src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.schemes;
  22
  23 import jalview.datamodel.AnnotatedCollectionI;
  24 import jalview.datamodel.SequenceCollectionI;
  25 import jalview.datamodel.SequenceI;
  26
  27 import java.awt.Color;
  28 import java.util.HashMap;
  29 import java.util.List;
  30 import java.util.Map;
  31
  32 public class ClustalxColourScheme extends ResidueColourScheme
  33 {
  34   private static final int EIGHTY_FIVE = 85;
  35
  36   private static final int FIFTY = 50;
  37
  38   private static final int EIGHTY = 80;
  39
  40   private static final int SIXTY = 60;
  41
  42   /*
  43    * Map from conventional colour names to Clustal version of the same
  44    */
  45   private static Map<Color, Color> colhash = new HashMap<Color, Color>();
  46
  47   private int[][] cons2;
  48
  49   private ConsensusColour[] colours;
  50
  51   private ConsensusColour[] residueColour;
  52
  53   private int size;
  54
  55   private Consensus[] conses = new Consensus[32];
  56
  57   private boolean includeGaps = true;
  58
  59   static
  60   {
  61     colhash.put(Color.RED, new Color(0.9f, 0.2f, 0.1f));
  62     colhash.put(Color.BLUE, new Color(0.5f, 0.7f, 0.9f));
  63     colhash.put(Color.GREEN, new Color(0.1f, 0.8f, 0.1f));
  64     colhash.put(Color.ORANGE, new Color(0.9f, 0.6f, 0.3f));
  65     colhash.put(Color.CYAN, new Color(0.1f, 0.7f, 0.7f));
  66     colhash.put(Color.PINK, new Color(0.9f, 0.5f, 0.5f));
  67     colhash.put(Color.MAGENTA, new Color(0.8f, 0.3f, 0.8f));
  68     colhash.put(Color.YELLOW, new Color(0.8f, 0.8f, 0.0f));
  69   }
  70
  71   public ClustalxColourScheme(AnnotatedCollectionI alignment,
  72           Map<SequenceI, SequenceCollectionI> hiddenReps)
  73   {
  74     alignmentChanged(alignment, hiddenReps);
  75   }
  76
  77   public void alignmentChanged(AnnotatedCollectionI alignment,
  78           Map<SequenceI, SequenceCollectionI> hiddenReps)
  79   {
  80     int maxWidth = alignment.getWidth();
  81     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
  82     cons2 = new int[maxWidth][24];
  83     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
  84     // get the current setting of the
  85     // includeGaps param.
  86     int start = 0;
  87
  88     // Initialize the array
  89     for (int j = 0; j < 24; j++)
  90     {
  91       for (int i = 0; i < maxWidth; i++)
  92       {
  93         cons2[i][j] = 0;
  94       }
  95     }
  96
  97     int res;
  98     int i;
  99     int j = 0;
 100     char[] seq;
 101
 102     for (SequenceI sq : seqs)
 103     {
 104       seq = sq.getSequence();
 105
 106       int end_j = seq.length - 1;
 107
 108       for (i = start; i <= end_j; i++)
 109       {
 110         if ((seq.length - 1) < i)
 111         {
 112           res = 23;
 113         }
 114         else
 115         {
 116           res = ResidueProperties.aaIndex[seq[i]];
 117         }
 118
 119         cons2[i][res]++;
 120       }
 121
 122       j++;
 123     }
 124
 125     this.size = seqs.size();
 126     makeColours();
 127   }
 128
 129   public void makeColours()
 130   {
 131     conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
 132     conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
 133     conses[2] = new Consensus("ED", FIFTY);
 134     conses[3] = new Consensus("KR", SIXTY);
 135     conses[4] = new Consensus("G", FIFTY);
 136     conses[5] = new Consensus("N", FIFTY);
 137     conses[6] = new Consensus("QE", FIFTY);
 138     conses[7] = new Consensus("P", FIFTY);
 139     conses[8] = new Consensus("TS", FIFTY);
 140
 141     conses[26] = new Consensus("A", EIGHTY_FIVE);
 142     conses[27] = new Consensus("C", EIGHTY_FIVE);
