src/jalview/schemes/ClustalxColourScheme.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 package jalview.schemes;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import java.awt.*;\r
  24 \r
  25 import java.util.*;\r
  26 \r
  27 \r
  28 public class ClustalxColourScheme extends ResidueColourScheme {\r
  29     public static Hashtable colhash = new Hashtable();\r
  30     Hashtable[] cons;\r
  31     int[][] cons2;\r
  32     ConsensusColour[] colours;\r
  33     ConsensusColour[] ResidueColour;\r
  34     int size;\r
  35     Consensus[] conses = new Consensus[32];\r
  36     Vector colourTable = new Vector();\r
  37 \r
  38     {\r
  39         colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));\r
  40         colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));\r
  41         colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));\r
  42         colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));\r
  43         colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));\r
  44         colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));\r
  45         colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));\r
  46         colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));\r
  47     }\r
  48 \r
  49     public ClustalxColourScheme(Vector seqs, int maxWidth) {\r
  50         resetClustalX(seqs, maxWidth);\r
  51     }\r
  52 \r
  53     public void resetClustalX(Vector seqs, int maxWidth) {\r
  54         cons2 = new int[maxWidth][24];\r
  55 \r
  56         int start = 0;\r
  57 \r
  58         // Initialize the array\r
  59         for (int j = 0; j < 24; j++)\r
  60             for (int i = 0; i < maxWidth; i++)\r
  61                 cons2[i][j] = 0;\r
  62 \r
  63         int res;\r
  64         int i;\r
  65         int j = 0;\r
  66         String seq;\r
  67 \r
  68         while (j < seqs.size()) {\r
  69             seq = ((SequenceI) seqs.elementAt(j)).getSequence();\r
  70 \r
  71             int end_j = seq.length() - 1;\r
  72 \r
  73             for (i = start; i <= end_j; i++) {\r
  74                 if ((seq.length() - 1) < i) {\r
  75                     res = 23;\r
  76                 } else {\r
  77                     res = ((Integer) ResidueProperties.aaHash.get(seq.charAt(i) +\r
  78                             "")).intValue();\r
  79                 }\r
  80 \r
  81                 cons2[i][res]++;\r
  82             }\r
  83 \r
  84             j++;\r
  85         }\r
  86 \r
  87         this.size = seqs.size();\r
  88         makeColours();\r
  89     }\r
  90 \r
  91     public void makeColours() {\r
  92         conses[0] = new Consensus("WLVIMAFCYHP", 60);\r
  93         conses[1] = new Consensus("WLVIMAFCYHP", 80);\r
  94         conses[2] = new Consensus("ED", 50);\r
  95         conses[3] = new Consensus("KR", 60);\r
  96         conses[4] = new Consensus("G", 50);\r
  97         conses[5] = new Consensus("N", 50);\r
  98         conses[6] = new Consensus("QE", 50);\r
  99         conses[7] = new Consensus("P", 50);\r
 100         conses[8] = new Consensus("TS", 50);\r
 101 \r
 102         conses[26] = new Consensus("A", 85);\r
 103         conses[27] = new Consensus("C", 85);\r
 104         conses[10] = new Consensus("E", 85);\r
 105         conses[11] = new Consensus("F", 85);\r
 106         conses[12] = new Consensus("G", 85);\r
 107         conses[13] = new Consensus("H", 85);\r
 108         conses[14] = new Consensus("I", 85);\r
 109         conses[15] = new Consensus("L", 85);\r
 110         conses[16] = new Consensus("M", 85);\r
 111         conses[17] = new Consensus("N", 85);\r
 112         conses[18] = new Consensus("P", 85);\r
 113         conses[19] = new Consensus("Q", 85);\r
 114         conses[20] = new Consensus("R", 85);\r
 115         conses[21] = new Consensus("S", 85);\r
 116         conses[22] = new Consensus("T", 85);\r
 117         conses[23] = new Consensus("V", 85);\r
 118         conses[24] = new Consensus("W", 85);\r
 119         conses[25] = new Consensus("Y", 85);\r
 120         conses[28] = new Consensus("K", 85);\r
 121         conses[29] = new Consensus("D", 85);\r
 122 \r
 123         conses[30] = new Consensus("G", 0);\r
 124         conses[31] = new Consensus("P", 0);\r
 125 \r
 126         // We now construct the colours\r
 127         colours = new ConsensusColour[11];\r
 128 \r
 129         Consensus[] tmp8 = new Consensus[1];\r
 130         tmp8[0] = conses[30]; //G\r
 131         colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);\r
 132 \r
 133         Consensus[] tmp9 = new Consensus[1];\r
 134         tmp9[0] = conses[31]; //P\r
 135         colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);\r
 136 \r
 137         Consensus[] tmp10 = new Consensus[1];\r
 138         tmp10[0] = conses[27]; //C\r
 139         colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);\r
 140 \r
 141         Consensus[] tmp1 = new Consensus[14];\r
 142         tmp1[0] = conses[0]; //%\r
 143         tmp1[1] = conses[1]; //#\r
