X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=d34b316c3bfc50cda974528b7b5fcd0a8474f912;hb=1e4f81da4ca1c584213557180c1358ede40880d4;hp=f0d99e5ab6cc0970998dab4c23829dc4b752710d;hpb=7e9e238cd202a04c405adee8fa95cc68546c3ec5;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index f0d99e5..d34b316 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import jalview.util.Comparison;
@@ -8,85 +28,159 @@ import java.util.BitSet;
 import java.util.Collections;
 import java.util.List;
 import java.util.Vector;
+import java.util.concurrent.locks.ReentrantReadWriteLock;
 
 public class HiddenColumns
 {
+  private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+  
   /*
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
    */
-  private Vector<int[]> hiddenColumns;
+  private ArrayList<int[]> hiddenColumns;
 
   /**
-   * This Method is used to return all the HiddenColumn regions
-   * 
-   * @return empty list or List of hidden column intervals
+   * Constructor
    */
-  public List<int[]> getHiddenRegions()
+  public HiddenColumns()
   {
-    return hiddenColumns == null ? Collections.<int[]> emptyList()
-            : hiddenColumns;
   }
 
   /**
-   * Find the number of hidden columns
+   * Copy constructor
    * 
-   * @return number of hidden columns
+   * @param copy
    */
-  public int getSize()
+  public HiddenColumns(HiddenColumns copy)
   {
-    int size = 0;
-    if (hasHidden())
+    try
     {
-      for (int[] range : hiddenColumns)
+      LOCK.writeLock().lock();
+      if (copy != null)
       {
-        size += range[1] - range[0] + 1;
+        if (copy.hiddenColumns != null)
+        {
+          hiddenColumns = copy.copyHiddenRegionsToArrayList();
+        }
       }
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
-    return size;
   }
 
   /**
-   * Answers if there are any hidden columns
+   * This method is used to return all the HiddenColumn regions and is intended
+   * to remain private. External callers which need a copy of the regions can
+   * call getHiddenColumnsCopyAsList.
    * 
-   * @return true if there are hidden columns
+   * @return empty list or List of hidden column intervals
    */
-  public boolean hasHidden()
+  private List<int[]> getHiddenRegions()
   {
-    return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : hiddenColumns;
   }
 
-  @Override
-  public boolean equals(Object obj)
+  /**
+   * Output regions data as a string. String is in the format:
+   * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
+   * 
+   * @param delimiter
+   *          string to delimit regions
+   * @param betweenstring
+   *          to put between start and end region values
+   * @return regions formatted according to delimiter and between strings
+   */
+  public String regionsToString(String delimiter, String between)
   {
-    if (!(obj instanceof HiddenColumns))
+    try
+    {
+      LOCK.readLock().lock();
+      StringBuilder regionBuilder = new StringBuilder();
+      if (hiddenColumns != null)
+      {
+        for (int[] range : hiddenColumns)
+        {
+          regionBuilder.append(delimiter).append(range[0]).append(between)
+                  .append(range[1]);
+        }
+
+        regionBuilder.deleteCharAt(0);
+      }
+      return regionBuilder.toString();
+    } finally
     {
-      return false;
+      LOCK.readLock().unlock();
     }
-    HiddenColumns that = (HiddenColumns) obj;
+  }
 
-    /*
-     * check hidden columns are either both null, or match
-     */
-    if (this.hiddenColumns == null)
+  /**
+   * Find the number of hidden columns
+   * 
+   * @return number of hidden columns
+   */
+  public int getSize()
+  {
+    try
     {
-      return (that.hiddenColumns == null);
+      LOCK.readLock().lock();
+      int size = 0;
+      if (hasHiddenColumns())
+      {
+        for (int[] range : hiddenColumns)
+        {
+          size += range[1] - range[0] + 1;
+        }
+      }
+      return size;
     }
-    if (that.hiddenColumns == null
-            || that.hiddenColumns.size() != this.hiddenColumns.size())
+    finally
     {
-      return false;
+      LOCK.readLock().unlock();
     }
-    int i = 0;
-    for (int[] thisRange : hiddenColumns)
+  }
+
+  @Override
+  public boolean equals(Object obj)
+  {
+    try
     {
-      int[] thatRange = that.hiddenColumns.get(i++);
-      if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+      LOCK.readLock().lock();
+
+      if (!(obj instanceof HiddenColumns))
+      {
+        return false;
+      }
+      HiddenColumns that = (HiddenColumns) obj;
+
+      /*
+       * check hidden columns are either both null, or match
+       */
+      if (this.hiddenColumns == null)
+      {
+        return (that.hiddenColumns == null);
+      }
+      if (that.hiddenColumns == null
+              || that.hiddenColumns.size() != this.hiddenColumns.size())
       {
         return false;
       }
+      int i = 0;
+      for (int[] thisRange : hiddenColumns)
+      {
+        int[] thatRange = that.hiddenColumns.get(i++);
+        if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+        {
+          return false;
+        }
+      }
+      return true;
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-    return true;
   }
 
