+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ void applyConservation(int i)\r
+ {\r
+ if ((conservation[i] != '*') && (conservation[i] != '+'))\r
+ {\r
+ int tmp = 10;\r
+ int t = 0;\r
+\r
+ if (!jalview.util.Comparison.isGap(conservation[i]))\r
+ {\r
+ t = conservation[i]-'0';\r
+ }\r
+\r
+ while (tmp >= t)\r
+ {\r
+ lighter(inc);\r
+ tmp--;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ * @param inc DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ void lighter(int inc)\r
+ {\r
+ int red = currentColour.getRed();\r
+ int blue = currentColour.getBlue();\r
+ int green = currentColour.getGreen();\r
+\r
+ if (red < (255 - inc))\r
+ {\r
+ red = red + inc;\r
+ }\r
+ else\r
+ {\r
+ red = 255;\r
+ }\r
+\r
+ if (blue < (255 - inc))\r
+ {\r
+ blue = blue + inc;\r
+ }\r
+ else\r
+ {\r
+ blue = 255;\r
+ }\r
+\r
+ if (green < (255 - inc))\r
+ {\r
+ green = green + inc;\r
+ }\r
+ else\r
+ {\r
+ green = 255;\r
+ }\r
+\r
+ currentColour = new Color(red, green, blue);\r
+ }\r
+\r
+\r