1 /* Jalview - a java multiple alignment editor
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2 * Copyright (C) 1998 Michele Clamp
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4 * This program is free software; you can redistribute it and/or
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5 * modify it under the terms of the GNU General Public License
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6 * as published by the Free Software Foundation; either version 2
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7 * of the License, or (at your option) any later version.
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9 * This program is distributed in the hope that it will be useful,
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10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 * GNU General Public License for more details.
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14 * You should have received a copy of the GNU General Public License
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15 * along with this program; if not, write to the Free Software
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16 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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19 package jalview.schemes;
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21 import jalview.datamodel.*;
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25 public class ClustalxColourScheme implements ColourSchemeI
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29 ConsensusColour[] colours;
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30 ConsensusColour[] ResidueColour;
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32 Consensus[] conses = new Consensus[32];
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33 public static Hashtable colhash = new Hashtable();
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36 colhash.put("RED",new Color((float)0.9,(float)0.2,(float)0.1));
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37 colhash.put("BLUE",new Color((float)0.5,(float)0.7,(float)0.9));
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38 colhash.put("GREEN",new Color((float)0.1,(float)0.8,(float)0.1));
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39 colhash.put("ORANGE",new Color((float)0.9,(float)0.6,(float)0.3));
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40 colhash.put("CYAN",new Color((float)0.1,(float)0.7,(float)0.7));
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41 colhash.put("PINK",new Color((float)0.9,(float)0.5,(float)0.5));
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42 colhash.put("MAGENTA",new Color((float)0.8,(float)0.3,(float)0.8));
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43 colhash.put("YELLOW",new Color((float)0.8,(float)0.8,(float)0.0));
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46 Vector colourTable = new Vector();
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49 public ClustalxColourScheme(Vector seqs, int maxWidth)
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51 cons2 = new int[maxWidth][24];
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52 int start = 0, end = maxWidth-1;
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54 // Initialize the array
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55 for (int j=0;j<24;j++)
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56 for (int i=0; i < maxWidth;i++)
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61 while(j < seqs.size())
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63 seq = ( (SequenceI) seqs.get(j)).getSequence();
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64 for (i = start; i <= end; i++)
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66 if(seq.length()-1<i)
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69 res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();
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75 this.size = seqs.size();
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78 public void makeColours() {
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79 conses[0] = new Consensus("WLVIMAFCYHP",60);
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80 conses[1] = new Consensus("WLVIMAFCYHP",80);
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81 conses[2] = new Consensus("ED",50);
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82 conses[3] = new Consensus("KR",60);
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83 conses[4] = new Consensus("G",50);
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84 conses[5] = new Consensus("N",50);
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85 conses[6] = new Consensus("QE",50);
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86 conses[7] = new Consensus("P",50);
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87 conses[8] = new Consensus("TS",50);
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89 conses[26] = new Consensus("A",85);
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90 conses[27] = new Consensus("C",85);
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91 conses[10] = new Consensus("E",85);
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92 conses[11] = new Consensus("F",85);
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93 conses[12] = new Consensus("G",85);
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94 conses[13] = new Consensus("H",85);
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95 conses[14] = new Consensus("I",85);
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96 conses[15] = new Consensus("L",85);
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97 conses[16] = new Consensus("M",85);
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98 conses[17] = new Consensus("N",85);
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99 conses[18] = new Consensus("P",85);
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100 conses[19] = new Consensus("Q",85);
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101 conses[20] = new Consensus("R",85);
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102 conses[21] = new Consensus("S",85);
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103 conses[22] = new Consensus("T",85);
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104 conses[23] = new Consensus("V",85);
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105 conses[24] = new Consensus("W",85);
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106 conses[25] = new Consensus("Y",85);
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107 conses[28] = new Consensus("K",85);
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108 conses[29] = new Consensus("D",85);
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110 conses[30] = new Consensus("G",0);
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111 conses[31] = new Consensus("P",0);
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113 // We now construct the colours
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114 colours = new ConsensusColour[11];
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117 Consensus[] tmp8 = new Consensus[1];
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118 tmp8[0] = conses[30];//G
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119 colours[7] =new ConsensusColour((Color)colhash.get("ORANGE"),tmp8);
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121 Consensus[] tmp9 = new Consensus[1];
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122 tmp9[0] = conses[31];//P
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123 colours[8] =new ConsensusColour((Color)colhash.get("YELLOW"),tmp9);
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125 Consensus[] tmp10 = new Consensus[1];
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126 tmp10[0] = conses[27];//C
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127 colours[9] =new ConsensusColour((Color)colhash.get("PINK"),tmp8);
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129 Consensus[] tmp1 = new Consensus[14];
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130 tmp1[0] = conses[0]; //%
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131 tmp1[1] = conses[1]; //#
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132 tmp1[2] = conses[26]; //A
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133 tmp1[3] = conses[27]; //C
