src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.schemes;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23
  24 import jalview.datamodel.*;
  25
  26 public class ClustalxColourScheme extends ResidueColourScheme // implements
  27 // IParameterizable
  28 {
  29   public static Hashtable colhash = new Hashtable();
  30
  31   Hashtable[] cons;
  32
  33   int[][] cons2;
  34
  35   ConsensusColour[] colours;
  36
  37   ConsensusColour[] ResidueColour;
  38
  39   int size;
  40
  41   Consensus[] conses = new Consensus[32];
  42
  43   Vector colourTable = new Vector();
  44
  45   private boolean includeGaps = true;
  46
  47   {
  48     colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
  49     colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
  50     colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
  51     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
  52     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
  53     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
  54     colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
  55     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
  56   }
  57
  58   public ClustalxColourScheme(Vector seqs, int maxWidth)
  59   {
  60     resetClustalX(seqs, maxWidth);
  61   }
  62
  63   public void resetClustalX(Vector seqs, int maxWidth)
  64   {
  65     cons2 = new int[maxWidth][24];
  66     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
  67     // get the current setting of the
  68     // includeGaps param.
  69     int start = 0;
  70
  71     // Initialize the array
  72     for (int j = 0; j < 24; j++)
  73     {
  74       for (int i = 0; i < maxWidth; i++)
  75       {
  76         cons2[i][j] = 0;
  77       }
  78     }
  79
  80     int res;
  81     int i;
  82     int j = 0;
  83     char[] seq;
  84
  85     while (j < seqs.size())
  86     {
  87       seq = ((SequenceI) seqs.elementAt(j)).getSequence();
  88
  89       int end_j = seq.length - 1;
  90
  91       for (i = start; i <= end_j; i++)
  92       {
  93         if ((seq.length - 1) < i)
  94         {
  95           res = 23;
  96         }
  97         else
  98         {
  99           res = ResidueProperties.aaIndex[seq[i]];
 100         }
 101
 102         cons2[i][res]++;
 103       }
 104
 105       j++;
 106     }
 107
 108     this.size = seqs.size();
 109     makeColours();
 110   }
 111
 112   public void makeColours()
 113   {
 114     conses[0] = new Consensus("WLVIMAFCYHP", 60);
 115     conses[1] = new Consensus("WLVIMAFCYHP", 80);
 116     conses[2] = new Consensus("ED", 50);
 117     conses[3] = new Consensus("KR", 60);
 118     conses[4] = new Consensus("G", 50);
 119     conses[5] = new Consensus("N", 50);
 120     conses[6] = new Consensus("QE", 50);
 121     conses[7] = new Consensus("P", 50);
 122     conses[8] = new Consensus("TS", 50);
 123
 124     conses[26] = new Consensus("A", 85);
 125     conses[27] = new Consensus("C", 85);
 126     conses[10] = new Consensus("E", 85);
 127     conses[11] = new Consensus("F", 85);
 128     conses[12] = new Consensus("G", 85);
 129     conses[13] = new Consensus("H", 85);
 130     conses[14] = new Consensus("I", 85);
 131     conses[15] = new Consensus("L", 85);
 132     conses[16] = new Consensus("M", 85);
 133     conses[17] = new Consensus("N", 85);
 134     conses[18] = new Consensus("P", 85);
 135     conses[19] = new Consensus("Q", 85);
 136     conses[20] = new Consensus("R", 85);
 137     conses[21] = new Consensus("S", 85);
 138     conses[22] = new Consensus("T", 85);
 139     conses[23] = new Consensus("V", 85);
 140     conses[24] = new Consensus("W", 85);
 141     conses[25] = new Consensus("Y", 85);
 142     conses[28] = new Consensus("K", 85);
 143     conses[29] = new Consensus("D", 85);
 144
 145     conses[30] = new Consensus("G", 0);
 146     conses[31] = new Consensus("P", 0);
 147
 148     // We now construct the colours
 149     colours = new ConsensusColour[11];
 150
 151     Consensus[] tmp8 = new Consensus[1];
 152     tmp8[0] = conses[30]; // G
 153     colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 154
 155     Consensus[] tmp9 = new Consensus[1];
 156     tmp9[0] = conses[31]; // P
 157     colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 158
 159     Consensus[] tmp10 = new Consensus[1];
 160     tmp10[0] = conses[27]; // C
 161     colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 162
 163     Consensus[] tmp1 = new Consensus[14];
 164     tmp1[0] = conses[0]; // %
 165     tmp1[1] = conses[1]; // #
 166     tmp1[2] = conses[26]; // A
 167     tmp1[3] = conses[27]; // C
 168     tmp1[4] = conses[11]; // F
 169     tmp1[5] = conses[13]; // H
 170     tmp1[6] = conses[14]; // I
 171     tmp1[7] = conses[15]; // L
 172     tmp1[8] = conses[16]; // M
 173     tmp1[9] = conses[23]; // V