 143     conses[10] = new Consensus("E", EIGHTY_FIVE);
 144     conses[11] = new Consensus("F", EIGHTY_FIVE);
 145     conses[12] = new Consensus("G", EIGHTY_FIVE);
 146     conses[13] = new Consensus("H", EIGHTY_FIVE);
 147     conses[14] = new Consensus("I", EIGHTY_FIVE);
 148     conses[15] = new Consensus("L", EIGHTY_FIVE);
 149     conses[16] = new Consensus("M", EIGHTY_FIVE);
 150     conses[17] = new Consensus("N", EIGHTY_FIVE);
 151     conses[18] = new Consensus("P", EIGHTY_FIVE);
 152     conses[19] = new Consensus("Q", EIGHTY_FIVE);
 153     conses[20] = new Consensus("R", EIGHTY_FIVE);
 154     conses[21] = new Consensus("S", EIGHTY_FIVE);
 155     conses[22] = new Consensus("T", EIGHTY_FIVE);
 156     conses[23] = new Consensus("V", EIGHTY_FIVE);
 157     conses[24] = new Consensus("W", EIGHTY_FIVE);
 158     conses[25] = new Consensus("Y", EIGHTY_FIVE);
 159     conses[28] = new Consensus("K", EIGHTY_FIVE);
 160     conses[29] = new Consensus("D", EIGHTY_FIVE);
 161
 162     conses[30] = new Consensus("G", 0);
 163     conses[31] = new Consensus("P", 0);
 164
 165     // We now construct the colours
 166     colours = new ConsensusColour[11];
 167
 168     Consensus[] tmp8 = new Consensus[1];
 169     tmp8[0] = conses[30]; // G
 170     colours[7] = new ConsensusColour(colhash.get(Color.ORANGE), tmp8);
 171
 172     Consensus[] tmp9 = new Consensus[1];
 173     tmp9[0] = conses[31]; // P
 174     colours[8] = new ConsensusColour(colhash.get(Color.YELLOW), tmp9);
 175
 176     Consensus[] tmp10 = new Consensus[1];
 177     tmp10[0] = conses[27]; // C
 178     colours[9] = new ConsensusColour(colhash.get(Color.PINK), tmp8);
 179
 180     Consensus[] tmp1 = new Consensus[14];
 181     tmp1[0] = conses[0]; // %
 182     tmp1[1] = conses[1]; // #
 183     tmp1[2] = conses[26]; // A
 184     tmp1[3] = conses[27]; // C
 185     tmp1[4] = conses[11]; // F
 186     tmp1[5] = conses[13]; // H
 187     tmp1[6] = conses[14]; // I
 188     tmp1[7] = conses[15]; // L
 189     tmp1[8] = conses[16]; // M
 190     tmp1[9] = conses[23]; // V
 191     tmp1[10] = conses[24]; // W
 192     tmp1[11] = conses[25]; // Y
 193     tmp1[12] = conses[18]; // P
 194     tmp1[13] = conses[19]; // p
 195     colours[0] = new ConsensusColour(colhash.get(Color.BLUE), tmp1);
 196
 197     colours[10] = new ConsensusColour(colhash.get(Color.CYAN), tmp1);
 198
 199     Consensus[] tmp2 = new Consensus[5];
 200     tmp2[0] = conses[8]; // t
 201     tmp2[1] = conses[21]; // S
 202     tmp2[2] = conses[22]; // T
 203     tmp2[3] = conses[0]; // %
 204     tmp2[4] = conses[1]; // #
 205     colours[1] = new ConsensusColour(colhash.get(Color.GREEN), tmp2);
 206
 207     Consensus[] tmp3 = new Consensus[3];
 208
 209     tmp3[0] = conses[17]; // N
 210     tmp3[1] = conses[29]; // D
 211     tmp3[2] = conses[5]; // n
 212     colours[2] = new ConsensusColour(colhash.get(Color.GREEN), tmp3);
 213
 214     Consensus[] tmp4 = new Consensus[6];
 215     tmp4[0] = conses[6]; // q = QE
 216     tmp4[1] = conses[19]; // Q
 217     tmp4[2] = conses[22]; // E
 218     tmp4[3] = conses[3]; // +
 219     tmp4[4] = conses[28]; // K
 220     tmp4[5] = conses[20]; // R
 221     colours[3] = new ConsensusColour(colhash.get(Color.GREEN), tmp4);
 222
 223     Consensus[] tmp5 = new Consensus[4];
 224     tmp5[0] = conses[3]; // +
 225     tmp5[1] = conses[28]; // K
 226     tmp5[2] = conses[20]; // R
 227     tmp5[3] = conses[19]; // Q
 228     colours[4] = new ConsensusColour(colhash.get(Color.RED), tmp5);
 229
 230     Consensus[] tmp6 = new Consensus[6];
 231     tmp6[0] = conses[3]; // -
 232     tmp6[1] = conses[29]; // D
 233     tmp6[2] = conses[10]; // E
