--- /dev/null
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over visible regions in a range. Provides a
+ * special "endsAtHidden" indicator to allow callers to determine if the final
+ * visible column is adjacent to a hidden region.
+ */
+public class VisibleContigsIterator implements Iterator<int[]>
+{
+ private List<int[]> vcontigs = new ArrayList<>();
+
+ private int currentPosition = 0;
+
+ private boolean endsAtHidden = false;
+
+ VisibleContigsIterator(int start, int end,
+ List<int[]> hiddenColumns)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ int vstart = start;
+ int hideStart;
+ int hideEnd;
+
+ for (int[] region : hiddenColumns)
+ {
+ endsAtHidden = false;
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ // navigate to start
+ if (hideEnd < vstart)
+ {
+ continue;
+ }
+ if (hideStart > vstart)
+ {
+ if (end - 1 > hideStart - 1)
+ {
+ int[] contig = new int[] { vstart, hideStart - 1 };
+ vcontigs.add(contig);
+ endsAtHidden = true;
+ }
+ else
+ {
+ int[] contig = new int[] { vstart, end - 1 };
+ vcontigs.add(contig);
+ }
+ }
+ vstart = hideEnd + 1;
+
+ // exit if we're past the end
+ if (vstart >= end)
+ {
+ break;
+ }
+ }
+
+ if (vstart < end)
+ {
+ int[] contig = new int[] { vstart, end - 1 };
+ vcontigs.add(contig);
+ endsAtHidden = false;
+ }
+ }
+ else
+ {
+ int[] contig = new int[] { start, end - 1 };
+ vcontigs.add(contig);
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (currentPosition < vcontigs.size());
+ }
+
+ @Override
+ public int[] next()
+ {
+ int[] result = vcontigs.get(currentPosition);
+ currentPosition++;
+ return result;
+ }
+
+ public boolean endsAtHidden()
+ {
+ return endsAtHidden;
+ }
+}
+