   /**
@@ -98,19 +192,26 @@ public class HiddenColumns
    */
   public int adjustForHiddenColumns(int column)
   {
-    int result = column;
-    if (hiddenColumns != null)
+    try
     {
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      LOCK.readLock().lock();
+      int result = column;
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(i);
-        if (result >= region[0])
+        for (int i = 0; i < hiddenColumns.size(); i++)
         {
-          result += region[1] - region[0] + 1;
+          int[] region = hiddenColumns.get(i);
+          if (result >= region[0])
+          {
+            result += region[1] - region[0] + 1;
+          }
         }
       }
+      return result;
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-    return result;
   }
 
   /**
@@ -124,42 +225,52 @@ public class HiddenColumns
    */
   public int findColumnPosition(int hiddenColumn)
   {
-    int result = hiddenColumn;
-    if (hiddenColumns != null)
+    try
     {
-      int index = 0;
-      int[] region;
-      do
+      LOCK.readLock().lock();
+      int result = hiddenColumn;
+      if (hiddenColumns != null)
       {
-        region = hiddenColumns.elementAt(index++);
-        if (hiddenColumn > region[1])
+        int index = 0;
+        int[] region;
+        do
         {
-          result -= region[1] + 1 - region[0];
-        }
-      } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+          region = hiddenColumns.get(index++);
+          if (hiddenColumn > region[1])
+          {
+            result -= region[1] + 1 - region[0];
+          }
+        } while ((hiddenColumn > region[1])
+                && (index < hiddenColumns.size()));
 
-      if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
-      {
-        // Here the hidden column is within a region, so
-        // we want to return the position of region[0]-1, adjusted for any
-        // earlier hidden columns.
-        // Calculate the difference between the actual hidden col position
-        // and region[0]-1, and then subtract from result to convert result from
-        // the adjusted hiddenColumn value to the adjusted region[0]-1 value
-
-        // However, if the region begins at 0 we cannot return region[0]-1
-        // just return 0
-        if (region[0] == 0)
-        {
-          return 0;
-        }
-        else
+        if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
         {
-          return result - (hiddenColumn - region[0] + 1);
+          // Here the hidden column is within a region, so
+          // we want to return the position of region[0]-1, adjusted for any
+          // earlier hidden columns.
+          // Calculate the difference between the actual hidden col position
+          // and region[0]-1, and then subtract from result to convert result
+          // from
+          // the adjusted hiddenColumn value to the adjusted region[0]-1 value
+
+          // However, if the region begins at 0 we cannot return region[0]-1
+          // just return 0
+          if (region[0] == 0)
+          {
+            return 0;
+          }
+          else
+          {
+            return result - (hiddenColumn - region[0] + 1);
+          }
         }
       }
+      return result; // return the shifted position after removing hidden
+                     // columns.
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
-    return result; // return the shifted position after removing hidden columns.
   }
 
   /**
@@ -175,6 +286,10 @@ public class HiddenColumns
    */
   public int subtractVisibleColumns(int visibleDistance, int startColumn)
   {
+    try
+    {
+
+      LOCK.readLock().lock();
     int distance = visibleDistance;
 
     // in case startColumn is in a hidden region, move it to the left
@@ -216,40 +331,62 @@ public class HiddenColumns
       return nextstart - distance;
     }
     return start - distance;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
 
   }
 
   /**
-   * Use this method to determine where the next hiddenRegion starts
+   * Use this method to determine the set of hiddenRegion start positions
    * 
-   * @param hiddenRegion
-   *          index of hidden region (counts from 0)
-   * @return column number in visible view
+   * @return list of column number in visible view where hidden regions start
    */
-  public int findHiddenRegionPosition(int hiddenRegion)
+  public List<Integer> findHiddenRegionPositions()
   {
-    int result = 0;
-    if (hiddenColumns != null)
+    try
     {
-      int index = 0;
-      int gaps = 0;
-      do
+      LOCK.readLock().lock();
+      List<Integer> positions = null;
+
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (hiddenRegion == 0)
+        positions = new ArrayList<>(hiddenColumns.size());
+
+        positions.add(hiddenColumns.get(0)[0]);
+        for (int i = 1; i < hiddenColumns.size(); ++i)
         {
-          return region[0];
-        }
 
-        gaps += region[1] + 1 - region[0];
-        result = region[1] + 1;
-        index++;
-      } while (index <= hiddenRegion);
+          int result = 0;
+          if (hiddenColumns != null)
+          {
+            int index = 0;
+            int gaps = 0;
+            do
+            {
+              int[] region = hiddenColumns.get(index);
+              gaps += region[1] + 1 - region[0];
+              result = region[1] + 1;
+              index++;
+            } while (index <= i);
 
-      result -= gaps;
-    }
+            result -= gaps;
+          }
+          positions.add(result);
+        }
+      }
+      else
+      {
+        positions = new ArrayList<>();
+      }
 
-    return result;
+      return positions;
+    }
+    finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
@@ -261,22 +398,29 @@ public class HiddenColumns
    */
   public int getHiddenBoundaryRight(int alPos)
   {
-    if (hiddenColumns != null)
+    try
     {
-      int index = 0;
-      do
+      LOCK.readLock().lock();
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (alPos < region[0])
+        int index = 0;
+        do
         {
-          return region[0];
-        }
+          int[] region = hiddenColumns.get(index);
+          if (alPos < region[0])
+          {
+            return region[0];
+          }
 
-        index++;
-      } while (index < hiddenColumns.size());
-    }
+          index++;
+        } while (index < hiddenColumns.size());
+      }
 
