+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ *
+ * @param inserts
+ * BitSet where hidden columns will be marked
+ */
+ public void markHiddenRegions(BitSet inserts)
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ if (hiddenColumns == null)
+ {
+ return;
+ }
+ for (int[] range : hiddenColumns)
+ {
+ inserts.set(range[0], range[1] + 1);
+ }
+ }
+ finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
+ /**
+ * 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)