+
+ /**
+ * construct and call the calculation methods on a new Conservation object
+ *
+ * @param name
+ * - name of conservation
+ * @param threshold
+ * - minimum number of conserved residues needed to indicate
+ * conservation (typically 3)
+ * @param seqs
+ * @param start
+ * first column in calculation window
+ * @param end
+ * last column in calculation window
+ * @param posOrNeg
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
+ * @return Conservation object ready for use in visualization
+ */
+ public static Conservation calculateConservation(String name,
+ int threshold, List<SequenceI> seqs, int start, int end,
+ boolean posOrNeg, int consPercGaps, boolean calcQuality)
+ {
+ Conservation cons = new Conservation(name, threshold, seqs, start, end);
+ cons.calculate();
+ cons.verdict(posOrNeg, consPercGaps);
+
+ if (calcQuality)
+ {
+ cons.findQuality();
+ }
+
+ return cons;
+ }