+\r
+ public void setConservationInc(int i)\r
+ {\r
+ inc = i;\r
+ }\r
+\r
+ public int getConservationInc()\r
+ {\r
+ return inc;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param consensus DOCUMENT ME!\r
+ */\r
+ public void setConsensus(Vector vconsensus)\r
+ {\r
+ int i, iSize=vconsensus.size();\r
+ consensus = new Hashtable[iSize];\r
+ for(i=0; i<iSize; i++)\r
+ consensus[i] = (Hashtable)vconsensus.elementAt(i);\r
+ }\r
+\r
+\r
+ public void setConservation(Conservation cons)\r
+ {\r
+ if(cons==null)\r
+ {\r
+ conservationColouring = false;\r
+ conservation = null;\r
+ }\r
+ else\r
+ {\r
+ conservationColouring = true;\r
+ int i, iSize = cons.getConsSequence().getLength();\r
+ conservation = new char[iSize];\r
+ for (i = 0; i < iSize; i++)\r
+ conservation[i] = cons.getConsSequence().getCharAt(i);\r
+ }\r
+\r
+ }\r
+\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