 174     tmp1[10] = conses[24]; // W
 175     tmp1[11] = conses[25]; // Y
 176     tmp1[12] = conses[18]; // P
 177     tmp1[13] = conses[19]; // p
 178     colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
 179
 180     colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 181
 182     Consensus[] tmp2 = new Consensus[5];
 183     tmp2[0] = conses[8]; // t
 184     tmp2[1] = conses[21]; // S
 185     tmp2[2] = conses[22]; // T
 186     tmp2[3] = conses[0]; // %
 187     tmp2[4] = conses[1]; // #
 188     colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 189
 190     Consensus[] tmp3 = new Consensus[3];
 191
 192     tmp3[0] = conses[17]; // N
 193     tmp3[1] = conses[29]; // D
 194     tmp3[2] = conses[5]; // n
 195     colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 196
 197     Consensus[] tmp4 = new Consensus[6];
 198     tmp4[0] = conses[6]; // q = QE
 199     tmp4[1] = conses[19]; // Q
 200     tmp4[2] = conses[22]; // E
 201     tmp4[3] = conses[3]; // +
 202     tmp4[4] = conses[28]; // K
 203     tmp4[5] = conses[20]; // R
 204     colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 205
 206     Consensus[] tmp5 = new Consensus[4];
 207     tmp5[0] = conses[3]; // +
 208     tmp5[1] = conses[28]; // K
 209     tmp5[2] = conses[20]; // R
 210     tmp5[3] = conses[19]; // Q
 211     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 212
 213     Consensus[] tmp6 = new Consensus[6];
 214     tmp6[0] = conses[3]; // -
 215     tmp6[1] = conses[29]; // D
 216     tmp6[2] = conses[10]; // E
 217     tmp6[3] = conses[6]; // QE
 218     tmp6[4] = conses[19]; // Q
 219     tmp6[5] = conses[2]; // DE
 220     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 221
 222     Consensus[] tmp7 = new Consensus[5];
 223     tmp7[0] = conses[3]; // -
 224     tmp7[1] = conses[29]; // D
 225     tmp7[2] = conses[10]; // E
 226     tmp7[3] = conses[17]; // N
 227     tmp7[4] = conses[2]; // DE
 228     colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 229
 230     // Now attach the ConsensusColours to the residue letters
 231     ResidueColour = new ConsensusColour[20];
 232     ResidueColour[0] = colours[0]; // A
 233     ResidueColour[1] = colours[4]; // R
 234     ResidueColour[2] = colours[2]; // N
 235     ResidueColour[3] = colours[6]; // D
 236     ResidueColour[4] = colours[0]; // C
 237     ResidueColour[5] = colours[3]; // Q
 238     ResidueColour[6] = colours[5]; // E
 239     ResidueColour[7] = colours[7]; // G
 240     ResidueColour[8] = colours[10]; // H
 241     ResidueColour[9] = colours[0]; // I
 242     ResidueColour[10] = colours[0]; // L
 243     ResidueColour[11] = colours[4]; // K
 244     ResidueColour[12] = colours[0]; // M
 245     ResidueColour[13] = colours[0]; // F
 246     ResidueColour[14] = colours[8]; // P
 247     ResidueColour[15] = colours[1]; // S
 248     ResidueColour[16] = colours[1]; // T
 249     ResidueColour[17] = colours[0]; // W
 250     ResidueColour[18] = colours[10]; // Y
 251     ResidueColour[19] = colours[0]; // V
 252   }
 253
 254   public Color findColour(char c)
 255   {
 256     return Color.pink;
 257   }
 258
 259   public Color findColour(char c, int j)
 260   {
 261     Color currentColour;
 262
 263     if (cons2.length <= j
 264             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 265     {
 266       return Color.white;
 267     }
 268
 269     int i = ResidueProperties.aaIndex[c];
 270
 271     currentColour = Color.white;
 272
 273     if (i > 19)
 274     {
 275       return currentColour;
 276     }
 277
 278     for (int k = 0; k < ResidueColour[i].conses.length; k++)
 279     {
 280       if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
 281               includeGaps))
 282       {
 283         currentColour = ResidueColour[i].c;
 284       }
 285     }
 286
 287     if (i == 4)
 288     {
 289       if (conses[27].isConserved(cons2, j, size, includeGaps))
 290       {
 291         currentColour = (Color) colhash.get("PINK");
 292       }
 293     }
 294
 295     if (conservationColouring)
 296     {
 297       currentColour = applyConservation(currentColour, j);
 298     }
 299
 300     return currentColour;
 301   }
 302
 303   /**
 304    * @return the includeGaps
 305    */
 306   protected boolean isIncludeGaps()
 307   {
 308     return includeGaps;
 309   }
 310
 311   /**
 312    * @param includeGaps
 313    *          the includeGaps to set
 314    */
 315   protected void setIncludeGaps(boolean includeGaps)
 316   {
 317     this.includeGaps = includeGaps;
 318   }
 319 }
 320
 321 class ConsensusColour
 322 {
 323   Consensus[] conses;
 324
 325   Color c;
 326
 327   public ConsensusColour(Color c, Consensus[] conses)
 328   {
 329     this.conses = conses;
 330
 331     // this.list = list;
 332     this.c = c;
 333   }
 334 }