From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 6 Jun 2017 14:44:04 +0000 (+0100)
Subject: JAL-2591 Added readwrite locking on HiddenColumns
X-Git-Tag: Release_2_10_3b1~183^2~18
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=defcce0ef74ffc0923b4387bcb5f0d867bf64831

JAL-2591 Added readwrite locking on HiddenColumns
---

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index f0d99e5..da0b854 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -8,9 +8,12 @@ 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
@@ -35,15 +38,23 @@ public class HiddenColumns
    */
   public int getSize()
   {
-    int size = 0;
-    if (hasHidden())
+    try
     {
-      for (int[] range : hiddenColumns)
+      lock.readLock().lock();
+      int size = 0;
+      if (hasHidden())
       {
-        size += range[1] - range[0] + 1;
+        for (int[] range : hiddenColumns)
+        {
+          size += range[1] - range[0] + 1;
+        }
       }
+      return size;
+    }
+    finally
+    {
+      lock.readLock().unlock();
     }
-    return size;
   }
 
   /**
@@ -53,40 +64,56 @@ public class HiddenColumns
    */
   public boolean hasHidden()
   {
-    return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
+    try
+    {
+      lock.readLock().lock();
+      return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
+    } finally
+    {
+      lock.readLock().unlock();
+    }
+
   }
 
   @Override
   public boolean equals(Object obj)
   {
-    if (!(obj instanceof HiddenColumns))
+    try
     {
-      return false;
-    }
-    HiddenColumns that = (HiddenColumns) obj;
+      lock.readLock().lock();
 
-    /*
-     * 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])
+      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 +125,26 @@ 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.elementAt(i);
+          if (result >= region[0])
+          {
+            result += region[1] - region[0] + 1;
+          }
         }
       }
+      return result;
+    } finally
+    {
+      lock.readLock().unlock();
     }
-    return result;
   }
 
   /**
@@ -124,42 +158,52 @@ 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.elementAt(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)
+        if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
         {
-          return 0;
-        }
-        else
-        {
-          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 +219,10 @@ 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
@@ -216,6 +264,10 @@ public class HiddenColumns
       return nextstart - distance;
     }
     return start - distance;
+    } finally
+    {
+      lock.readLock().unlock();
+    }
 
   }
 
@@ -228,28 +280,36 @@ public class HiddenColumns
    */
   public int findHiddenRegionPosition(int hiddenRegion)
   {
-    int result = 0;
-    if (hiddenColumns != null)
+    try
     {
-      int index = 0;
-      int gaps = 0;
-      do
+      lock.readLock().lock();
+      int result = 0;
+      if (hiddenColumns != null)
       {
-        int[] region = hiddenColumns.elementAt(index);
-        if (hiddenRegion == 0)
+        int index = 0;
+        int gaps = 0;
+        do
         {
-          return region[0];
-        }
+          int[] region = hiddenColumns.elementAt(index);
+          if (hiddenRegion == 0)
+          {
+            return region[0];
+          }
 
-        gaps += region[1] + 1 - region[0];
-        result = region[1] + 1;
-        index++;
-      } while (index <= hiddenRegion);
+          gaps += region[1] + 1 - region[0];
+          result = region[1] + 1;
+          index++;
+        } while (index <= hiddenRegion);
 
-      result -= gaps;
-    }
+        result -= gaps;
+      }
 
-    return result;
+      return result;
+    }
+    finally
+    {
+      lock.readLock().unlock();
+    }
   }
 
   /**
@@ -261,22 +321,29 @@ 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.elementAt(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();
+    }
 
   }
 
@@ -289,6 +356,10 @@ public class HiddenColumns
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
+    try
+    {
+      lock.readLock().lock();
+
     if (hiddenColumns != null)
     {
       int index = hiddenColumns.size() - 1;
@@ -305,7 +376,10 @@ public class HiddenColumns
     }
 
     return alPos;
-
+    } finally
+    {
+      lock.readLock().unlock();
+    }
   }
 
   /**
@@ -318,6 +392,10 @@ public class HiddenColumns
    */
   private int getHiddenIndexLeft(int pos)
   {
+    try
+    {
+
+      lock.readLock().lock();
     if (hiddenColumns != null)
     {
       int index = hiddenColumns.size() - 1;
@@ -334,6 +412,10 @@ public class HiddenColumns
     }
 
     return -1;
+    } finally
+    {
+      lock.readLock().unlock();
+    }
 
   }
 
@@ -345,9 +427,28 @@ public class HiddenColumns
    */
   public void hideColumns(int start, int end)
   {
+    hideColumns(start, end, false);
+  }
+
+  /**
+   * Adds the specified column range to the hidden columns
+   * 
+   * @param start
+   * @param end
+   */
+  private void hideColumns(int start, int end, boolean alreadyLocked)
+  {
+    try
+    {
+
+      if (!alreadyLocked)
+      {
+        lock.writeLock().lock();
+      }
+
     if (hiddenColumns == null)
     {
-      hiddenColumns = new Vector<int[]>();
+      hiddenColumns = new Vector<>();
     }
 
