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 \r
  20 package jalview.schemes;\r
  21 \r
  22 import jalview.datamodel.*;\r
  23 import java.util.*;\r
  24 import java.awt.*;\r
  25 \r
  26 public class ClustalxColourScheme extends ResidueColourScheme\r
  27 {\r
  28   Hashtable[] cons;\r
  29   int[][] cons2;\r
  30   ConsensusColour[] colours;\r
  31   ConsensusColour[] ResidueColour;\r
  32   int size;\r
  33     Consensus[] conses = new Consensus[32];\r
  34     public static Hashtable colhash = new Hashtable();\r
  35 \r
  36     {\r
  37         colhash.put("RED",new Color((float)0.9,(float)0.2,(float)0.1));\r
  38         colhash.put("BLUE",new Color((float)0.5,(float)0.7,(float)0.9));\r
  39         colhash.put("GREEN",new Color((float)0.1,(float)0.8,(float)0.1));\r
  40         colhash.put("ORANGE",new Color((float)0.9,(float)0.6,(float)0.3));\r
  41         colhash.put("CYAN",new Color((float)0.1,(float)0.7,(float)0.7));\r
  42         colhash.put("PINK",new Color((float)0.9,(float)0.5,(float)0.5));\r
  43         colhash.put("MAGENTA",new Color((float)0.8,(float)0.3,(float)0.8));\r
  44         colhash.put("YELLOW",new Color((float)0.8,(float)0.8,(float)0.0));\r
  45 \r
  46     }\r
  47   Vector colourTable = new Vector();\r
  48 \r
  49   public ClustalxColourScheme(Vector seqs, int maxWidth)\r
  50   {\r
  51     resetClustalX(seqs, maxWidth);\r
  52   }\r
  53 \r
  54   public void resetClustalX(Vector seqs, int maxWidth)\r
  55   {\r
  56     cons2 = new int[maxWidth][24];\r
  57     int start = 0;\r
  58 \r
  59     // Initialize the array\r
  60     for (int j=0;j<24;j++)\r
  61       for (int i=0; i < maxWidth;i++)\r
  62         cons2[i][j] = 0;\r
  63 \r
  64       int res,i, j = 0;\r
  65       String seq;\r
  66       while(j < seqs.size())\r
  67       {\r
  68         seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
  69         int end_j = seq.length()-1;\r
  70         for (i = start; i <= end_j; i++)\r
  71         {\r
  72           if(seq.length()-1<i)\r
  73             res = 23;\r
  74           else\r
  75             res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();\r
  76           cons2[i][res]++;\r
  77         }\r
  78         j++;\r
  79       }\r
  80 \r
  81     this.size = seqs.size();\r
  82     makeColours();\r
  83   }\r
  84   public void makeColours() {\r
  85     conses[0] = new Consensus("WLVIMAFCYHP",60);\r
  86     conses[1] = new Consensus("WLVIMAFCYHP",80);\r
  87     conses[2] = new Consensus("ED",50);\r
  88     conses[3] = new Consensus("KR",60);\r
  89     conses[4] = new Consensus("G",50);\r
  90     conses[5] = new Consensus("N",50);\r
  91     conses[6] = new Consensus("QE",50);\r
  92     conses[7] = new Consensus("P",50);\r
  93     conses[8] = new Consensus("TS",50);\r
  94 \r
  95     conses[26] = new Consensus("A",85);\r
  96     conses[27] = new Consensus("C",85);\r
  97     conses[10] = new Consensus("E",85);\r
  98     conses[11] = new Consensus("F",85);\r
  99     conses[12] = new Consensus("G",85);\r
 100     conses[13] = new Consensus("H",85);\r
 101     conses[14] = new Consensus("I",85);\r
