+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+
+ newhidden.hideColumns(left, right);
+ padGaps(left, right, profileseq);
+ }
+ return newhidden;
+ }
+
+ /**
+ * Pad gaps in all sequences in alignment except profileseq
+ *
+ * @param left
+ * position of first gap to insert
+ * @param right
+ * position of last gap to insert
+ * @param profileseq
+ * sequence not to pad
+ */
+ private void padGaps(int left, int right, SequenceI profileseq)
+ {
+ char gc = getGapCharacter();
+
+ // make a string with number of gaps = length of hidden region
+ StringBuilder sb = new StringBuilder();
+ for (int g = 0; g < right - left + 1; g++)
+ {
+ sb.append(gc);
+ }
+
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = getSequenceAt(s);
+ if ((sqobj != profileseq) && (sqobj.getLength() >= left))