+
+  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);
+        }
+        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) {
+  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) {
+        if (hiddenColumns != null)
+        {
           pruneIntervalVector(shifts, hiddenColumns);
-          if (hiddenColumns!=null && hiddenColumns.size()==0) {
-            hiddenColumns=null;
+          if (hiddenColumns != null && hiddenColumns.size() == 0)
+          {
+            hiddenColumns = null;
           }
         }
-        if (selected!=null && selected.size()>0) {
+        if (selected != null && selected.size() > 0)
+        {
           pruneColumnList(shifts, selected);
-          if (selected!=null && selected.size()==0)
-            selected=null;
+          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.
@@ -406,6 +466,7 @@ public class ColumnSelection
   {
     return hiddenColumns;
   }
+
   /**
    * Return absolute column index for a visible column index
    * @param column int column index in alignment view
@@ -446,7 +507,7 @@ public class ColumnSelection
         int[] region = (int[]) hiddenColumns.elementAt(index);
         if (hiddenColumn > region[1])
         {
-          result -= region[1]+1-region[0];
+          result -= region[1] + 1 - region[0];
         }
         index++;
       }
@@ -471,16 +532,16 @@ public class ColumnSelection
       do
       {
         int[] region = (int[]) hiddenColumns.elementAt(index);
-        if(hiddenRegion==0)
+        if (hiddenRegion == 0)
         {
           return region[0];
         }
 
-        gaps +=  region[1] +1 - region[0];
-        result = region[1] +1;
+        gaps += region[1] + 1 - region[0];
+        result = region[1] + 1;
         index++;
       }
-      while(index < hiddenRegion+1);
+      while (index < hiddenRegion + 1);
 
       result -= gaps;
     }
@@ -502,37 +563,42 @@ public class ColumnSelection
       do
       {
         int[] region = (int[]) hiddenColumns.elementAt(index);
-        if(alPos < region[0])
+        if (alPos < region[0])
+        {
           return region[0];
+        }
 
         index++;
       }
-      while(index < hiddenColumns.size());
+      while (index < hiddenColumns.size());
     }
 
     return alPos;
 
   }
+
   /**
-   * THis method returns the rightmost limit of a
+   * This method returns the leftmost limit of a
    * region of an alignment with hidden columns.
-   * In otherwords, the next hidden column.
+   * In otherwords, the previous hidden column.
    * @param index int
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
     if (hiddenColumns != null)
     {
-      int index = hiddenColumns.size()-1;
+      int index = hiddenColumns.size() - 1;
       do
       {
         int[] region = (int[]) hiddenColumns.elementAt(index);
-        if(alPos > region[1])
+        if (alPos > region[1])
+        {
           return region[1];
+        }
 
         index--;
       }
-      while(index >-1);
+      while (index > -1);
     }
 
     return alPos;
@@ -551,8 +617,10 @@ public class ColumnSelection
 
   public void hideColumns(int start, int end)
   {
-    if(hiddenColumns==null)
+    if (hiddenColumns == null)
+    {
       hiddenColumns = new Vector();
+    }
 
     boolean added = false;
     boolean overlap = false;
@@ -560,7 +628,7 @@ public class ColumnSelection
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
       int[] region = (int[]) hiddenColumns.elementAt(i);
-      if ( start<=region[1] && end>=region[0])
+      if (start <= region[1] && end >= region[0])
       {
         hiddenColumns.removeElementAt(i);
         overlap = true;
@@ -569,18 +637,21 @@ public class ColumnSelection
       else if (end < region[0] && start < region[0])
       {
         hiddenColumns.insertElementAt(new int[]
-                                              {start, end}, i);
+                                      {start, end}, i);
         added = true;
         break;
       }
     }
 
-    if(overlap)
+    if (overlap)
     {
       hideColumns(start, end);
     }
     else if (!added)
-      hiddenColumns.addElement(new int[] {start, end});
+    {
+      hiddenColumns.addElement(new int[]
+                               {start, end});
+    }
 