-    return alPos;
+      return alPos;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
 
   }
 
@@ -289,12 +433,16 @@ public class HiddenColumns
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
+    try
+    {
+      LOCK.readLock().lock();
+
     if (hiddenColumns != null)
     {
       int index = hiddenColumns.size() - 1;
       do
       {
-        int[] region = hiddenColumns.elementAt(index);
+          int[] region = hiddenColumns.get(index);
         if (alPos > region[1])
         {
           return region[1];
@@ -305,7 +453,10 @@ public class HiddenColumns
     }
 
     return alPos;
-
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
@@ -318,12 +469,16 @@ public class HiddenColumns
    */
   private int getHiddenIndexLeft(int pos)
   {
+    try
+    {
+
+      LOCK.readLock().lock();
     if (hiddenColumns != null)
     {
       int index = hiddenColumns.size() - 1;
       do
       {
-        int[] region = hiddenColumns.elementAt(index);
+          int[] region = hiddenColumns.get(index);
         if (pos > region[1])
         {
           return index;
@@ -334,6 +489,10 @@ public class HiddenColumns
     }
 
     return -1;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
 
   }
 
@@ -345,76 +504,101 @@ public class HiddenColumns
    */
   public void hideColumns(int start, int end)
   {
-    if (hiddenColumns == null)
-    {
-      hiddenColumns = new Vector<int[]>();
-    }
-
-    /*
-     * traverse existing hidden ranges and insert / amend / append as
-     * appropriate
-     */
-    for (int i = 0; i < hiddenColumns.size(); i++)
+    boolean wasAlreadyLocked = false;
+    try
     {
-      int[] region = hiddenColumns.elementAt(i);
-
-      if (end < region[0] - 1)
+      // check if the write lock was already locked by this thread,
+      // as this method can be called internally in loops within HiddenColumns
+      if (!LOCK.isWriteLockedByCurrentThread())
       {
-        /*
-         * insert discontiguous preceding range
-         */
-        hiddenColumns.insertElementAt(new int[] { start, end }, i);
-        return;
+        LOCK.writeLock().lock();
+      }
+      else
+      {
+        wasAlreadyLocked = true;
       }
 
-      if (end <= region[1])
+      if (hiddenColumns == null)
       {
-        /*
-         * new range overlaps existing, or is contiguous preceding it - adjust
-         * start column
-         */
-        region[0] = Math.min(region[0], start);
-        return;
+        hiddenColumns = new ArrayList<>();
       }
 
-      if (start <= region[1] + 1)
+      /*
+       * traverse existing hidden ranges and insert / amend / append as
+       * appropriate
+       */
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        /*
-         * new range overlaps existing, or is contiguous following it - adjust
-         * start and end columns
-         */
-        region[0] = Math.min(region[0], start);
-        region[1] = Math.max(region[1], end);
-
-        /*
-         * also update or remove any subsequent ranges 
-         * that are overlapped
-         */
-        while (i < hiddenColumns.size() - 1)
+        int[] region = hiddenColumns.get(i);
+
+        if (end < region[0] - 1)
+        {
+          /*
+           * insert discontiguous preceding range
+           */
+          hiddenColumns.add(i, new int[] { start, end });
+          return;
+        }
+
+        if (end <= region[1])
+        {
+          /*
+           * new range overlaps existing, or is contiguous preceding it - adjust
+           * start column
+           */
+          region[0] = Math.min(region[0], start);
+          return;
+        }
+
+        if (start <= region[1] + 1)
         {
-          int[] nextRegion = hiddenColumns.get(i + 1);
-          if (nextRegion[0] > end + 1)
+          /*
+           * new range overlaps existing, or is contiguous following it - adjust
+           * start and end columns
+           */
+          region[0] = Math.min(region[0], start);
+          region[1] = Math.max(region[1], end);
+
+          /*
+           * also update or remove any subsequent ranges 
+           * that are overlapped
+           */
+          while (i < hiddenColumns.size() - 1)
           {
-            /*
-             * gap to next hidden range - no more to update
-             */
-            break;
+            int[] nextRegion = hiddenColumns.get(i + 1);
+            if (nextRegion[0] > end + 1)
+            {
+              /*
+               * gap to next hidden range - no more to update
+               */
+              break;
+            }
+            region[1] = Math.max(nextRegion[1], end);
+            hiddenColumns.remove(i + 1);
           }
-          region[1] = Math.max(nextRegion[1], end);
-          hiddenColumns.remove(i + 1);
+          return;
         }
-        return;
-      }
     }
 
     /*
      * remaining case is that the new range follows everything else
      */
-    hiddenColumns.addElement(new int[] { start, end });
+      hiddenColumns.add(new int[] { start, end });
+    } finally
+    {
+      if (!wasAlreadyLocked)
+      {
+        LOCK.writeLock().unlock();
+      }
+    }
   }
 
   public boolean isVisible(int column)
   {
+    try
+    {
+      LOCK.readLock().lock();
+
     if (hiddenColumns != null)
     {
       for (int[] region : hiddenColumns)
@@ -427,39 +611,54 @@ public class HiddenColumns
     }
 
     return true;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
-  /**
-   * ColumnSelection
-   */
-  public HiddenColumns()
+  private ArrayList<int[]> copyHiddenRegionsToArrayList()
   {
-  }
+    int size = 0;
+    if (hiddenColumns != null)
+    {
+      size = hiddenColumns.size();
+    }
+    ArrayList<int[]> copy = new ArrayList<>(size);
+
+    for (int i = 0, j = size; i < j; i++)
+    {
+      int[] rh;
+      int[] cp;
+      rh = hiddenColumns.get(i);
+      if (rh != null)
+      {
+        cp = new int[rh.length];
+        System.arraycopy(rh, 0, cp, 0, rh.length);
+        copy.add(cp);
+      }
+    }
 
