src/jalview/schemes/ClustalxColourScheme.java

   1 /* Jalview - a java multiple alignment editor\r
   2  * Copyright (C) 1998  Michele Clamp\r
   3  *\r
   4  * This program is free software; you can redistribute it and/or\r
   5  * modify it under the terms of the GNU General Public License\r
   6  * as published by the Free Software Foundation; either version 2\r
   7  * of the License, or (at your option) any later version.\r
   8  *\r
   9  * This program is distributed in the hope that it will be useful,\r
  10  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  11  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  12  * GNU General Public License for more details.\r
  13  *\r
  14  * You should have received a copy of the GNU General Public License\r
  15  * along with this program; if not, write to the Free Software\r
  16  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.\r
  17  */\r
  18 /*\r
  19 package jalview.schemes;\r
  20 import java.util.*;\r
  21 import java.awt.*;\r
  22 \r
  23 public class ClustalxColourScheme implements ColourSchemeI\r
  24 {\r
  25   Hashtable[] cons;\r
  26   int[][] cons2;\r
  27   ConsensusColour[] colours;\r
  28   ConsensusColour[] ResidueColour;\r
  29   int size;\r
  30     Consensus[] conses = new Consensus[32];\r
  31     public static Hashtable colhash = new Hashtable();\r
  32 \r
  33     {\r
  34         colhash.put("RED",new Color((float)0.9,(float)0.2,(float)0.1));\r
  35         colhash.put("BLUE",new Color((float)0.5,(float)0.7,(float)0.9));\r
  36         colhash.put("GREEN",new Color((float)0.1,(float)0.8,(float)0.1));\r
  37         colhash.put("ORANGE",new Color((float)0.9,(float)0.6,(float)0.3));\r
  38         colhash.put("CYAN",new Color((float)0.1,(float)0.7,(float)0.7));\r
  39         colhash.put("PINK",new Color((float)0.9,(float)0.5,(float)0.5));\r
  40         colhash.put("MAGENTA",new Color((float)0.8,(float)0.3,(float)0.8));\r
  41         colhash.put("YELLOW",new Color((float)0.8,(float)0.8,(float)0.0));\r
  42 \r
  43     }\r
  44   Vector colourTable = new Vector();\r
  45   public ClustalxColourScheme() {\r
  46     this.cons2 = null;\r
  47     this.size = 0;\r
  48     makeColours();\r
  49   }\r
  50   public ClustalxColourScheme(int[][] cons2, int size) {\r
  51     this.cons2 = cons2;\r
  52     this.size = size;\r
  53     makeColours();\r
  54   }\r
  55   public void makeColours() {\r
  56     conses[0] = new Consensus("WLVIMAFCYHP",60);\r
  57     conses[1] = new Consensus("WLVIMAFCYHP",80);\r
  58     conses[2] = new Consensus("ED",50);\r
  59     conses[3] = new Consensus("KR",60);\r
  60     conses[4] = new Consensus("G",50);\r
  61     conses[5] = new Consensus("N",50);\r
  62     conses[6] = new Consensus("QE",50);\r
  63     conses[7] = new Consensus("P",50);\r
  64     conses[8] = new Consensus("TS",50);\r
  65 \r
  66     conses[26] = new Consensus("A",85);\r
  67     conses[27] = new Consensus("C",85);\r
  68     conses[10] = new Consensus("E",85);\r
  69     conses[11] = new Consensus("F",85);\r
  70     conses[12] = new Consensus("G",85);\r
  71     conses[13] = new Consensus("H",85);\r
  72     conses[14] = new Consensus("I",85);\r
  73     conses[15] = new Consensus("L",85);\r
  74     conses[16] = new Consensus("M",85);\r
