+ * 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;
+ }
+ }
+ // Change GAP_SPACE to GAP_DASH if we adopt - for gap in matrices
+ char c1 = i >= len1 ? Comparison.GAP_SPACE : seq1.charAt(i);
+ char c2 = i >= len2 ? Comparison.GAP_SPACE : 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.includesGaps())
+ {
+ continue;
+ }
+ }
+ float score = getPairwiseScore(c1, c2);
+ total += score;
+ }
+ return total;
+ }
+
+ /**