+    return copy;
+  }
+  
   /**
-   * Copy constructor
+   * Returns a copy of the vector of hidden regions, as an ArrayList. Before
+   * using this method please consider if you really need access to the hidden
+   * regions - a new (or existing!) method on HiddenColumns might be more
+   * appropriate.
    * 
-   * @param copy
+   * @return hidden regions as an ArrayList of [start,end] pairs
    */
-  public HiddenColumns(HiddenColumns copy)
+  public ArrayList<int[]> getHiddenColumnsCopy()
   {
-    if (copy != null)
+    try
     {
-      if (copy.hiddenColumns != null)
-      {
-        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
-        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
-        {
-          int[] rh, cp;
-          rh = copy.hiddenColumns.elementAt(i);
-          if (rh != null)
-          {
-            cp = new int[rh.length];
-            System.arraycopy(rh, 0, cp, 0, rh.length);
-            hiddenColumns.addElement(cp);
-          }
-        }
-      }
+      LOCK.readLock().lock();
+      return copyHiddenRegionsToArrayList();
+    } finally
+    {
+      LOCK.readLock().unlock();
     }
   }
 
@@ -474,42 +673,49 @@ public class HiddenColumns
   public List<int[]> compensateForEdit(int start, int change,
           ColumnSelection sel)
   {
-    List<int[]> deletedHiddenColumns = null;
-
-    if (hiddenColumns != null)
+    try
     {
-      deletedHiddenColumns = new ArrayList<int[]>();
-      int hSize = hiddenColumns.size();
-      for (int i = 0; i < hSize; i++)
+      LOCK.writeLock().lock();
+      List<int[]> deletedHiddenColumns = null;
+
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(i);
-        if (region[0] > start && start + change > region[1])
+        deletedHiddenColumns = new ArrayList<>();
+        int hSize = hiddenColumns.size();
+        for (int i = 0; i < hSize; i++)
         {
-          deletedHiddenColumns.add(region);
+          int[] region = hiddenColumns.get(i);
+          if (region[0] > start && start + change > region[1])
+          {
+            deletedHiddenColumns.add(region);
 
-          hiddenColumns.removeElementAt(i);
-          i--;
-          hSize--;
-          continue;
-        }
+            hiddenColumns.remove(i);
+            i--;
+            hSize--;
+            continue;
+          }
 
-        if (region[0] > start)
-        {
-          region[0] -= change;
-          region[1] -= change;
-        }
+          if (region[0] > start)
+          {
+            region[0] -= change;
+            region[1] -= change;
+          }
+
+          if (region[0] < 0)
+          {
+            region[0] = 0;
+          }
 
-        if (region[0] < 0)
-        {
-          region[0] = 0;
         }
 
+        this.revealHiddenColumns(0, sel);
       }
 
-      this.revealHiddenColumns(0, sel);
+      return deletedHiddenColumns;
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
-
-    return deletedHiddenColumns;
   }
 
   /**
@@ -523,34 +729,42 @@ public class HiddenColumns
    */
   public void compensateForDelEdits(int start, int change)
   {
-    if (hiddenColumns != null)
+    try
     {
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      LOCK.writeLock().lock();
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(i);
-        if (region[0] >= start)
-        {
-          region[0] -= change;
-        }
-        if (region[1] >= start)
-        {
-          region[1] -= change;
-        }
-        if (region[1] < region[0])
+        for (int i = 0; i < hiddenColumns.size(); i++)
         {
-          hiddenColumns.removeElementAt(i--);
-        }
+          int[] region = hiddenColumns.get(i);
+          if (region[0] >= start)
+          {
+            region[0] -= change;
+          }
+          if (region[1] >= start)
+          {
+            region[1] -= change;
+          }
+          if (region[1] < region[0])
+          {
+            hiddenColumns.remove(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;
+          }
         }
       }
     }
+    finally
+    {
+      LOCK.writeLock().unlock();
+    }
   }
 
   /**
@@ -565,111 +779,130 @@ public class HiddenColumns
    */
   public int[] getVisibleContigs(int start, int end)
   {
-    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    try
     {
-      List<int[]> visiblecontigs = new ArrayList<int[]>();
-      List<int[]> regions = getHiddenRegions();
+      LOCK.readLock().lock();
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
+      {
+        List<int[]> visiblecontigs = new ArrayList<>();
+        List<int[]> regions = getHiddenRegions();
 
-      int vstart = start;
-      int[] region;
-      int hideStart, hideEnd;
+        int vstart = start;
+        int[] region;
+        int hideStart;
+        int hideEnd;
 
