+ sb.append("ScoreMatrix ").append(getName()).append("\n");
+ }
+ for (char sym : symbols)
+ {
+ if (html)
+ {
+ sb.append("<th> ").append(sym).append(" </th>");
+ }
+ else
+ {
+ sb.append("\t").append(sym);
+ }
+ }
+ sb.append(html ? "</tr>\n" : "\n");
+
+ /*
+ * table of scores
+ */
+ for (char c1 : symbols)
+ {
+ if (html)
+ {
+ sb.append("<tr><td>");
+ }
+ sb.append(c1).append(html ? "</td>" : "");
+ for (char c2 : symbols)
+ {
+ sb.append(html ? "<td>" : "\t")
+ .append(matrix[symbolIndex[c1]][symbolIndex[c2]])
+ .append(html ? "</td>" : "");
+ }
+ sb.append(html ? "</tr>\n" : "\n");
+ }
+ if (html)
+ {
+ sb.append("</table>");
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Answers the number of symbols coded for (also equal to the number of rows
+ * and columns of the score matrix)
+ *
+ * @return
+ */
+ public int getSize()
+ {
+ return symbols.length;
+ }
+
+ /**
+ * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
+ * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
+ * computed using the current score matrix. For example
+ * <ul>
+ * <li>Sequences:</li>
+ * <li>FKL</li>
+ * <li>R-D</li>
+ * <li>QIA</li>
+ * <li>GWC</li>
+ * <li>Score matrix is BLOSUM62</li>
+ * <li>Gaps treated same as X (unknown)</li>
+ * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
+ * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
+ * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
+ * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
+ * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
+ * <li>and so on</li>
+ * </ul>
+ * This method is thread-safe.
+ */
+ @Override
+ public MatrixI findSimilarities(AlignmentView seqstrings,
+ SimilarityParamsI options)
+ {
+ char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
+ : GAP_CHARACTER;
+ String[] seqs = seqstrings.getSequenceStrings(gapChar);
+ return findSimilarities(seqs, options);
+ }
+
+ /**
+ * Computes pairwise similarities of a set of sequences using the given
+ * parameters
+ *
+ * @param seqs
+ * @param params
+ * @return
+ */
+ protected MatrixI findSimilarities(String[] seqs,
+ SimilarityParamsI params)
+ {
+ double[][] values = new double[seqs.length][];
+ for (int row = 0; row < seqs.length; row++)
+ {
+ values[row] = new double[seqs.length];
+ for (int col = 0; col < seqs.length; col++)
+ {
+ double total = computeSimilarity(seqs[row], seqs[col], params);
+ values[row][col] = total;
+ }
+ }
+ return new Matrix(values);
+ }
+
+ /**
+ * Calculates the pairwise similarity of two strings using the given
+ * calculation parameters
+ *
+ * @param seq1
+ * @param seq2
+ * @param params
+ * @return
+ */
+ protected double computeSimilarity(String seq1, String seq2,
+ SimilarityParamsI params)
+ {
+ int len1 = seq1.length();
+ int len2 = seq2.length();
+ double total = 0;
+
+ int width = Math.max(len1, len2);
+ for (int i = 0; i < width; i++)
+ {
+ if (i >= len1 || i >= len2)