   }
 
@@ -592,26 +663,37 @@ public class ColumnSelection
   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 --;  }
+    int min = col, max = col + 1;
+    while (contains(min))
+    {
+      removeElement(min);
+      min--;
+    }
 
-    while( contains(max) )
-    { removeElement(max);  max ++;  }
+    while (contains(max))
+    {
+      removeElement(max);
+      max++;
+    }
 
-    min++; max--;
+    min++;
+    max--;
+    if (min > max)
+    {
+      min = max;
+    }
 
     hideColumns(min, max);
   }
 
   public void revealAllHiddenColumns()
   {
-    if(hiddenColumns!=null)
+    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++)
+        for (int j = region[0]; j < region[1] + 1; j++)
         {
           addElement(j);
         }
@@ -623,12 +705,12 @@ public class ColumnSelection
 
   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);
         }
@@ -637,40 +719,52 @@ public class ColumnSelection
         break;
       }
     }
-    if(hiddenColumns.size()==0)
+    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])
+    if (hiddenColumns != null)
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        return false;
+        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) {
+  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++) {
+        for (int i = 0, j = copy.selected.size(); i < j; i++)
+        {
           selected.addElement(copy.selected.elementAt(i));
         }
       }
-      if (copy.hiddenColumns!=null) {
-        hiddenColumns=new Vector(copy.hiddenColumns.size());
-        for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
-          int[] rh,cp;
-          rh = (int[])copy.hiddenColumns.elementAt(i);
-          if (rh!=null) {
+      if (copy.hiddenColumns != null)
+      {
+        hiddenColumns = new Vector(copy.hiddenColumns.size());
+        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+        {
+          int[] rh, cp;
+          rh = (int[]) copy.hiddenColumns.elementAt(i);
+          if (rh != null)
+          {
             cp = new int[rh.length];
             System.arraycopy(rh, 0, cp, 0, rh.length);
             hiddenColumns.addElement(cp);
@@ -679,6 +773,7 @@ public class ColumnSelection
       }
     }
   }
+
   /**
    * ColumnSelection
    */
@@ -686,17 +781,20 @@ public class ColumnSelection
   {
   }
 
-  public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
-    int i,iSize=seqs.length;
+  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)
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      for (i=0; i<iSize; i++) {
+      for (i = 0; i < iSize; i++)
+      {
         StringBuffer visibleSeq = new StringBuffer();
         Vector regions = getHiddenColumns();
 
-        int blockStart = start, blockEnd=end;
-        int [] region;
+        int blockStart = start, blockEnd = end;
+        int[] region;
         int hideStart, hideEnd;
 
         for (int j = 0; j < regions.size(); j++)
@@ -705,42 +803,44 @@ public class ColumnSelection
           hideStart = region[0];
           hideEnd = region[1];
 
-          if(hideStart < start)
+          if (hideStart < start)
           {
             continue;
           }
 
-          blockStart = Math.min(blockStart, hideEnd+1);
+          blockStart = Math.min(blockStart, hideEnd + 1);
           blockEnd = Math.min(blockEnd, hideStart);
 
-          if(blockStart>blockEnd)
+          if (blockStart > blockEnd)
           {
             break;
           }
 
-
           visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
 
-          blockStart = hideEnd+1;
+          blockStart = hideEnd + 1;
           blockEnd = end;
         }
 
-        if(end>blockStart)
+        if (end > blockStart)
+        {
           visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        }
 
         selection[i] = visibleSeq.toString();
       }
     }
     else
     {
-      for(i=0; i<iSize; i++)
+      for (i = 0; i < iSize; i++)
       {
-        selection[i] = seqs[i].getSequence(start, end);
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
     }
 
     return selection;
   }
+
   /**
    * return all visible segments between the given start and end boundaries
    *
@@ -748,47 +848,169 @@ public class ColumnSelection
    * @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)
+  public int[] getVisibleContigs(int start, int end)
+  {
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      Vector visiblecontigs=new Vector();
+      Vector visiblecontigs = new Vector();
       Vector regions = getHiddenColumns();
 
       int vstart = start;
-      int [] region;
+      int[] region;
       int hideStart, hideEnd;
 
