From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 7 Jun 2017 14:32:30 +0000 (+0100)
Subject: JAL-2591 More refactoring (incomplete)
X-Git-Tag: Release_2_10_3b1~183^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab67e99fb7336d0f4411488d9f843c720ab6b418;p=jalview.git

JAL-2591 More refactoring (incomplete)
---

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 9ba9cce..0971e56 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -837,8 +837,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
             + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      av.getAlignment().getHiddenColumns().getHiddenColumnsCopy(
-              jalview.appletgui.AlignFrame.copiedHiddenColumns);
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = av.getAlignment()
+              .getHiddenColumns().getHiddenColumnsCopy();
     }
   }
 
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f5e6fc7..098222f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1916,42 +1916,6 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
-  {
-    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
-    int startPos = alignmentStartEnd[0];
-    int endPos = alignmentStartEnd[1];
-
-    int[] lowestRange = new int[] { -1, -1 };
-    int[] higestRange = new int[] { -1, -1 };
-
-    for (int[] hiddenCol : hiddenCols)
-    {
-      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 };
-  }
-
-  @Override
   public void setHiddenColumns(HiddenColumns cols)
   {
     hiddenCols = cols;
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2e61f9d..1b5207f 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -580,15 +580,6 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
-  /**
-   * Calculate the visible start and end index of an alignment. The result is
-   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
-   * 
-   * @param hiddenCols
-   * @return
-   */
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
-
   public void setHiddenColumns(HiddenColumns cols);
 
 }
diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 0036402..be10721 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;
@@ -6,14 +26,13 @@ import jalview.util.ShiftList;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Collections;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 
-public class HiddenColumns implements Iterable<int[]>
+public class HiddenColumns
 {
-  private static final ReentrantReadWriteLock lock = new ReentrantReadWriteLock();
+  private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
   
   /*
    * list of hidden column [start, end] ranges; the list is maintained in
@@ -46,7 +65,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       StringBuilder regionBuilder = new StringBuilder();
       for (int[] range : hiddenColumns)
       {
@@ -58,7 +77,7 @@ public class HiddenColumns implements Iterable<int[]>
       return regionBuilder.toString();
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -71,7 +90,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int size = 0;
       if (hasHidden())
       {
@@ -84,7 +103,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -97,11 +116,11 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
 
   }
@@ -111,7 +130,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
       if (!(obj instanceof HiddenColumns))
       {
@@ -143,7 +162,7 @@ public class HiddenColumns implements Iterable<int[]>
       return true;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -158,7 +177,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int result = column;
       if (hiddenColumns != null)
       {
@@ -174,7 +193,7 @@ public class HiddenColumns implements Iterable<int[]>
       return result;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -191,7 +210,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int result = hiddenColumn;
       if (hiddenColumns != null)
       {
@@ -233,7 +252,7 @@ public class HiddenColumns implements Iterable<int[]>
                      // columns.
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -253,7 +272,7 @@ public class HiddenColumns implements Iterable<int[]>
     try
     {
 
-      lock.readLock().lock();
+      LOCK.readLock().lock();
     int distance = visibleDistance;
 
     // in case startColumn is in a hidden region, move it to the left
@@ -297,7 +316,7 @@ public class HiddenColumns implements Iterable<int[]>
     return start - distance;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
 
   }
@@ -311,7 +330,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       List<Integer> positions = new ArrayList<>(
               hiddenColumns.size());
 
@@ -341,7 +360,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -356,7 +375,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (hiddenColumns != null)
       {
         int index = 0;
@@ -375,7 +394,7 @@ public class HiddenColumns implements Iterable<int[]>
       return alPos;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
 
   }
@@ -391,7 +410,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
     if (hiddenColumns != null)
     {
@@ -411,7 +430,7 @@ public class HiddenColumns implements Iterable<int[]>
     return alPos;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -428,7 +447,7 @@ public class HiddenColumns implements Iterable<int[]>
     try
     {
 
-      lock.readLock().lock();
+      LOCK.readLock().lock();
     if (hiddenColumns != null)
     {
       int index = hiddenColumns.size() - 1;
@@ -447,7 +466,7 @@ public class HiddenColumns implements Iterable<int[]>
     return -1;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
 
