+ }
+
+ /**
+ * 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