/** prints the alignment of the two sequences */ public String printAlignment() { String res = ""; if (pointer == 0) { calculateAlignmentRecursive(m, n); alignments = transformer.retransform(alignments); } for (int i = pointer - 1; i >= 0; i--) { String s1 = alignments[0][i].getName(); String s2 = alignments[1][i].getName(); // maximum of 50 characters for (int k = 50 - s1.length(); k > 0; k--) { res += " "; } res += s1 + " - " + s2 + "\n"; } res += "\nLength seq1 = " + m + "; length seq2 = " + n + "\n"; double score = this.getScore(); res += "alignment score: " + score + "\n\n"; System.out.println(res); return res; }