     /*
@@ -411,10 +512,21 @@ public class HiddenColumns
      * remaining case is that the new range follows everything else
      */
     hiddenColumns.addElement(new int[] { start, end });
+    } finally
+    {
+      if (!alreadyLocked)
+      {
+        lock.writeLock().unlock();
+      }
+    }
   }
 
   public boolean isVisible(int column)
   {
+    try
+    {
+      lock.readLock().lock();
+
     if (hiddenColumns != null)
     {
       for (int[] region : hiddenColumns)
@@ -427,6 +539,10 @@ public class HiddenColumns
     }
 
     return true;
+    } finally
+    {
+      lock.readLock().unlock();
+    }
   }
 
   /**
@@ -443,24 +559,33 @@ public class HiddenColumns
    */
   public HiddenColumns(HiddenColumns copy)
   {
-    if (copy != null)
+    try
     {
-      if (copy.hiddenColumns != null)
+
+      lock.readLock().lock();
+      if (copy != null)
       {
-        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
-        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+        if (copy.hiddenColumns != null)
         {
-          int[] rh, cp;
-          rh = copy.hiddenColumns.elementAt(i);
-          if (rh != null)
+          hiddenColumns = new Vector<>(copy.hiddenColumns.size());
+          for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
           {
-            cp = new int[rh.length];
-            System.arraycopy(rh, 0, cp, 0, rh.length);
-            hiddenColumns.addElement(cp);
+            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);
+            }
           }
         }
       }
     }
+    finally
+    {
+      lock.readLock().unlock();
+    }
   }
 
   /**
@@ -474,42 +599,49 @@ 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.elementAt(i);
+          if (region[0] > start && start + change > region[1])
+          {
+            deletedHiddenColumns.add(region);
 
-          hiddenColumns.removeElementAt(i);
-          i--;
-          hSize--;
-          continue;
-        }
+            hiddenColumns.removeElementAt(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 +655,42 @@ 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)
+        for (int i = 0; i < hiddenColumns.size(); i++)
         {
-          region[0] -= change;
-        }
-        if (region[1] >= start)
-        {
-          region[1] -= change;
-        }
-        if (region[1] < region[0])
-        {
-          hiddenColumns.removeElementAt(i--);
-        }
+          int[] region = hiddenColumns.elementAt(i);
+          if (region[0] >= start)
+          {
+            region[0] -= change;
+          }
+          if (region[1] >= start)
+          {
+            region[1] -= change;
+          }
+          if (region[1] < region[0])
+          {
+            hiddenColumns.removeElementAt(i--);
+          }
 
-        if (region[0] < 0)
-        {
-          region[0] = 0;
-        }
-        if (region[1] < 0)
-        {
-          region[1] = 0;
+          if (region[0] < 0)
+          {
+            region[0] = 0;
+          }
+          if (region[1] < 0)
+          {
+            region[1] = 0;
+          }
         }
       }
     }
+    finally
+    {
+      lock.writeLock().unlock();
+    }
   }
 
   /**
@@ -565,111 +705,127 @@ 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, 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 i, 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 (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, blockEnd = end;
+          int[] region;
+          int hideStart, 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 (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 +840,79 @@ 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(), 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,
+                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, 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 (!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 +940,97 @@ public class HiddenColumns
   public void makeVisibleAnnotation(int start, int end,
           AlignmentAnnotation alignmentAnnotation)
   {
-    if (alignmentAnnotation.annotations == null)
-    {
-      return;
-    }
-    if (start == end && end == -1)
+    try
     {
-      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, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd, 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 +1040,14 @@ 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 +1056,14 @@ 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 +1074,17 @@ 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], true);
+      }
+    } finally
+    {
+      lock.writeLock().unlock();
     }
   }
 
@@ -898,19 +1093,27 @@ 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.elementAt(i);
+          for (int j = region[0]; j < region[1] + 1; j++)
+          {
+            sel.addElement(j);
+          }
         }
       }
-    }
 
-    hiddenColumns = null;
+      hiddenColumns = null;
+    }
+    finally
+    {
+      lock.writeLock().unlock();
+    }
   }
 
   /**
@@ -921,23 +1124,31 @@ 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.elementAt(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.removeElement(region);
+          break;
+        }
+      }
+      if (hiddenColumns.size() == 0)
+      {
+        hiddenColumns = null;
       }
     }
-    if (hiddenColumns.size() == 0)
+    finally
     {
-      hiddenColumns = null;
+      lock.writeLock().unlock();
     }
   }
 
@@ -1044,15 +1255,23 @@ 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;
+        pruneIntervalVector(shifts, hiddenColumns);
+        if (hiddenColumns != null && hiddenColumns.size() == 0)
+        {
+          hiddenColumns = null;
+        }
       }
     }
+    finally
+    {
+      lock.writeLock().unlock();
+    }
   }
 
   /**
@@ -1251,16 +1470,24 @@ 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 +1498,19 @@ 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, true);
+      }
+    } finally
+    {
+      lock.writeLock().unlock();
     }
   }
 
@@ -1286,13 +1521,21 @@ public class HiddenColumns
    */
   public void markHiddenRegions(BitSet inserts)
   {
-    if (hiddenColumns == null)
+    try
     {
-      return;
+      lock.readLock().lock();
+      if (hiddenColumns == null)
+      {
+        return;
+      }
+      for (int[] range : hiddenColumns)
+      {
+        inserts.set(range[0], range[1] + 1);
+      }
     }
-    for (int[] range : hiddenColumns)
+    finally
     {
-      inserts.set(range[0], range[1] + 1);
+      lock.readLock().unlock();
     }
   }