+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void recalcConservation()\r
+ {\r
+ if (cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
+ }\r
+\r
+ if (cs.conservationApplied())\r
+ {\r
+ Conservation c = new Conservation(groupName,\r
+ ResidueProperties.propHash, 3,\r
+ sequences,\r
+ startRes, endRes + 1);\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+\r
+ cs.setConservation(c);\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences,\r
+ getWidth());\r
+ }\r
+ }\r
+ }\r
+ catch (java.lang.OutOfMemoryError err)\r
+ {\r
+ System.out.println("Out of memory loading groups: " + err);\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param recalc DOCUMENT ME!\r
+ */\r
+ public void addOrRemove(SequenceI s, boolean recalc)\r
+ {\r
+ if (sequences.contains(s))\r
+ {\r
+ deleteSequence(s, recalc);\r
+ }\r
+ else\r
+ {\r
+ addSequence(s, recalc);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param recalc DOCUMENT ME!\r
+ */\r
+ public void deleteSequence(SequenceI s, boolean recalc)\r
+ {\r
+ sequences.removeElement(s);\r
+\r
+ if (recalc)\r
+ {\r
+ recalcConservation();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r