-      for (int j = 0; vstart < end && j < regions.size(); j++)
-      {
-        region = regions.get(j);
-        hideStart = region[0];
-        hideEnd = region[1];
+        for (int j = 0; vstart < end && j < regions.size(); j++)
+        {
+          region = regions.get(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+
+          if (hideEnd < vstart)
+          {
+            continue;
+          }
+          if (hideStart > vstart)
+          {
+            visiblecontigs.add(new int[] { vstart, hideStart - 1 });
+          }
+          vstart = hideEnd + 1;
+        }
 
-        if (hideEnd < vstart)
+        if (vstart < end)
         {
-          continue;
+          visiblecontigs.add(new int[] { vstart, end - 1 });
         }
-        if (hideStart > vstart)
+        int[] vcontigs = new int[visiblecontigs.size() * 2];
+        for (int i = 0, j = visiblecontigs.size(); i < j; i++)
         {
-          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
+          int[] vc = visiblecontigs.get(i);
+          visiblecontigs.set(i, null);
+          vcontigs[i * 2] = vc[0];
+          vcontigs[i * 2 + 1] = vc[1];
         }
-        vstart = hideEnd + 1;
-      }
-
-      if (vstart < end)
-      {
-        visiblecontigs.add(new int[] { vstart, end - 1 });
+        visiblecontigs.clear();
+        return vcontigs;
       }
-      int[] vcontigs = new int[visiblecontigs.size() * 2];
-      for (int i = 0, j = visiblecontigs.size(); i < j; i++)
+      else
       {
-        int[] vc = visiblecontigs.get(i);
-        visiblecontigs.set(i, null);
-        vcontigs[i * 2] = vc[0];
-        vcontigs[i * 2 + 1] = vc[1];
+        return new int[] { start, end - 1 };
       }
-      visiblecontigs.clear();
-      return vcontigs;
     }
-    else
+    finally
     {
-      return new int[] { start, end - 1 };
+      LOCK.readLock().unlock();
     }
   }
 
   public String[] getVisibleSequenceStrings(int start, int end,
           SequenceI[] seqs)
   {
-    int i, iSize = seqs.length;
-    String selections[] = new String[iSize];
-    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    try
     {
-      for (i = 0; i < iSize; i++)
+      LOCK.readLock().lock();
+      int iSize = seqs.length;
+      String[] selections = new String[iSize];
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
-        StringBuffer visibleSeq = new StringBuffer();
-        List<int[]> regions = getHiddenRegions();
-
-        int blockStart = start, blockEnd = end;
-        int[] region;
-        int hideStart, hideEnd;
-
-        for (int j = 0; j < regions.size(); j++)
+        for (int i = 0; i < iSize; i++)
         {
-          region = regions.get(j);
-          hideStart = region[0];
-          hideEnd = region[1];
+          StringBuffer visibleSeq = new StringBuffer();
+          List<int[]> regions = getHiddenRegions();
 
-          if (hideStart < start)
+          int blockStart = start;
+          int blockEnd = end;
+          int[] region;
+          int hideStart;
+          int hideEnd;
+
+          for (int j = 0; j < regions.size(); j++)
           {
-            continue;
-          }
+            region = regions.get(j);
+            hideStart = region[0];
+            hideEnd = region[1];
 
-          blockStart = Math.min(blockStart, hideEnd + 1);
-          blockEnd = Math.min(blockEnd, hideStart);
+            if (hideStart < start)
+            {
+              continue;
+            }
 
-          if (blockStart > blockEnd)
-          {
-            break;
+            blockStart = Math.min(blockStart, hideEnd + 1);
+            blockEnd = Math.min(blockEnd, hideStart);
+
+            if (blockStart > blockEnd)
+            {
+              break;
+            }
+
+            visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+            blockStart = hideEnd + 1;
+            blockEnd = end;
           }
 
-          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+          if (end > blockStart)
+          {
+            visibleSeq.append(seqs[i].getSequence(blockStart, end));
+          }
 
-          blockStart = hideEnd + 1;
-          blockEnd = end;
+          selections[i] = visibleSeq.toString();
         }
-
-        if (end > blockStart)
+      }
+      else
+      {
+        for (int i = 0; i < iSize; i++)
         {
-          visibleSeq.append(seqs[i].getSequence(blockStart, end));
+          selections[i] = seqs[i].getSequenceAsString(start, end);
         }
-
-        selections[i] = visibleSeq.toString();
       }
+
+      return selections;
     }
-    else
+    finally
     {
-      for (i = 0; i < iSize; i++)
-      {
-        selections[i] = seqs[i].getSequenceAsString(start, end);
-      }
+      LOCK.readLock().unlock();
     }
-
-    return selections;
   }
 
   /**
@@ -684,70 +917,86 @@ public class HiddenColumns
    */
   public int[] locateVisibleBoundsOfSequence(SequenceI seq)
   {
-    int fpos = seq.getStart(), lpos = seq.getEnd();
-    int start = 0;
-
-    if (hiddenColumns == null || hiddenColumns.size() == 0)
+    try
     {
-      int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
-      return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
-    }
+      LOCK.readLock().lock();
+      int fpos = seq.getStart();
+      int lpos = seq.getEnd();
+      int start = 0;
 
