- * @param b 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(Conservation cons, boolean b, int consPercGaps, boolean calcQuality)
- {
- cons.calculate();
- cons.verdict(b, consPercGaps);
+ * @param b
+ * 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(Conservation cons,
+ boolean b, int consPercGaps, boolean calcQuality)
+ {
+ cons.calculate();
+ cons.verdict(b, consPercGaps);