- * @param originalSequences - sequences in alignment that are to filtered
- * @param omitHidden - null or strings to be analysed (typically, visible portion of each sequence in alignment)
- * @param start - first column in window for calculation
- * @param end - last column in window for calculation
- * @param ungapped - if true then use ungapped sequence to compute PID
- * @return vector containing maximum PID for i-th sequence and any sequences longer than that seuqence
+ *
+ * @param originalSequences
+ * - sequences in alignment that are to filtered
+ * @param omitHidden
+ * - null or strings to be analysed (typically, visible portion of
+ * each sequence in alignment)
+ * @param start
+ * - first column in window for calculation
+ * @param end
+ * - last column in window for calculation
+ * @param ungapped
+ * - if true then use ungapped sequence to compute PID
+ * @return vector containing maximum PID for i-th sequence and any sequences
+ * longer than that seuqence