-    // Simply walk along the sequence whilst watching for hidden column
-    // boundaries
-    List<int[]> regions = getHiddenRegions();
-    int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
-            .getLength(), hideEnd = -1;
-    int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
-    boolean foundStart = false;
-    for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
-            && p < pLen; p++)
-    {
-      if (!Comparison.isGap(seq.getCharAt(p)))
+      if (hiddenColumns == null || hiddenColumns.size() == 0)
       {
-        // keep track of first/last column
-        // containing sequence data regardless of visibility
-        if (firstP == -1)
-        {
-          firstP = p;
-        }
-        lastP = p;
-        // update hidden region start/end
-        while (hideEnd < p && rcount < regions.size())
-        {
-          int[] region = regions.get(rcount++);
-          visPrev = visNext;
-          visNext += region[0] - visPrev;
-          hideStart = region[0];
-          hideEnd = region[1];
-        }
-        if (hideEnd < p)
-        {
-          hideStart = seq.getLength();
-        }
-        // update visible boundary for sequence
-        if (p < hideStart)
+        int ifpos = seq.findIndex(fpos) - 1;
+        int ilpos = seq.findIndex(lpos) - 1;
+        return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
+      }
+
+      // Simply walk along the sequence whilst watching for hidden column
+      // boundaries
+      List<int[]> regions = getHiddenRegions();
+      int spos = fpos;
+      int lastvispos = -1;
+      int rcount = 0;
+      int hideStart = seq.getLength();
+      int hideEnd = -1;
+      int visPrev = 0;
+      int visNext = 0;
+      int firstP = -1;
+      int lastP = -1;
+      boolean foundStart = false;
+      for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+              && p < pLen; p++)
+      {
+        if (!Comparison.isGap(seq.getCharAt(p)))
         {
-          if (!foundStart)
+          // keep track of first/last column
+          // containing sequence data regardless of visibility
+          if (firstP == -1)
+          {
+            firstP = p;
+          }
+          lastP = p;
+          // update hidden region start/end
+          while (hideEnd < p && rcount < regions.size())
+          {
+            int[] region = regions.get(rcount++);
+            visPrev = visNext;
+            visNext += region[0] - visPrev;
+            hideStart = region[0];
+            hideEnd = region[1];
+          }
+          if (hideEnd < p)
           {
-            fpos = spos;
-            start = p;
-            foundStart = true;
+            hideStart = seq.getLength();
           }
-          lastvispos = p;
-          lpos = spos;
+          // update visible boundary for sequence
+          if (p < hideStart)
+          {
+            if (!foundStart)
+            {
+              fpos = spos;
+              start = p;
+              foundStart = true;
+            }
+            lastvispos = p;
+            lpos = spos;
+          }
+          // look for next sequence position
+          spos++;
         }
-        // look for next sequence position
-        spos++;
       }
+      if (foundStart)
+      {
+        return new int[] { findColumnPosition(start),
+            findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+      }
+      // otherwise, sequence was completely hidden
+      return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
     }
-    if (foundStart)
+    finally
     {
-      return new int[] { findColumnPosition(start),
-          findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+      LOCK.readLock().unlock();
     }
-    // otherwise, sequence was completely hidden
-    return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
   }
 
   /**
@@ -775,88 +1024,100 @@ public class HiddenColumns
   public void makeVisibleAnnotation(int start, int end,
           AlignmentAnnotation alignmentAnnotation)
   {
-    if (alignmentAnnotation.annotations == null)
+    try
     {
-      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<Annotation[]> annels = new Vector<Annotation[]>();
-      Annotation[] els = null;
-      List<int[]> regions = getHiddenRegions();
-      int blockStart = start, blockEnd = end;
-      int[] region;
-      int hideStart, hideEnd, w = 0;
-
-      for (int j = 0; j < regions.size(); j++)
+      LOCK.readLock().lock();
+      if (alignmentAnnotation.annotations == null)
       {
-        region = regions.get(j);
-        hideStart = region[0];
-        hideEnd = region[1];
+        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<Annotation[]> annels = new Vector<>();
+        Annotation[] els = null;
+        List<int[]> regions = getHiddenRegions();
+        int blockStart = start;
+        int blockEnd = end;
+        int[] region;
+        int hideStart;
+        int hideEnd;
+        int w = 0;
 
-        if (hideStart < start)
+        for (int j = 0; j < regions.size(); j++)
         {
-          continue;
-        }
+          region = regions.get(j);
+          hideStart = region[0];
+          hideEnd = region[1];
 
-        blockStart = Math.min(blockStart, hideEnd + 1);
-        blockEnd = Math.min(blockEnd, hideStart);
+          if (hideStart < start)
+          {
+            continue;
+          }
 
-        if (blockStart > blockEnd)
-        {
-          break;
-        }
+          blockStart = Math.min(blockStart, hideEnd + 1);
+          blockEnd = Math.min(blockEnd, hideStart);
 
-        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 (blockStart > blockEnd)
+          {
+            break;
+          }
 
