+
+ /**
+ * 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)
+ {
+ /*
+ * off the end of one sequence; stop if we are only matching
+ * on the shorter sequence length, else treat as trailing gap
+ */
+ if (params.denominateByShortestLength())
+ {
+ break;
+ }
+ }
+
+ char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
+ char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
+ boolean gap1 = Comparison.isGap(c1);
+ boolean gap2 = Comparison.isGap(c2);
+
+ if (gap1 && gap2)
+ {
+ /*
+ * gap-gap: include if options say so, else ignore
+ */
+ if (!params.includeGappedColumns())
+ {
+ continue;
+ }
+ }
+ else if (gap1 || gap2)
+ {
+ /*
+ * gap-residue: score if options say so
+ */
+ if (!params.includeGaps())
+ {
+ continue;
+ }
+ }
+ float score = getPairwiseScore(c1, c2);
+ total += score;
+ }
+ return total;
+ }
+
+ /**
+ * Answers a hashcode computed from the symbol alphabet and the matrix score
+ * values
+ */
+ @Override
+ public int hashCode()
+ {
+ int hs = Arrays.hashCode(symbols);
+ for (float[] row : matrix)
+ {
+ hs = hs * 31 + Arrays.hashCode(row);
+ }
+ return hs;
+ }
+
+ /**
+ * Answers true if the argument is a ScoreMatrix with the same symbol alphabet
+ * and score values, else false
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof ScoreMatrix))
+ {
+ return false;
+ }
+ ScoreMatrix sm = (ScoreMatrix) obj;
+ if (Arrays.equals(symbols, sm.symbols)
+ && Arrays.deepEquals(matrix, sm.matrix))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the alphabet the matrix scores for, as a string of characters
+ *
+ * @return
+ */
+ String getSymbols()
+ {
+ return new String(symbols);
+ }
+
+ public float getMinimumScore()
+ {
+ return minValue;
+ }
+
+ public float getMaximumScore()
+ {
+ return maxValue;
+ }
+
+ @Override
+ public ScoreModelI getInstance(AlignmentViewPanel avp)
+ {
+ return this;
+ }