  75     conses[17] = new Consensus("N",85);\r
  76     conses[18] = new Consensus("P",85);\r
  77     conses[19] = new Consensus("Q",85);\r
  78     conses[20] = new Consensus("R",85);\r
  79     conses[21] = new Consensus("S",85);\r
  80     conses[22] = new Consensus("T",85);\r
  81     conses[23] = new Consensus("V",85);\r
  82     conses[24] = new Consensus("W",85);\r
  83     conses[25] = new Consensus("Y",85);\r
  84     conses[28] = new Consensus("K",85);\r
  85     conses[29] = new Consensus("D",85);\r
  86 \r
  87     conses[30] = new Consensus("G",0);\r
  88     conses[31] = new Consensus("P",0);\r
  89 \r
  90     // We now construct the colours\r
  91     colours = new ConsensusColour[11];\r
  92 \r
  93 \r
  94     Consensus[] tmp8 = new Consensus[1];\r
  95     tmp8[0] = conses[30];//G\r
  96     colours[7] =new ConsensusColour((Color)colhash.get("ORANGE"),tmp8);\r
  97 \r
  98     Consensus[] tmp9 = new Consensus[1];\r
  99     tmp9[0] = conses[31];//P\r
 100     colours[8] =new ConsensusColour((Color)colhash.get("YELLOW"),tmp9);\r
 101 \r
 102     Consensus[] tmp10 = new Consensus[1];\r
 103     tmp10[0] = conses[27];//C\r
 104     colours[9] =new ConsensusColour((Color)colhash.get("PINK"),tmp8);\r
 105 \r
 106     Consensus[] tmp1 = new Consensus[14];\r
 107     tmp1[0] = conses[0]; //%\r
 108     tmp1[1] = conses[1]; //#\r
 109     tmp1[2] = conses[26]; //A\r
 110     tmp1[3] = conses[27]; //C\r
 111     tmp1[4] = conses[11]; //F\r
 112     tmp1[5] = conses[13]; //H\r
 113     tmp1[6] = conses[14]; //I\r
 114     tmp1[7] = conses[15]; //L\r
 115     tmp1[8] = conses[16]; //M\r
 116     tmp1[9] = conses[23]; //V\r
 117     tmp1[10] = conses[24]; //W\r
 118     tmp1[11] = conses[25]; //Y\r
 119     tmp1[12] = conses[18]; //P\r
 120     tmp1[13] = conses[19]; //p\r
 121     colours[0] = new ConsensusColour((Color)colhash.get("BLUE"),tmp1);\r
 122 \r
 123     colours[10] = new ConsensusColour((Color)colhash.get("CYAN"),tmp1);\r
 124 \r
 125     Consensus[] tmp2 = new Consensus[5];\r
 126     tmp2[0] = conses[8];  //t\r
 127     tmp2[1] = conses[21]; //S\r
 128     tmp2[2] = conses[22]; //T\r
 129     tmp2[3] = conses[0];  //%\r
 130     tmp2[4] = conses[1];  //#\r
 131     colours[1] = new ConsensusColour((Color)colhash.get("GREEN"),tmp2);\r
 132 \r
 133     Consensus[] tmp3 = new Consensus[3];\r
 134 \r
 135     tmp3[0] = conses[17]; //N\r
 136     tmp3[1] = conses[29]; //D\r
 137     tmp3[2] = conses[5];  //n\r
 138     colours[2] = new ConsensusColour((Color)colhash.get("GREEN"),tmp3);\r
 139 \r
 140     Consensus[] tmp4 = new Consensus[6];\r
 141     tmp4[0] = conses[6];  // q = QE\r
 142     tmp4[1] = conses[19]; //Q\r
 143     tmp4[2] = conses[22]; //E\r
 144     tmp4[3] = conses[3];  //+\r
 145     tmp4[4] = conses[28]; //K\r
 146     tmp4[5] = conses[20]; //R\r
 147     colours[3] = new ConsensusColour((Color)colhash.get("GREEN"),tmp4);\r
 148     Consensus[] tmp5 = new Consensus[4];\r
 149     tmp5[0] = conses[3];  //+\r
 150     tmp5[1] = conses[28]; //K\r
 151     tmp5[2] = conses[20]; //R\r
 152     tmp5[3] = conses[19]; //Q\r
 153     colours[4] = new ConsensusColour((Color)colhash.get("RED"),tmp5);\r
 154     Consensus[] tmp6 = new Consensus[5];\r
 155     tmp6[0] = conses[3];  //-\r