-      if (end > blockStart)
-      {
-        annels.addElement(els = new Annotation[end - blockStart + 1]);
-        if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+          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)
         {
-          // copy just the visible segment of the annotation row
-          System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                  els, 0, els.length);
+          annels.addElement(els = new Annotation[end - blockStart + 1]);
+          if ((els.length
+                  + blockStart) <= alignmentAnnotation.annotations.length)
+          {
+            // copy just the visible segment of the annotation row
+            System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                    els, 0, els.length);
+          }
+          else
+          {
+            // copy to the end of the annotation row
+            System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                    els, 0,
+                    (alignmentAnnotation.annotations.length - blockStart));
+          }
+          w += els.length;
         }
-        else
+        if (w == 0)
         {
-          // copy to the end of the annotation row
-          System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                  els, 0,
-                  (alignmentAnnotation.annotations.length - blockStart));
+          return;
         }
-        w += els.length;
-      }
-      if (w == 0)
-      {
-        return;
-      }
 
-      alignmentAnnotation.annotations = new Annotation[w];
-      w = 0;
+        alignmentAnnotation.annotations = new Annotation[w];
+        w = 0;
 
-      for (Annotation[] chnk : annels)
+        for (Annotation[] chnk : annels)
+        {
+          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                  chnk.length);
+          w += chnk.length;
+        }
+      }
+      else
       {
-        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
-                chnk.length);
-        w += chnk.length;
+        alignmentAnnotation.restrict(start, end);
       }
     }
-    else
+    finally
     {
-      alignmentAnnotation.restrict(start, end);
+      LOCK.readLock().unlock();
     }
   }
 
@@ -866,7 +1127,14 @@ public class HiddenColumns
    */
   public boolean hasHiddenColumns()
   {
-    return hiddenColumns != null && hiddenColumns.size() > 0;
+    try
+    {
+      LOCK.readLock().lock();
+      return hiddenColumns != null && hiddenColumns.size() > 0;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
@@ -875,7 +1143,14 @@ public class HiddenColumns
    */
   public boolean hasManyHiddenColumns()
   {
-    return hiddenColumns != null && hiddenColumns.size() > 1;
+    try
+    {
+      LOCK.readLock().lock();
+      return hiddenColumns != null && hiddenColumns.size() > 1;
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
@@ -886,10 +1161,17 @@ public class HiddenColumns
    */
   public void hideInsertionsFor(SequenceI sr)
   {
-    List<int[]> inserts = sr.getInsertions();
-    for (int[] r : inserts)
+    try
     {
-      hideColumns(r[0], r[1]);
+      LOCK.writeLock().lock();
+      List<int[]> inserts = sr.getInsertions();
+      for (int[] r : inserts)
+      {
+        hideColumns(r[0], r[1]);
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -898,19 +1180,27 @@ public class HiddenColumns
    */
   public void revealAllHiddenColumns(ColumnSelection sel)
   {
-    if (hiddenColumns != null)
+    try
     {
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      LOCK.writeLock().lock();
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(i);
-        for (int j = region[0]; j < region[1] + 1; j++)
+        for (int i = 0; i < hiddenColumns.size(); i++)
         {
-          sel.addElement(j);
+          int[] region = hiddenColumns.get(i);
+          for (int j = region[0]; j < region[1] + 1; j++)
+          {
+            sel.addElement(j);
+          }
         }
       }
-    }
 
-    hiddenColumns = null;
+      hiddenColumns = null;
+    }
+    finally
+    {
+      LOCK.writeLock().unlock();
+    }
   }
 
   /**
@@ -921,23 +1211,31 @@ public class HiddenColumns
    */
   public void revealHiddenColumns(int start, ColumnSelection sel)
   {
-    for (int i = 0; i < hiddenColumns.size(); i++)
+    try
     {
-      int[] region = hiddenColumns.elementAt(i);
-      if (start == region[0])
+      LOCK.writeLock().lock();
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        for (int j = region[0]; j < region[1] + 1; j++)
+        int[] region = hiddenColumns.get(i);
+        if (start == region[0])
         {
-          sel.addElement(j);
-        }
+          for (int j = region[0]; j < region[1] + 1; j++)
+          {
+            sel.addElement(j);
+          }
 
-        hiddenColumns.removeElement(region);
-        break;
+          hiddenColumns.remove(region);
+          break;
+        }
+      }
+      if (hiddenColumns.size() == 0)
+      {
+        hiddenColumns = null;
       }
     }
-    if (hiddenColumns.size() == 0)
+    finally
     {
-      hiddenColumns = null;
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -949,13 +1247,16 @@ public class HiddenColumns
    * @param intervals
    * @return
    */
-  private boolean pruneIntervalVector(final List<int[]> shifts,
-          Vector<int[]> intervals)
+  private boolean pruneIntervalList(final List<int[]> shifts,
+          ArrayList<int[]> intervals)
   {
     boolean pruned = false;
-    int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
-    int hr[] = intervals.elementAt(i);
-    int sr[] = shifts.get(s);
+    int i = 0;
+    int j = intervals.size() - 1;
+    int s = 0;
+    int t = shifts.size() - 1;
+    int[] hr = intervals.get(i);
+    int[] sr = shifts.get(s);
     while (i <= j && s <= t)
     {
       boolean trailinghn = hr[1] >= sr[0];
@@ -963,7 +1264,7 @@ public class HiddenColumns
       {
         if (i < j)
         {
-          hr = intervals.elementAt(++i);
+          hr = intervals.get(++i);
         }
         else
         {
@@ -991,12 +1292,12 @@ public class HiddenColumns
       {
         if (trailinghc)
         { // deleted hidden region.
-          intervals.removeElementAt(i);
+          intervals.remove(i);
           pruned = true;
           j--;
           if (i <= j)
           {
-            hr = intervals.elementAt(i);
+            hr = intervals.get(i);
           }
           continue;
         }
@@ -1044,15 +1345,23 @@ public class HiddenColumns
    */
   public void pruneDeletions(List<int[]> shifts)
   {
-    // delete any intervals intersecting.
-    if (hiddenColumns != null)
+    try
     {
-      pruneIntervalVector(shifts, hiddenColumns);
-      if (hiddenColumns != null && hiddenColumns.size() == 0)
+      LOCK.writeLock().lock();
+      // delete any intervals intersecting.
+      if (hiddenColumns != null)
       {
-        hiddenColumns = null;
+        pruneIntervalList(shifts, hiddenColumns);
+        if (hiddenColumns != null && hiddenColumns.size() == 0)
+        {
+          hiddenColumns = null;
+        }
       }
     }
+    finally
+    {
+      LOCK.writeLock().unlock();
+    }
   }
 