   }
@@ -476,69 +495,69 @@ public class HiddenColumns implements Iterable<int[]>
 
       if (!alreadyLocked)
       {
-        lock.writeLock().lock();
+        LOCK.writeLock().lock();
       }
 
-    if (hiddenColumns == null)
-    {
-      hiddenColumns = new Vector<>();
-    }
-
-    /*
-     * traverse existing hidden ranges and insert / amend / append as
-     * appropriate
-     */
-    for (int i = 0; i < hiddenColumns.size(); i++)
-    {
-      int[] region = hiddenColumns.elementAt(i);
-
-      if (end < region[0] - 1)
+      if (hiddenColumns == null)
       {
-        /*
-         * insert discontiguous preceding range
-         */
-        hiddenColumns.insertElementAt(new int[] { start, end }, i);
-        return;
+        hiddenColumns = new Vector<>();
       }
 
-      if (end <= region[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 preceding it - adjust
-         * start column
-         */
-        region[0] = Math.min(region[0], start);
-        return;
-      }
+        int[] region = hiddenColumns.elementAt(i);
 
-      if (start <= region[1] + 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)
+        if (end < region[0] - 1)
+        {
+          /*
+           * insert discontiguous preceding range
+           */
+          hiddenColumns.insertElementAt(new int[] { start, end }, i);
+          return;
+        }
+
+        if (end <= region[1])
         {
-          int[] nextRegion = hiddenColumns.get(i + 1);
-          if (nextRegion[0] > end + 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)
+        {
+          /*
+           * 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;
-      }
     }
 
     /*
@@ -549,7 +568,7 @@ public class HiddenColumns implements Iterable<int[]>
     {
       if (!alreadyLocked)
       {
-        lock.writeLock().unlock();
+        LOCK.writeLock().unlock();
       }
     }
   }
@@ -558,7 +577,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
 
     if (hiddenColumns != null)
     {
@@ -574,7 +593,7 @@ public class HiddenColumns implements Iterable<int[]>
     return true;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -595,7 +614,7 @@ public class HiddenColumns implements Iterable<int[]>
     try
     {
 
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (copy != null)
       {
         if (copy.hiddenColumns != null)
@@ -606,7 +625,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -615,7 +634,8 @@ public class HiddenColumns implements Iterable<int[]>
     Vector<int[]> copy = new Vector<>(hiddenColumns.size());
     for (int i = 0, j = hiddenColumns.size(); i < j; i++)
     {
-      int[] rh, cp;
+      int[] rh;
+      int[] cp;
       rh = hiddenColumns.elementAt(i);
       if (rh != null)
       {
@@ -632,7 +652,8 @@ public class HiddenColumns implements Iterable<int[]>
     ArrayList<int[]> copy = new ArrayList<>(hiddenColumns.size());
     for (int i = 0, j = hiddenColumns.size(); i < j; i++)
     {
-      int[] rh, cp;
+      int[] rh;
+      int[] cp;
       rh = hiddenColumns.elementAt(i);
       if (rh != null)
       {
@@ -644,27 +665,27 @@ public class HiddenColumns implements Iterable<int[]>
     return copy;
   }
 
-  public void getHiddenColumnsCopy(Vector<int[]> copy)
+  public Vector<int[]> getHiddenColumnsCopy()
   {
     try
     {
-      lock.readLock().lock();
-      copy = copyHiddenRegions();
+      LOCK.readLock().lock();
+      return copyHiddenRegions();
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
-  public void getHiddenColumnsCopy(ArrayList<int[]> copy)
+  public ArrayList<int[]> getHiddenColumnsCopyAsList()
   {
     try
     {
-      lock.readLock().lock();
-      copy = copyHiddenRegionsToArrayList();
+      LOCK.readLock().lock();
+      return copyHiddenRegionsToArrayList();
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -681,7 +702,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       List<int[]> deletedHiddenColumns = null;
 
       if (hiddenColumns != null)
@@ -720,7 +741,7 @@ public class HiddenColumns implements Iterable<int[]>
       return deletedHiddenColumns;
     } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -737,7 +758,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       if (hiddenColumns != null)
       {
         for (int i = 0; i < hiddenColumns.size(); i++)
@@ -769,7 +790,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -787,7 +808,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
         List<int[]> visiblecontigs = new ArrayList<>();
@@ -795,7 +816,8 @@ public class HiddenColumns implements Iterable<int[]>
 