 156     tmp6[1] = conses[29]; //D\r
 157     tmp6[2] = conses[10]; //E\r
 158     tmp6[3] = conses[6];  //q\r
 159     tmp6[4] = conses[19]; //Q\r
 160     colours[5] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp6);\r
 161 \r
 162     Consensus[] tmp7 = new Consensus[5];\r
 163     tmp7[0] = conses[3];  //-\r
 164     tmp7[1] = conses[29]; //D\r
 165     tmp7[2] = conses[10]; //E\r
 166     tmp7[3] = conses[17];  //N\r
 167     tmp7[4] = conses[2]; //DE\r
 168     colours[6] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp7);\r
 169 \r
 170     // Now attach the ConsensusColours to the residue letters\r
 171     ResidueColour = new ConsensusColour[20];\r
 172     ResidueColour[0] = colours[0]; // A\r
 173     ResidueColour[1] = colours[4]; // R\r
 174     ResidueColour[2] = colours[2]; // N\r
 175     ResidueColour[3] = colours[6]; // D\r
 176     ResidueColour[4] = colours[0]; // C\r
 177     ResidueColour[5] = colours[3]; // Q\r
 178     ResidueColour[6] = colours[5]; // E\r
 179     ResidueColour[7] = colours[7]; // G\r
 180     ResidueColour[8] = colours[10]; // H\r
 181     ResidueColour[9] = colours[0]; // I\r
 182     ResidueColour[10] = colours[0]; // L\r
 183     ResidueColour[11] = colours[4]; // K\r
 184     ResidueColour[12] = colours[0]; // M\r
 185     ResidueColour[13] = colours[0]; // F\r
 186     ResidueColour[14] = colours[8]; // P\r
 187     ResidueColour[15] = colours[1]; // S\r
 188     ResidueColour[16] = colours[1]; // T\r
 189     ResidueColour[17] = colours[0]; // W\r
 190     ResidueColour[18] = colours[10]; // Y\r
 191     ResidueColour[19] = colours[0]; // V\r
 192   }\r
 193 \r
 194   public Color findColour(DrawableSequence seq, String s, int j) {\r
 195     // System.out.println("Finding colour for " + s + " " + j);\r
 196     int i = seq.num[j];\r
 197     Color c = Color.white;\r
 198     for (int k=0; k < ResidueColour[i].conses.length ; k++) {\r
 199       if (ResidueColour[i].conses[k].isConserved(cons2,j,seq.num[j],size)) {\r
 200         c =  ResidueColour[i].c;\r
 201       }\r
 202     }\r
 203     if (i ==4) {\r
 204       if (conses[27].isConserved(cons2,j,seq.num[j],size)) {\r
 205         c = (Color)colhash.get("PINK");\r
 206       }\r
 207     }\r
 208     return c;\r
 209   }\r
 210 \r
 211   public void setColours(DrawableSequence seq, int j) {\r
 212     Color c = Color.white;\r
 213 \r
 214     String s = seq.getSequence().substring(j,j+1);\r
 215     try {\r
 216       c = findColour(seq,s,j);\r
 217       seq.setResidueBoxColour(j,c);\r
 218     } catch (Exception e) {\r
 219       seq.setResidueBoxColour(j,Color.white);\r
 220     }\r
 221   }\r
 222 \r
 223   public void setColours(DrawableSequence s) {\r
 224     for (int j = 0; j < s.sequence.length(); j++) {\r
 225       setColours(s,j);\r
 226     }\r
 227   }\r
 228 \r
 229   public void setColours(SequenceGroup sg) {\r
 230     for (int j = 0; j < sg.sequences.size(); j++) {\r
 231 \r
 232       DrawableSequence s = (DrawableSequence)sg.sequences.elementAt(j);\r
 233       for (int i = 0; i < s.getSequence().length();i++) {\r
 234         setColours(s,i);\r
 235       }\r
 236     }\r
 237   }\r
 238 \r
 239 \r
 240 }\r
 241 \r
 242 */\r
 243 \r
 244 \r
 245 \r
 246 \r
 247 \r