+ /**
+ * Justify the sequences to the left or right by deleting and inserting gaps
+ * before the initial residue or after the terminal residue
+ *
+ * @param right
+ * true if alignment padded to right, false to justify to left
+ * @return true if alignment was changed
+ */
+ public boolean justify(boolean right)
+ {
+ boolean modified = false;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
+ int ends[] = new int[sequences.size() * 2];
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ // This should really be a sequence method
+ ends[i * 2] = current.findIndex(current.getStart());
+ ends[i * 2 + 1] = current.findIndex(current.getStart()
+ + current.getLength());
+ boolean hitres = false;
+ for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
+ {
+ if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ if (!hitres)
+ {
+ ends[i * 2] = j;
+ hitres = true;
+ }
+ else
+ {
+ ends[i * 2 + 1] = j;
+ if (j - ends[i * 2] > maxLength)
+ {
+ maxLength = j - ends[i * 2];
+ }
+ }
+ }
+ }
+ }
+
+ maxLength++;
+ // now edit the flanking gaps to justify to either left or right
+ int cLength, extent, diff;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+
+ cLength = 1 + ends[i * 2 + 1] - ends[i * 2];
+ diff = maxLength - cLength; // number of gaps to indent
+ extent = current.getLength();
+ if (right)
+ {
+ // right justify
+ if (extent > ends[i * 2 + 1])
+ {
+ current.deleteChars(ends[i * 2 + 1] + 1, extent);
+ modified = true;
+ }
+ if (ends[i * 2] > diff)
+ {
+ current.deleteChars(0, ends[i * 2] - diff);
+ modified = true;
+ }
+ else
+ {
+ if (ends[i * 2] < diff)
+ {
+ current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ else
+ {
+ // left justify
+ if (ends[i * 2] > 0)
+ {
+ current.deleteChars(0, ends[i * 2]);
+ modified = true;
+ ends[i * 2 + 1] -= ends[i * 2];
+ extent -= ends[i * 2];
+ }
+ if (extent > maxLength)
+ {
+ current.deleteChars(maxLength + 1, extent);
+ modified = true;
+ }
+ else
+ {
+ if (extent < maxLength)
+ {
+ current.insertCharAt(extent, maxLength - extent, gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ }
+ return modified;
+ }
+