         int vstart = start;
         int[] region;
-        int hideStart, hideEnd;
+        int hideStart;
+        int hideEnd;
 
         for (int j = 0; vstart < end && j < regions.size(); j++)
         {
@@ -836,7 +858,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -845,19 +867,21 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
-      int i, iSize = seqs.length;
+      LOCK.readLock().lock();
+      int iSize = seqs.length;
       String selections[] = new String[iSize];
       if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
-        for (i = 0; i < iSize; i++)
+        for (int i = 0; i < iSize; i++)
         {
           StringBuffer visibleSeq = new StringBuffer();
           List<int[]> regions = getHiddenRegions();
 
-          int blockStart = start, blockEnd = end;
+          int blockStart = start;
+          int blockEnd = end;
           int[] region;
-          int hideStart, hideEnd;
+          int hideStart;
+          int hideEnd;
 
           for (int j = 0; j < regions.size(); j++)
           {
@@ -894,7 +918,7 @@ public class HiddenColumns implements Iterable<int[]>
       }
       else
       {
-        for (i = 0; i < iSize; i++)
+        for (int i = 0; i < iSize; i++)
         {
           selections[i] = seqs[i].getSequenceAsString(start, end);
         }
@@ -904,7 +928,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -922,23 +946,30 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
-      int fpos = seq.getStart(), lpos = seq.getEnd();
+      LOCK.readLock().lock();
+      int fpos = seq.getStart();
+      int lpos = seq.getEnd();
       int start = 0;
 
       if (hiddenColumns == null || hiddenColumns.size() == 0)
       {
-        int ifpos = seq.findIndex(fpos) - 1,
-                ilpos = seq.findIndex(lpos) - 1;
+        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, lastvispos = -1, rcount = 0,
-              hideStart = seq.getLength(), hideEnd = -1;
-      int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
+      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++)
@@ -991,7 +1022,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1022,7 +1053,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (alignmentAnnotation.annotations == null)
       {
         return;
@@ -1038,9 +1069,12 @@ public class HiddenColumns implements Iterable<int[]>
         Vector<Annotation[]> annels = new Vector<>();
         Annotation[] els = null;
         List<int[]> regions = getHiddenRegions();
-        int blockStart = start, blockEnd = end;
+        int blockStart = start;
+        int blockEnd = end;
         int[] region;
-        int hideStart, hideEnd, w = 0;
+        int hideStart;
+        int hideEnd;
+        int w = 0;
 
         for (int j = 0; j < regions.size(); j++)
         {
@@ -1110,7 +1144,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1122,11 +1156,11 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       return hiddenColumns != null && hiddenColumns.size() > 0;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1138,11 +1172,11 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       return hiddenColumns != null && hiddenColumns.size() > 1;
     } finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1156,7 +1190,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       List<int[]> inserts = sr.getInsertions();
       for (int[] r : inserts)
       {
@@ -1164,7 +1198,7 @@ public class HiddenColumns implements Iterable<int[]>
       }
     } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1175,7 +1209,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       if (hiddenColumns != null)
       {
         for (int i = 0; i < hiddenColumns.size(); i++)
@@ -1192,7 +1226,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1206,7 +1240,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
         int[] region = hiddenColumns.elementAt(i);
@@ -1228,7 +1262,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1244,7 +1278,10 @@ public class HiddenColumns implements Iterable<int[]>
           Vector<int[]> intervals)
   {
     boolean pruned = false;
-    int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+    int i = 0;
+    int j = intervals.size() - 1;
+    int s = 0;
+    int t = shifts.size() - 1;
     int hr[] = intervals.elementAt(i);
     int sr[] = shifts.get(s);
     while (i <= j && s <= t)
@@ -1337,7 +1374,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       // delete any intervals intersecting.
       if (hiddenColumns != null)
       {
@@ -1350,7 +1387,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1552,7 +1589,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       int hashCode = 1;
       if (hiddenColumns != null)
       {
@@ -1566,7 +1603,7 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
@@ -1580,7 +1617,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.writeLock().lock();
+      LOCK.writeLock().lock();
       for (int firstSet = inserts
               .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
                       .nextSetBit(lastSet))
@@ -1590,7 +1627,7 @@ public class HiddenColumns implements Iterable<int[]>
       }
     } finally
     {
-      lock.writeLock().unlock();
+      LOCK.writeLock().unlock();
     }
   }
 
