From b2d54d33d6313efd9da96bd7586dfaa7a0d7a182 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 22 Aug 2006 08:34:04 +0000
Subject: [PATCH] hidden region recovery in JPred and new hidden region
 pruning function

---
 src/jalview/datamodel/ColumnSelection.java | 1181 ++++++++++++++++------------
 src/jalview/util/ShiftList.java            |  248 +++---
 src/jalview/ws/JPredClient.java            |    4 +-
 3 files changed, 792 insertions(+), 641 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 39d7a8d..bd06ca3 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,510 +1,671 @@
-/*
- * 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 change shift in edit (-ve or +ve number of columns)
-     */
-    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;
-          }
-        }
-    }
-    public ShiftList compensateForEdits(ShiftList shiftrecord) {
-      if (shiftrecord!=null) {
-        Vector shifts = shiftrecord.shifts;
-        if (shifts!=null && shifts.size()>0) {
-          for (int i=0,j=shifts.size(); i<j; i++) {
-            int[] sh = (int[]) shifts.elementAt(i);
-            compensateForEdit(sh[0], sh[1]);
-          }
-        }
-        return shiftrecord.getInverse();
-      }
-      return null;
-    }
-    /**
-     * 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()
-  {
-  }
-}
+/*
+ * 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.get(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.get(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.set(i, ((Integer) copy.selected.get(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.get(i);
+            if (rh!=null) {
+              cp = new int[rh.length];
+              System.arraycopy(rh, 0, cp, 0, rh.length);
+              hiddenColumns.set(i, cp);
+            }
+          }
+        }
+      }
+    }
+
+  /**
+   * ColumnSelection
+   */
+  public ColumnSelection()
+  {
+  }
+}
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 5c1d572..0c78ca1 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,129 +1,119 @@
-/*
- * 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.util;
-
-import jalview.datamodel.SequenceI;
-
-import java.util.*;
-
-/**
- * ShiftList
- * Simple way of mapping a linear series to a new linear range with new points introduced.
- * Use at your own risk!
- * <p>Title: ShiftList</p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class ShiftList
-{
-    public Vector shifts;
-  public ShiftList()
-  {
-    shifts = new Vector();
-  }
-
-  /**
-   * addShift
-   * @param pos start position for shift (in original reference frame)
-   * @param shift length of shift
-   */
-  public void addShift(int pos, int shift)
-  {
-    int sidx = 0;
-    int[] rshift=null;
-    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
-      sidx++;
-    if (sidx==shifts.size())
-      shifts.insertElementAt(new int[] { pos, shift}, sidx);
-    else
-      rshift[1]+=shift;
-  }
-
-  /**
-   * shift
-   *
-   * @param pos int
-   * @return int shifted position
-   */
-  public int shift(int pos)
-  {
-    if (shifts.size()==0)
-      return pos;
-    int shifted=pos;
-    int sidx=0;
-    int rshift[];
-    while (sidx<shifts.size()
-           &&
-           (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
-      shifted += rshift[1];
-    }
-    return shifted;
-  }
-
-  /**
-   * clear all shifts
-   */
-  public void clear()
-  {
-    shifts.removeAllElements();
-  }
-  /**
-   * invert the shifts
-   * @return ShiftList with inverse shift operations
-   */
-  public ShiftList getInverse() {
-    ShiftList inverse=new ShiftList();
-    if (shifts!=null) {
-      for (int i=0,j=shifts.size(); i<j; i++) {
-        int[] sh=(int[]) shifts.elementAt(i);
-        if (sh!=null)
-          inverse.shifts.addElement(new int[] {sh[0], -sh[1]});
-      }
-    }
-    return inverse;
-  }
-
-  /**
-   * parse a 1d map of position 1<i<n to L<pos[i]<N
-   * such as that returned from SequenceI.gapMap()
-   * @param gapMap
-   * @return
-   */
-  public static ShiftList parseMap(int[] gapMap) {
-    ShiftList shiftList = null;
-    if (gapMap!=null && gapMap.length>0) {
-      shiftList=new ShiftList();
-
-      for (int i=0,p=0; i<gapMap.length; p++,i++) {
-        if (p!=gapMap[i]) {
-          shiftList.addShift(p, gapMap[i]-p);
-          p=gapMap[i];
-        }
-      }
-    }
-    return shiftList;
-  }
-}
+/*
+ * 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.util;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.*;
+
+/**
+ * ShiftList
+ * Simple way of mapping a linear series to a new linear range with new points introduced.
+ * Use at your own risk!
+ * Now growing to be used for interval ranges (position, offset) storing deletions/insertions
+ */
+public class ShiftList
+{
+    public Vector shifts;
+  public ShiftList()
+  {
+    shifts = new Vector();
+  }
+
+  /**
+   * addShift
+   * @param pos start position for shift (in original reference frame)
+   * @param shift length of shift
+   */
+  public void addShift(int pos, int shift)
+  {
+    int sidx = 0;
+    int[] rshift=null;
+    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+      sidx++;
+    if (sidx==shifts.size())
+      shifts.insertElementAt(new int[] { pos, shift}, sidx);
+    else
+      rshift[1]+=shift;
+  }
+
+  /**
+   * shift
+   *
+   * @param pos int
+   * @return int shifted position
+   */
+  public int shift(int pos)
+  {
+    if (shifts.size()==0)
+      return pos;
+    int shifted=pos;
+    int sidx=0;
+    int rshift[];
+    while (sidx<shifts.size()
+           &&
+           (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
+      shifted += rshift[1];
+    }
+    return shifted;
+  }
+
+  /**
+   * clear all shifts
+   */
+  public void clear()
+  {
+    shifts.removeAllElements();
+  }
+  /**
+   * invert the shifts
+   * @return ShiftList with inverse shift operations
+   */
+  public ShiftList getInverse() {
+    ShiftList inverse=new ShiftList();
+    if (shifts!=null) {
+      for (int i=0,j=shifts.size(); i<j; i++) {
+        int[] sh=(int[]) shifts.get(i);
+        if (sh!=null)
+          inverse.shifts.add(new int[] {sh[0], -sh[1]});
+      }
+    }
+    return inverse;
+  }
+
+  /**
+   * parse a 1d map of position 1<i<n to L<pos[i]<N
+   * such as that returned from SequenceI.gapMap()
+   * @param gapMap
+   * @return shifts from map index to mapped position
+   */
+  public static ShiftList parseMap(int[] gapMap) {
+    ShiftList shiftList = null;
+    if (gapMap!=null && gapMap.length>0) {
+      shiftList=new ShiftList();
+      for (int i=0,p=0; i<gapMap.length; p++,i++) {
+        if (p!=gapMap[i]) {
+          shiftList.addShift(p, gapMap[i]-p);
+          p=gapMap[i];
+        }
+      }
+    }
+    return shiftList;
+  }
+}
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 72bef07..55e65a5 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -547,7 +547,7 @@ public class JPredClient
         else
           if (job.sequence!=null)
           {
-            job.jobId = server.predict(job.sequence);
+            job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//
           }
 
         if (job.jobId != null)
@@ -729,7 +729,7 @@ public class JPredClient
                  throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
                } else {
                  // test this.
-                 ((ColumnSelection) alandcolsel[1]).compensateForEdits(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
+                 ((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));//gapMap returns insert list, interpreted as delete list by pruneDeletions
                }
              }
              af = new AlignFrame(res, (ColumnSelection) alandcolsel[1]);
-- 
1.7.10.2