   /**
@@ -1251,16 +1560,24 @@ public class HiddenColumns
   @Override
   public int hashCode()
   {
-    int hashCode = 1;
-    if (hiddenColumns != null)
+    try
     {
-      for (int[] hidden : hiddenColumns)
+      LOCK.readLock().lock();
+      int hashCode = 1;
+      if (hiddenColumns != null)
       {
-        hashCode = 31 * hashCode + hidden[0];
-        hashCode = 31 * hashCode + hidden[1];
+        for (int[] hidden : hiddenColumns)
+        {
+          hashCode = 31 * hashCode + hidden[0];
+          hashCode = 31 * hashCode + hidden[1];
+        }
       }
+      return hashCode;
+    }
+    finally
+    {
+      LOCK.readLock().unlock();
     }
-    return hashCode;
   }
 
   /**
@@ -1271,11 +1588,19 @@ public class HiddenColumns
    */
   public void hideMarkedBits(BitSet inserts)
   {
-    for (int firstSet = inserts.nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
-            .nextSetBit(lastSet))
+    try
     {
-      lastSet = inserts.nextClearBit(firstSet);
-      hideColumns(firstSet, lastSet - 1);
+      LOCK.writeLock().lock();
+      for (int firstSet = inserts
+              .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
+                      .nextSetBit(lastSet))
+      {
+        lastSet = inserts.nextClearBit(firstSet);
+        hideColumns(firstSet, lastSet - 1);
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1286,13 +1611,109 @@ public class HiddenColumns
    */
   public void markHiddenRegions(BitSet inserts)
   {
-    if (hiddenColumns == null)
+    try
+    {
+      LOCK.readLock().lock();
+      if (hiddenColumns == null)
+      {
+        return;
+      }
+      for (int[] range : hiddenColumns)
+      {
+        inserts.set(range[0], range[1] + 1);
+      }
+    }
+    finally
     {
-      return;
+      LOCK.readLock().unlock();
     }
-    for (int[] range : hiddenColumns)
+  }
+
+  /**
+   * Calculate the visible start and end index of an alignment.
+   * 
+   * @param width
+   *          full alignment width
+   * @return integer array where: int[0] = startIndex, and int[1] = endIndex
+   */
+  public int[] getVisibleStartAndEndIndex(int width)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int[] alignmentStartEnd = new int[] { 0, width - 1 };
+      int startPos = alignmentStartEnd[0];
+      int endPos = alignmentStartEnd[1];
+
+      int[] lowestRange = new int[] { -1, -1 };
+      int[] higestRange = new int[] { -1, -1 };
+
+      if (hiddenColumns == null)
+      {
+        return new int[] { startPos, endPos };
+      }
+
+      for (int[] hiddenCol : hiddenColumns)
+      {
+        lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+        higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+      }
+
+      if (lowestRange[0] == -1 && lowestRange[1] == -1)
+      {
+        startPos = alignmentStartEnd[0];
+      }
+      else
+      {
+        startPos = lowestRange[1] + 1;
+      }
+
+      if (higestRange[0] == -1 && higestRange[1] == -1)
+      {
+        endPos = alignmentStartEnd[1];
+      }
+      else
+      {
+        endPos = higestRange[0] - 1;
+      }
+      return new int[] { startPos, endPos };
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
+
+  }
+
+  /**
+   * Finds the hidden region (if any) which starts or ends at res
+   * 
+   * @param res
+   *          visible residue position, unadjusted for hidden columns
+   * @return region as [start,end] or null if no matching region is found
+   */
+  public int[] getRegionWithEdgeAtRes(int res)
+  {
+    try
+    {
+      LOCK.readLock().lock();
+      int adjres = adjustForHiddenColumns(res);
+
+      int[] reveal = null;
+      if (hiddenColumns != null)
+      {
+        for (int[] region : hiddenColumns)
+        {
+          if (adjres + 1 == region[0] || adjres - 1 == region[1])
+          {
+            reveal = region;
+            break;
+          }
+        }
+      }
+      return reveal;
+    } finally
     {
-      inserts.set(range[0], range[1] + 1);
+      LOCK.readLock().unlock();
     }
   }