@@ -1603,7 +1640,7 @@ public class HiddenColumns implements Iterable<int[]>
   {
     try
     {
-      lock.readLock().lock();
+      LOCK.readLock().lock();
       if (hiddenColumns == null)
       {
         return;
@@ -1615,18 +1652,63 @@ public class HiddenColumns implements Iterable<int[]>
     }
     finally
     {
-      lock.readLock().unlock();
+      LOCK.readLock().unlock();
     }
   }
 
-  @Override
-  public Iterator<int[]> iterator()
+  /**
+   * 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)
   {
-    if (hiddenColumns == null)
+    try
     {
-      return Collections.<int[]> emptyList().iterator();
+      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();
     }
-    return hiddenColumns.iterator();
+
   }
 
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e79e303..ae2e44a 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1320,10 +1320,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       alignmentToExport = viewport.getAlignment();
     }
-    alignmentStartEnd = alignmentToExport
-            .getVisibleStartAndEndIndex(viewport.getAlignment()
-                    .getHiddenColumns()
-                    .getHiddenRegions());
+    alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;
@@ -1885,8 +1883,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.hasHiddenColumns())
     {
       hiddenColumns = new ArrayList<>();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes(),
-              hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
       for (int[] region : viewport.getAlignment().getHiddenColumns())
       {
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 07a5ad9..7741956 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -52,7 +52,6 @@ import java.awt.image.BufferedImage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.List;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -953,13 +952,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
-    List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
-            .getHiddenRegions();
-    if (hiddenCols != null)
+    if (av.hasHiddenColumns())
     {
-      alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
-              hiddenCols);
+      alignmentStartEnd = av.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
     }
+
     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
             seqs, omitHidden, alignmentStartEnd);
 
@@ -970,8 +968,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     if (av.hasHiddenColumns())
     {
-      av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy(hiddenColumns);
+      hiddenColumns = av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopyAsList();
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 637b590..d18c9b3 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1421,7 +1421,9 @@ public class Jalview2XML
         }
         else
         {
-          for (int[] region : hidden)
+          ArrayList<int[]> hiddenRegions = hidden
+                  .getHiddenColumnsCopyAsList();
+          for (int[] region : hiddenRegions)
           {
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index d6e09fd..1cfa771 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -37,7 +37,6 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
@@ -1107,35 +1106,6 @@ public class AlignmentTest
             "addSequence broke dataset reference integrity");
   }
 
-  @Test(groups = "Functional")
-  public void getVisibleStartAndEndIndexTest()
-  {
-    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
-    AlignmentI align = new Alignment(new SequenceI[] { seq });
-    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
-
-    int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(0, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 0, 0 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(1, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 6, 9 });
-    hiddenCols.add(new int[] { 11, 12 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(1, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 24, 25 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    System.out.println(startEnd[0] + " : " + startEnd[1]);
-    assertEquals(1, startEnd[0]);
-    assertEquals(23, startEnd[1]);
-  }
-
   /**
    * Tests that dbrefs with mappings to sequence get updated if the sequence
    * acquires a dataset sequence
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 9f77eaa..5b92677 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -612,4 +612,34 @@ public class HiddenColumnsTest
     String result = hc.regionsToString(",", "--");
     assertEquals("3--7,10--10,14--15", result);
   }
+
+  @Test(groups = "Functional")
+  public void getVisibleStartAndEndIndexTest()
+  {
+    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    AlignmentI align = new Alignment(new SequenceI[] { seq });
+    HiddenColumns hc = new HiddenColumns();
+
+    int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    assertEquals(0, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hc.hideColumns(0, 0);
+    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hc.hideColumns(6, 9);
+    hc.hideColumns(11, 12);
+    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hc.hideColumns(24, 25);
+    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    System.out.println(startEnd[0] + " : " + startEnd[1]);
+    assertEquals(1, startEnd[0]);
+    assertEquals(23, startEnd[1]);
+  }
+
 }