 234     tmp6[3] = conses[6]; // QE
 235     tmp6[4] = conses[19]; // Q
 236     tmp6[5] = conses[2]; // DE
 237     colours[5] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp6);
 238
 239     Consensus[] tmp7 = new Consensus[5];
 240     tmp7[0] = conses[3]; // -
 241     tmp7[1] = conses[29]; // D
 242     tmp7[2] = conses[10]; // E
 243     tmp7[3] = conses[17]; // N
 244     tmp7[4] = conses[2]; // DE
 245     colours[6] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp7);
 246
 247     // Now attach the ConsensusColours to the residue letters
 248     residueColour = new ConsensusColour[20];
 249     residueColour[0] = colours[0]; // A
 250     residueColour[1] = colours[4]; // R
 251     residueColour[2] = colours[2]; // N
 252     residueColour[3] = colours[6]; // D
 253     residueColour[4] = colours[0]; // C
 254     residueColour[5] = colours[3]; // Q
 255     residueColour[6] = colours[5]; // E
 256     residueColour[7] = colours[7]; // G
 257     residueColour[8] = colours[10]; // H
 258     residueColour[9] = colours[0]; // I
 259     residueColour[10] = colours[0]; // L
 260     residueColour[11] = colours[4]; // K
 261     residueColour[12] = colours[0]; // M
 262     residueColour[13] = colours[0]; // F
 263     residueColour[14] = colours[8]; // P
 264     residueColour[15] = colours[1]; // S
 265     residueColour[16] = colours[1]; // T
 266     residueColour[17] = colours[0]; // W
 267     residueColour[18] = colours[10]; // Y
 268     residueColour[19] = colours[0]; // V
 269   }
 270
 271   @Override
 272   public Color findColour(char c)
 273   {
 274     return Color.pink;
 275   }
 276
 277   @Override
 278   public Color findColour(char c, int j, SequenceI seq)
 279   {
 280     Color currentColour;
 281
 282     if (cons2.length <= j
 283             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 284     {
 285       return Color.white;
 286     }
 287
 288     int i = ResidueProperties.aaIndex[c];
 289
 290     currentColour = Color.white;
 291
 292     if (i > 19)
 293     {
 294       return currentColour;
 295     }
 296
 297     for (int k = 0; k < residueColour[i].conses.length; k++)
 298     {
 299       if (residueColour[i].conses[k].isConserved(cons2, j, size,
 300               includeGaps))
 301       {
 302         currentColour = residueColour[i].c;
 303       }
 304     }
 305
 306     if (i == 4)
 307     {
 308       if (conses[27].isConserved(cons2, j, size, includeGaps))
 309       {
 310         currentColour = colhash.get(Color.PINK);
 311       }
 312     }
 313
 314     if (conservationColouring)
 315     {
 316       currentColour = applyConservation(currentColour, j);
 317     }
 318
 319     return currentColour;
 320   }
 321
 322   /**
 323    * @return the includeGaps
 324    */
 325   protected boolean isIncludeGaps()
 326   {
 327     return includeGaps;
 328   }
 329
 330   /**
 331    * @param includeGaps
 332    *          the includeGaps to set
 333    */
 334   protected void setIncludeGaps(boolean includeGaps)
 335   {
 336     this.includeGaps = includeGaps;
 337   }
 338
 339   @Override
 340   public ColourSchemeI applyTo(AnnotatedCollectionI sg,
 341           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
 342   {
 343     ClustalxColourScheme css = new ClustalxColourScheme(sg,
 344             hiddenRepSequences);
 345     css.includeGaps = includeGaps;
 346     return css;
 347   }
 348 }
 349
 350 class ConsensusColour
 351 {
 352   Consensus[] conses;
 353
 354   Color c;
 355
 356   public ConsensusColour(Color c, Consensus[] conses)
 357   {
 358     this.conses = conses;
 359
 360     // this.list = list;
 361     this.c = c;
 362   }
 363 }