JAL-2674 reverted attempt at visible regions iterator

[jalview.git] / src / jalview / datamodel / HiddenColumns.java

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 82e25b9..b915423 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1525,11 +1525,6 @@ public class HiddenColumns
     return new BoundedStartRegionIterator(start, end, useCopy);
   }
 
-  public Iterator<int[]> getBoundedVisRegionIterator(int start, int end)
-  {
-    return new BoundedVisRegionIterator(start, end, true);
-  }
-
   /**
    * An iterator which iterates over hidden column regions in a range.
    * 
@@ -1733,125 +1728,4 @@ public class HiddenColumns
       return result;
     }
   }
-
-  class BoundedVisRegionIterator implements Iterator<int[]>
-  {
-    private int start; // start position to iterate from
-
-    private int end; // end position to iterate to
-
-    // current region in visColumns
-    private int[] currentRegion;
-
-    // current index in visColumns
-    private int currentPosition = 0;
-
-    private List<int[]> vcontigs = null;
-
-    /**
-     * Construct an iterator over visibleColumn regions bounded at
-     * [lowerBound,upperBound]
-     * 
-     * @param lowerBound
-     *          lower bound to iterate from
-     * @param upperBound
-     *          upper bound to iterate to
-     * @param useCopyCols
-     *          whether to make a local copy for iteration (set to true if
-     *          calling from outwith the HiddenColumns class)
-     */
-    BoundedVisRegionIterator(int lowerBound, int upperBound,
-            boolean useCopy)
-    {
-      try
-      {
-        start = lowerBound;
-        end = upperBound;
-
-        if (useCopy)
-        {
-          // assume that if useCopy is false the calling code has locked
-          // hiddenColumns
-          LOCK.readLock().lock();
-        }
-
-        int visStart = start;
-
-        if (hiddenColumns != null)
-        {
-          vcontigs = new ArrayList<>(hiddenColumns.size() + 1);
-
-          // navigate to start, keeping count of hidden columns
-          int i = 0;
-          int[] region = null;
-          while ((i < hiddenColumns.size())
-                  && (hiddenColumns.get(i)[0] <= start))
-          {
-            i++;
-          }
-          // if there was a hidden region before (i>=1), and it ended after
-          // start
-          // and before end, adjust visStart to be just after that region
-          if (i > 0)
-          {
-            region = hiddenColumns.get(i - 1);
-            if ((region[1] > start) && (region[1] < end))
-            {
-              visStart = region[1] + 1;
-            }
-            else if (region[1] >= end)
-            {
-              // previous hidden region covers whole range [start,end]
-              // early exit - vcontigs is empty
-              return;
-            }
-          }
-
-          // iterate from start to end, adding start positions of each
-          // hidden region. Positions are visible columns count, not absolute
-          while (i < hiddenColumns.size()
-                  && (hiddenColumns.get(i)[0] < end))
-          {
-            region = hiddenColumns.get(i);
-            int[] prevVisibleRegion = new int[] { visStart, region[0] - 1 };
-            vcontigs.add(prevVisibleRegion);
-            visStart = region[1] + 1;
-            i++;
-          }
-          // add on a final visible region if needed
-          if (visStart <= end)
-          {
-            int[] lastRegion = new int[] { visStart, end };
-            vcontigs.add(lastRegion);
-          }
-        }
-        else
-        {
-          vcontigs = new ArrayList<>();
-          int[] lastRegion = new int[] { start, end };
-          vcontigs.add(lastRegion);
-        }
-      } finally
-      {
-        if (useCopy)
-        {
-          LOCK.readLock().unlock();
-        }
-      }
-    }
-
-    @Override
-    public boolean hasNext()
-    {
-      return (currentPosition < vcontigs.size());
-    }
-
-    @Override
-    public int[] next()
-    {
-      currentRegion = vcontigs.get(currentPosition);
-      currentPosition++;
-      return currentRegion;
-    }
-  }
 }