 102     conses[15] = new Consensus("L",85);\r
 103     conses[16] = new Consensus("M",85);\r
 104     conses[17] = new Consensus("N",85);\r
 105     conses[18] = new Consensus("P",85);\r
 106     conses[19] = new Consensus("Q",85);\r
 107     conses[20] = new Consensus("R",85);\r
 108     conses[21] = new Consensus("S",85);\r
 109     conses[22] = new Consensus("T",85);\r
 110     conses[23] = new Consensus("V",85);\r
 111     conses[24] = new Consensus("W",85);\r
 112     conses[25] = new Consensus("Y",85);\r
 113     conses[28] = new Consensus("K",85);\r
 114     conses[29] = new Consensus("D",85);\r
 115 \r
 116     conses[30] = new Consensus("G",0);\r
 117     conses[31] = new Consensus("P",0);\r
 118 \r
 119     // We now construct the colours\r
 120     colours = new ConsensusColour[11];\r
 121 \r
 122 \r
 123     Consensus[] tmp8 = new Consensus[1];\r
 124     tmp8[0] = conses[30];//G\r
 125     colours[7] =new ConsensusColour((Color)colhash.get("ORANGE"),tmp8);\r
 126 \r
 127     Consensus[] tmp9 = new Consensus[1];\r
 128     tmp9[0] = conses[31];//P\r
 129     colours[8] =new ConsensusColour((Color)colhash.get("YELLOW"),tmp9);\r
 130 \r
 131     Consensus[] tmp10 = new Consensus[1];\r
 132     tmp10[0] = conses[27];//C\r
 133     colours[9] =new ConsensusColour((Color)colhash.get("PINK"),tmp8);\r
 134 \r
 135     Consensus[] tmp1 = new Consensus[14];\r
 136     tmp1[0] = conses[0]; //%\r
 137     tmp1[1] = conses[1]; //#\r
 138     tmp1[2] = conses[26]; //A\r
 139     tmp1[3] = conses[27]; //C\r
 140     tmp1[4] = conses[11]; //F\r
 141     tmp1[5] = conses[13]; //H\r
 142     tmp1[6] = conses[14]; //I\r
 143     tmp1[7] = conses[15]; //L\r
 144     tmp1[8] = conses[16]; //M\r
 145     tmp1[9] = conses[23]; //V\r
 146     tmp1[10] = conses[24]; //W\r
 147     tmp1[11] = conses[25]; //Y\r
 148     tmp1[12] = conses[18]; //P\r
 149     tmp1[13] = conses[19]; //p\r
 150     colours[0] = new ConsensusColour((Color)colhash.get("BLUE"),tmp1);\r
 151 \r
 152     colours[10] = new ConsensusColour((Color)colhash.get("CYAN"),tmp1);\r
 153 \r
 154     Consensus[] tmp2 = new Consensus[5];\r
 155     tmp2[0] = conses[8];  //t\r
 156     tmp2[1] = conses[21]; //S\r
 157     tmp2[2] = conses[22]; //T\r
 158     tmp2[3] = conses[0];  //%\r
 159     tmp2[4] = conses[1];  //#\r
 160     colours[1] = new ConsensusColour((Color)colhash.get("GREEN"),tmp2);\r
 161 \r
 162     Consensus[] tmp3 = new Consensus[3];\r
 163 \r
 164     tmp3[0] = conses[17]; //N\r
 165     tmp3[1] = conses[29]; //D\r
 166     tmp3[2] = conses[5];  //n\r
 167     colours[2] = new ConsensusColour((Color)colhash.get("GREEN"),tmp3);\r
 168 \r
 169     Consensus[] tmp4 = new Consensus[6];\r
 170     tmp4[0] = conses[6];  // q = QE\r
 171     tmp4[1] = conses[19]; //Q\r
 172     tmp4[2] = conses[22]; //E\r
 173     tmp4[3] = conses[3];  //+\r
 174     tmp4[4] = conses[28]; //K\r
 175     tmp4[5] = conses[20]; //R\r
 176     colours[3] = new ConsensusColour((Color)colhash.get("GREEN"),tmp4);\r
 177     Consensus[] tmp5 = new Consensus[4];\r
 178     tmp5[0] = conses[3];  //+\r
 179     tmp5[1] = conses[28]; //K\r