-      for (int j = 0; vstart<end && j < regions.size(); j++)
+      for (int j = 0; vstart < end && j < regions.size(); j++)
       {
         region = (int[]) regions.elementAt(j);
         hideStart = region[0];
         hideEnd = region[1];
 
-        if(hideEnd < vstart)
+        if (hideEnd < vstart)
         {
           continue;
         }
-        if (hideStart>vstart) {
-          visiblecontigs.addElement(new int[] {vstart, hideStart-1});
+        if (hideStart > vstart)
+        {
+          visiblecontigs.addElement(new int[]
+                                    {vstart, hideStart - 1});
         }
-        vstart=hideEnd+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);
+      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];
+        vcontigs[i * 2] = vc[0];
+        vcontigs[i * 2 + 1] = vc[1];
       }
       visiblecontigs.removeAllElements();
       return vcontigs;
     }
     else
     {
-      return new int[] { start, end-1 };
+      return new int[]
+          {
+          start, end - 1};
+    }
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
+   * @param alignmentAnnotation
+   */
+  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    makeVisibleAnnotation(-1,-1,alignmentAnnotation);
+  }
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
+   * @param start remove any annotation to the right of this column
+   * @param end remove any annotation to the left of this column
+   * @param alignmentAnnotation the annotation to operate on
+   */
+  public void makeVisibleAnnotation(int start, int end, AlignmentAnnotation alignmentAnnotation)
+  {
+    if (alignmentAnnotation.annotations==null)
+    {
+      return;
+    }
+    if (start==end && end==-1)
+    {
+      start = 0;
+      end = alignmentAnnotation.annotations.length;
     }
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      // then mangle the alignmentAnnotation annotation array
+        Vector annels = new Vector();
+        Annotation[] els = null;
+        Vector regions = getHiddenColumns();
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd,w=0;
+
+        for (int j = 0; j < regions.size(); j++)
+        {
+          region = (int[]) regions.elementAt(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+
+          if (hideStart < start)
+          {
+            continue;
+          }
+
+          blockStart = Math.min(blockStart, hideEnd + 1);
+          blockEnd = Math.min(blockEnd, hideStart);
+
+          if (blockStart > blockEnd)
+          {
+            break;
+          }
+
+          annels.addElement(els = new Annotation[blockEnd-blockStart]);
+          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
+          w+=els.length;
+          blockStart = hideEnd + 1;
+          blockEnd = end;
+        }
+
+        if (end > blockStart)
+        {
+          annels.addElement(els = new Annotation[end-blockStart+1]);
+          if (end-blockStart+1<=alignmentAnnotation.annotations.length)
+          {
+            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
+          } else {
+            System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, (end-blockStart+1));
+          }
+          w+=els.length;
+        }
+        if (w==0)
+          return;
+        Enumeration e = annels.elements();
+        alignmentAnnotation.annotations = new Annotation[w];
+        w=0;
+        while (e.hasMoreElements())
+        {
+          Annotation[] chnk = (Annotation[]) e.nextElement();
+          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);
+          w+=chnk.length;
+        }
+    } else {
+      alignmentAnnotation.restrict(start, end);
+    }
+  }
+
+  /**
+   * Invert the column selection from first to end-1.
+   * leaves hiddenColumns untouched (and unselected)
+   * @param first
+   * @param end
+   */
+  public void invertColumnSelection(int first, int width)
+  {
+    boolean hasHidden = hiddenColumns!=null && hiddenColumns.size()>0;
+    for(int i=first; i<width; i++)
+    {
+      if(contains(i))
+    {
+        removeElement(i);
+    }
+      else
+      {
+        if (!hasHidden || isVisible(i))
+        {
+          addElement(i);
+        }
+      }
+    }    
   }
 }