+ this.size = seqs.size();\r
+ makeColours();\r
+ }\r
+\r
+ public void makeColours()\r
+ {\r
+ conses[0] = new Consensus("WLVIMAFCYHP", 60);\r
+ conses[1] = new Consensus("WLVIMAFCYHP", 80);\r
+ conses[2] = new Consensus("ED", 50);\r
+ conses[3] = new Consensus("KR", 60);\r
+ conses[4] = new Consensus("G", 50);\r
+ conses[5] = new Consensus("N", 50);\r
+ conses[6] = new Consensus("QE", 50);\r
+ conses[7] = new Consensus("P", 50);\r
+ conses[8] = new Consensus("TS", 50);\r
+\r
+ conses[26] = new Consensus("A", 85);\r
+ conses[27] = new Consensus("C", 85);\r
+ conses[10] = new Consensus("E", 85);\r
+ conses[11] = new Consensus("F", 85);\r
+ conses[12] = new Consensus("G", 85);\r
+ conses[13] = new Consensus("H", 85);\r
+ conses[14] = new Consensus("I", 85);\r
+ conses[15] = new Consensus("L", 85);\r
+ conses[16] = new Consensus("M", 85);\r
+ conses[17] = new Consensus("N", 85);\r
+ conses[18] = new Consensus("P", 85);\r
+ conses[19] = new Consensus("Q", 85);\r
+ conses[20] = new Consensus("R", 85);\r
+ conses[21] = new Consensus("S", 85);\r
+ conses[22] = new Consensus("T", 85);\r
+ conses[23] = new Consensus("V", 85);\r
+ conses[24] = new Consensus("W", 85);\r
+ conses[25] = new Consensus("Y", 85);\r
+ conses[28] = new Consensus("K", 85);\r
+ conses[29] = new Consensus("D", 85);\r
+\r
+ conses[30] = new Consensus("G", 0);\r
+ conses[31] = new Consensus("P", 0);\r
+\r
+ // We now construct the colours\r
+ colours = new ConsensusColour[11];\r
+\r
+ Consensus[] tmp8 = new Consensus[1];\r
+ tmp8[0] = conses[30]; //G\r
+ colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);\r
+\r
+ Consensus[] tmp9 = new Consensus[1];\r
+ tmp9[0] = conses[31]; //P\r
+ colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);\r
+\r
+ Consensus[] tmp10 = new Consensus[1];\r
+ tmp10[0] = conses[27]; //C\r
+ colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);\r
+\r
+ Consensus[] tmp1 = new Consensus[14];\r
+ tmp1[0] = conses[0]; //%\r
+ tmp1[1] = conses[1]; //#\r
+ tmp1[2] = conses[26]; //A\r
+ tmp1[3] = conses[27]; //C\r
+ tmp1[4] = conses[11]; //F\r
+ tmp1[5] = conses[13]; //H\r
+ tmp1[6] = conses[14]; //I\r
+ tmp1[7] = conses[15]; //L\r
+ tmp1[8] = conses[16]; //M\r
+ tmp1[9] = conses[23]; //V\r
+ tmp1[10] = conses[24]; //W\r
+ tmp1[11] = conses[25]; //Y\r
+ tmp1[12] = conses[18]; //P\r
+ tmp1[13] = conses[19]; //p\r
+ colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);\r
+\r
+ colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);\r
+\r
+ Consensus[] tmp2 = new Consensus[5];\r
+ tmp2[0] = conses[8]; //t\r
+ tmp2[1] = conses[21]; //S\r
+ tmp2[2] = conses[22]; //T\r
+ tmp2[3] = conses[0]; //%\r
+ tmp2[4] = conses[1]; //#\r
+ colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);\r
+\r
+ Consensus[] tmp3 = new Consensus[3];\r
+\r
+ tmp3[0] = conses[17]; //N\r
+ tmp3[1] = conses[29]; //D\r
+ tmp3[2] = conses[5]; //n\r
+ colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);\r
+\r
+ Consensus[] tmp4 = new Consensus[6];\r
+ tmp4[0] = conses[6]; // q = QE\r
+ tmp4[1] = conses[19]; //Q\r
+ tmp4[2] = conses[22]; //E\r
+ tmp4[3] = conses[3]; //+\r
+ tmp4[4] = conses[28]; //K\r
+ tmp4[5] = conses[20]; //R\r
+ colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);\r
+\r
+ Consensus[] tmp5 = new Consensus[4];\r
+ tmp5[0] = conses[3]; //+\r
+ tmp5[1] = conses[28]; //K\r
+ tmp5[2] = conses[20]; //R\r
+ tmp5[3] = conses[19]; //Q\r
+ colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);\r
+\r
+ Consensus[] tmp6 = new Consensus[5];\r
+ tmp6[0] = conses[3]; //-\r
+ tmp6[1] = conses[29]; //D\r
+ tmp6[2] = conses[10]; //E\r
+ tmp6[3] = conses[6]; //q\r
+ tmp6[4] = conses[19]; //Q\r
+ colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);\r
+\r
+ Consensus[] tmp7 = new Consensus[5];\r
+ tmp7[0] = conses[3]; //-\r
+ tmp7[1] = conses[29]; //D\r
+ tmp7[2] = conses[10]; //E\r
+ tmp7[3] = conses[17]; //N\r
+ tmp7[4] = conses[2]; //DE\r
+ colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);\r
+\r
+ // Now attach the ConsensusColours to the residue letters\r
+ ResidueColour = new ConsensusColour[20];\r
+ ResidueColour[0] = colours[0]; // A\r
+ ResidueColour[1] = colours[4]; // R\r
+ ResidueColour[2] = colours[2]; // N\r
+ ResidueColour[3] = colours[6]; // D\r
+ ResidueColour[4] = colours[0]; // C\r
+ ResidueColour[5] = colours[3]; // Q\r
+ ResidueColour[6] = colours[5]; // E\r
+ ResidueColour[7] = colours[7]; // G\r
+ ResidueColour[8] = colours[10]; // H\r
+ ResidueColour[9] = colours[0]; // I\r
+ ResidueColour[10] = colours[0]; // L\r
+ ResidueColour[11] = colours[4]; // K\r
+ ResidueColour[12] = colours[0]; // M\r
+ ResidueColour[13] = colours[0]; // F\r
+ ResidueColour[14] = colours[8]; // P\r
+ ResidueColour[15] = colours[1]; // S\r
+ ResidueColour[16] = colours[1]; // T\r
+ ResidueColour[17] = colours[0]; // W\r
+ ResidueColour[18] = colours[10]; // Y\r
+ ResidueColour[19] = colours[0]; // V\r
+ }\r
+\r
+ public Color findColour(String s)\r
+ {\r
+ return Color.pink;\r
+ }\r
+\r
+ public Color findColour(String s, int j)\r
+ {\r
+ if ( (threshold != 0) && !aboveThreshold(s, j))\r
+ {\r
+ return Color.white;\r