 180     tmp5[2] = conses[20]; //R\r
 181     tmp5[3] = conses[19]; //Q\r
 182     colours[4] = new ConsensusColour((Color)colhash.get("RED"),tmp5);\r
 183     Consensus[] tmp6 = new Consensus[5];\r
 184     tmp6[0] = conses[3];  //-\r
 185     tmp6[1] = conses[29]; //D\r
 186     tmp6[2] = conses[10]; //E\r
 187     tmp6[3] = conses[6];  //q\r
 188     tmp6[4] = conses[19]; //Q\r
 189     colours[5] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp6);\r
 190 \r
 191     Consensus[] tmp7 = new Consensus[5];\r
 192     tmp7[0] = conses[3];  //-\r
 193     tmp7[1] = conses[29]; //D\r
 194     tmp7[2] = conses[10]; //E\r
 195     tmp7[3] = conses[17];  //N\r
 196     tmp7[4] = conses[2]; //DE\r
 197     colours[6] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp7);\r
 198 \r
 199     // Now attach the ConsensusColours to the residue letters\r
 200     ResidueColour = new ConsensusColour[20];\r
 201     ResidueColour[0] = colours[0]; // A\r
 202     ResidueColour[1] = colours[4]; // R\r
 203     ResidueColour[2] = colours[2]; // N\r
 204     ResidueColour[3] = colours[6]; // D\r
 205     ResidueColour[4] = colours[0]; // C\r
 206     ResidueColour[5] = colours[3]; // Q\r
 207     ResidueColour[6] = colours[5]; // E\r
 208     ResidueColour[7] = colours[7]; // G\r
 209     ResidueColour[8] = colours[10]; // H\r
 210     ResidueColour[9] = colours[0]; // I\r
 211     ResidueColour[10] = colours[0]; // L\r
 212     ResidueColour[11] = colours[4]; // K\r
 213     ResidueColour[12] = colours[0]; // M\r
 214     ResidueColour[13] = colours[0]; // F\r
 215     ResidueColour[14] = colours[8]; // P\r
 216     ResidueColour[15] = colours[1]; // S\r
 217     ResidueColour[16] = colours[1]; // T\r
 218     ResidueColour[17] = colours[0]; // W\r
 219     ResidueColour[18] = colours[10]; // Y\r
 220     ResidueColour[19] = colours[0]; // V\r
 221   }\r
 222 \r
 223   public Color findColour(String s)\r
 224   {\r
 225     return Color.pink;\r
 226   }\r
 227 \r
 228   public Color findColour(String s, int j)\r
 229    {\r
 230      if( threshold!=0 && !aboveThreshold(s,j))\r
 231       return Color.white;\r
 232 \r
 233 \r
 234      int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
 235 \r
 236      Color c = Color.white;\r
 237 \r
 238      if(i>19)\r
 239        return c;\r
 240 \r
 241      for (int k=0; k < ResidueColour[i].conses.length ; k++)\r
 242        if (ResidueColour[i].conses[k].isConserved(cons2,j,size))\r
 243          c =  ResidueColour[i].c;\r
 244 \r
 245      if (i == 4)\r
 246     {\r
 247       if (conses[27].isConserved(cons2, j, size))\r
 248         c = (Color) colhash.get("PINK");\r
 249     }\r
 250 \r
 251 \r
 252      return c;\r
 253 \r
 254    }\r
 255 }\r
 256 \r
 257 class ConsensusColour {\r
 258 \r
 259   Consensus[] conses;\r
 260   Color c;\r
 261 \r
 262   public ConsensusColour(Color c,Consensus[] conses) {\r
 263     this.conses = conses;\r
 264     //    this.list = list;\r
 265     this.c = c;\r
 266   }\r
 267 }\r
 268 \r
 269 \r
 270 \r
 271 \r
 272 \r
 273 \r
 274 \r
 275 \r
 276 \r
 277 \r
 278 \r
 279 \r
 280 \r
 281 \r
 282 \r