/** 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;
}
// implementation of the needleman-wunsch-algorithm
protected void calculate(ActionSequence aSeq1, ActionSequence aSeq2, Ontology ontology) {
seq1 = aSeq1.getSequence();
seq2 = aSeq2.getSequence();
seq1 = transformer.transform(aSeq1.getSequence());
seq2 = transformer.transform(aSeq2.getSequence());
this.ontology = ontology;
m = seq1.size();
n = seq2.size();
matrix = new double[m + 1][n + 1];
traceback = new String[m + 1][n + 1];
alignments = new ActionElement[2][m + n];
// initialisation of the matrix + traceback
matrix[0][0] = 0;
traceback[0][0] = "done";
for (int j = 1; j <= n; j++) {
matrix[0][j] = j * gap;
traceback[0][j] = "left";
}
for (int i = 1; i <= m; i++) {
matrix[i][0] = i * gap;
traceback[i][0] = "up";
}
// recursive calculation of the remaining alignment-scores + traceback
for (int i = 1; i <= m; i++) {
for (int j = 1; j <= n; j++) {
double score1;
double d;
if (ontology == null) {
d = compareNoWUP(seq1.get(i - 1), seq2.get(j - 1));
score1 = matrix[i - 1][j - 1] + d;
} else {
d = compareWUP(seq1.get(i - 1), seq2.get(j - 1));
score1 = matrix[i - 1][j - 1] + d;
}
// if (d == match) {
// String s1 = seq1.get(i - 1).getHashMap().get("verb");
// String s2 = seq2.get(j - 1).getHashMap().get("verb");
// if (s1 != null && s2 != null) {
// if (s1.equals("none") && s2.equals("none")) {
// score1 -= 0.5;
// }
// }
// }
double score2 = matrix[i - 1][j] + gap;
double score3 = matrix[i][j - 1] + gap;
if (score1 > score2 && score1 > score3) {
matrix[i][j] = score1;
traceback[i][j] = "diag";
} else if (score2 > score3) {
matrix[i][j] = score2;
traceback[i][j] = "up";
} else {
matrix[i][j] = score3;
traceback[i][j] = "left";
}
}
}
// this.countNoneMatchings(m, n);
}