 144         tmp1[2] = conses[26]; //A\r
 145         tmp1[3] = conses[27]; //C\r
 146         tmp1[4] = conses[11]; //F\r
 147         tmp1[5] = conses[13]; //H\r
 148         tmp1[6] = conses[14]; //I\r
 149         tmp1[7] = conses[15]; //L\r
 150         tmp1[8] = conses[16]; //M\r
 151         tmp1[9] = conses[23]; //V\r
 152         tmp1[10] = conses[24]; //W\r
 153         tmp1[11] = conses[25]; //Y\r
 154         tmp1[12] = conses[18]; //P\r
 155         tmp1[13] = conses[19]; //p\r
 156         colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);\r
 157 \r
 158         colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);\r
 159 \r
 160         Consensus[] tmp2 = new Consensus[5];\r
 161         tmp2[0] = conses[8]; //t\r
 162         tmp2[1] = conses[21]; //S\r
 163         tmp2[2] = conses[22]; //T\r
 164         tmp2[3] = conses[0]; //%\r
 165         tmp2[4] = conses[1]; //#\r
 166         colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);\r
 167 \r
 168         Consensus[] tmp3 = new Consensus[3];\r
 169 \r
 170         tmp3[0] = conses[17]; //N\r
 171         tmp3[1] = conses[29]; //D\r
 172         tmp3[2] = conses[5]; //n\r
 173         colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);\r
 174 \r
 175         Consensus[] tmp4 = new Consensus[6];\r
 176         tmp4[0] = conses[6]; // q = QE\r
 177         tmp4[1] = conses[19]; //Q\r
 178         tmp4[2] = conses[22]; //E\r
 179         tmp4[3] = conses[3]; //+\r
 180         tmp4[4] = conses[28]; //K\r
 181         tmp4[5] = conses[20]; //R\r
 182         colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);\r
 183 \r
 184         Consensus[] tmp5 = new Consensus[4];\r
 185         tmp5[0] = conses[3]; //+\r
 186         tmp5[1] = conses[28]; //K\r
 187         tmp5[2] = conses[20]; //R\r
 188         tmp5[3] = conses[19]; //Q\r
 189         colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);\r
 190 \r
 191         Consensus[] tmp6 = new Consensus[5];\r
 192         tmp6[0] = conses[3]; //-\r
 193         tmp6[1] = conses[29]; //D\r
 194         tmp6[2] = conses[10]; //E\r
 195         tmp6[3] = conses[6]; //q\r
 196         tmp6[4] = conses[19]; //Q\r
 197         colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);\r
 198 \r
 199         Consensus[] tmp7 = new Consensus[5];\r
 200         tmp7[0] = conses[3]; //-\r
 201         tmp7[1] = conses[29]; //D\r
 202         tmp7[2] = conses[10]; //E\r
 203         tmp7[3] = conses[17]; //N\r
 204         tmp7[4] = conses[2]; //DE\r
 205         colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);\r
 206 \r
 207         // Now attach the ConsensusColours to the residue letters\r
 208         ResidueColour = new ConsensusColour[20];\r
 209         ResidueColour[0] = colours[0]; // A\r
 210         ResidueColour[1] = colours[4]; // R\r
 211         ResidueColour[2] = colours[2]; // N\r
 212         ResidueColour[3] = colours[6]; // D\r
 213         ResidueColour[4] = colours[0]; // C\r
 214         ResidueColour[5] = colours[3]; // Q\r
 215         ResidueColour[6] = colours[5]; // E\r
 216         ResidueColour[7] = colours[7]; // G\r
 217         ResidueColour[8] = colours[10]; // H\r
 218         ResidueColour[9] = colours[0]; // I\r
 219         ResidueColour[10] = colours[0]; // L\r
 220         ResidueColour[11] = colours[4]; // K\r
 221         ResidueColour[12] = colours[0]; // M\r
 222         ResidueColour[13] = colours[0]; // F\r
 223         ResidueColour[14] = colours[8]; // P\r
 224         ResidueColour[15] = colours[1]; // S\r
 225         ResidueColour[16] = colours[1]; // T\r
 226         ResidueColour[17] = colours[0]; // W\r
 227         ResidueColour[18] = colours[10]; // Y\r
 228         ResidueColour[19] = colours[0]; // V\r
 229     }\r
 230 \r
 231     public Color findColour(String s) {\r
 232         return Color.pink;\r
 233     }\r
 234 \r
 235     public Color findColour(String s, int j) {\r
 236         if ((threshold != 0) && !aboveThreshold(s, j)) {\r
 237             return Color.white;\r
 238         }\r
 239 \r
 240         int i = ((Integer) ResidueProperties.aaHash.get(s)).intValue();\r
 241 \r
 242         Color c = Color.white;\r
 243 \r
 244         if (i > 19) {\r
 245             return c;\r
 246         }\r
 247 \r
 248         for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
 249             if (ResidueColour[i].conses[k].isConserved(cons2, j, size)) {\r
 250                 c = ResidueColour[i].c;\r
 251             }\r
 252 \r
 253         if (i == 4) {\r
 254             if (conses[27].isConserved(cons2, j, size)) {\r
 255                 c = (Color) colhash.get("PINK");\r
 256             }\r
 257         }\r
 258 \r
 259         return c;\r
 260     }\r
 261 }\r
 262 \r
 263 \r
 264 class ConsensusColour {\r
 265     Consensus[] conses;\r
 266     Color c;\r
 267 \r
 268     public ConsensusColour(Color c, Consensus[] conses) {\r
 269         this.conses = conses;\r
 270 \r
 271         //    this.list = list;\r
 272         this.c = c;\r
 273     }\r
 274 }\r