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134 tmp1[4] = conses[11]; //F
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135 tmp1[5] = conses[13]; //H
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136 tmp1[6] = conses[14]; //I
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137 tmp1[7] = conses[15]; //L
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138 tmp1[8] = conses[16]; //M
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139 tmp1[9] = conses[23]; //V
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140 tmp1[10] = conses[24]; //W
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141 tmp1[11] = conses[25]; //Y
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142 tmp1[12] = conses[18]; //P
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143 tmp1[13] = conses[19]; //p
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144 colours[0] = new ConsensusColour((Color)colhash.get("BLUE"),tmp1);
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146 colours[10] = new ConsensusColour((Color)colhash.get("CYAN"),tmp1);
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148 Consensus[] tmp2 = new Consensus[5];
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149 tmp2[0] = conses[8]; //t
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150 tmp2[1] = conses[21]; //S
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151 tmp2[2] = conses[22]; //T
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152 tmp2[3] = conses[0]; //%
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153 tmp2[4] = conses[1]; //#
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154 colours[1] = new ConsensusColour((Color)colhash.get("GREEN"),tmp2);
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156 Consensus[] tmp3 = new Consensus[3];
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158 tmp3[0] = conses[17]; //N
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159 tmp3[1] = conses[29]; //D
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160 tmp3[2] = conses[5]; //n
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161 colours[2] = new ConsensusColour((Color)colhash.get("GREEN"),tmp3);
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163 Consensus[] tmp4 = new Consensus[6];
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164 tmp4[0] = conses[6]; // q = QE
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165 tmp4[1] = conses[19]; //Q
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166 tmp4[2] = conses[22]; //E
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167 tmp4[3] = conses[3]; //+
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168 tmp4[4] = conses[28]; //K
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169 tmp4[5] = conses[20]; //R
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170 colours[3] = new ConsensusColour((Color)colhash.get("GREEN"),tmp4);
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171 Consensus[] tmp5 = new Consensus[4];
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172 tmp5[0] = conses[3]; //+
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173 tmp5[1] = conses[28]; //K
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174 tmp5[2] = conses[20]; //R
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175 tmp5[3] = conses[19]; //Q
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176 colours[4] = new ConsensusColour((Color)colhash.get("RED"),tmp5);
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177 Consensus[] tmp6 = new Consensus[5];
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178 tmp6[0] = conses[3]; //-
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179 tmp6[1] = conses[29]; //D
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180 tmp6[2] = conses[10]; //E
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181 tmp6[3] = conses[6]; //q
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182 tmp6[4] = conses[19]; //Q
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183 colours[5] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp6);
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185 Consensus[] tmp7 = new Consensus[5];
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186 tmp7[0] = conses[3]; //-
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187 tmp7[1] = conses[29]; //D
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188 tmp7[2] = conses[10]; //E
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189 tmp7[3] = conses[17]; //N
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190 tmp7[4] = conses[2]; //DE
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191 colours[6] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp7);
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193 // Now attach the ConsensusColours to the residue letters
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194 ResidueColour = new ConsensusColour[20];
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195 ResidueColour[0] = colours[0]; // A
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196 ResidueColour[1] = colours[4]; // R
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197 ResidueColour[2] = colours[2]; // N
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198 ResidueColour[3] = colours[6]; // D
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199 ResidueColour[4] = colours[0]; // C
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200 ResidueColour[5] = colours[3]; // Q
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201 ResidueColour[6] = colours[5]; // E
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202 ResidueColour[7] = colours[7]; // G
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203 ResidueColour[8] = colours[10]; // H
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204 ResidueColour[9] = colours[0]; // I
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205 ResidueColour[10] = colours[0]; // L
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206 ResidueColour[11] = colours[4]; // K
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207 ResidueColour[12] = colours[0]; // M
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208 ResidueColour[13] = colours[0]; // F
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209 ResidueColour[14] = colours[8]; // P
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210 ResidueColour[15] = colours[1]; // S
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211 ResidueColour[16] = colours[1]; // T
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212 ResidueColour[17] = colours[0]; // W
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213 ResidueColour[18] = colours[10]; // Y
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214 ResidueColour[19] = colours[0]; // V
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217 public Color findColour(String s)
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222 public void setGroupSizeChanged(int i)
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227 public Color findColour(String s, int j, Vector seqs)
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229 int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
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231 Color c = Color.white;
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236 for (int k=0; k < ResidueColour[i].conses.length ; k++)
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237 if (ResidueColour[i].conses[k].isConserved(cons2,j,size))
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238 c = ResidueColour[i].c;
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242 if (conses[27].isConserved(cons2, j, size))
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243 c = (Color) colhash.get("PINK");
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252 public boolean canThreshold()
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257 public boolean isUserDefinable()
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265 class ConsensusColour {
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267 Consensus[] conses;
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270 public ConsensusColour(Color c,Consensus[] conses) {
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271 this.conses = conses;
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272 // this.list = list;
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