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.api.AlignViewportI;
  24 import jalview.datamodel.AnnotatedCollectionI;
  25 import jalview.datamodel.SequenceCollectionI;
  26 import jalview.datamodel.SequenceI;
  27 import jalview.util.Comparison;
  28
  29 import java.awt.Color;
  30 import java.util.List;
  31 import java.util.Map;
  32
  33 public class ClustalxColourScheme extends ResidueColourScheme
  34 {
  35   private static final int EIGHTY_FIVE = 85;
  36
  37   private static final int FIFTY = 50;
  38
  39   private static final int EIGHTY = 80;
  40
  41   private static final int SIXTY = 60;
  42
  43   enum ClustalColour
  44   {
  45     RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
  46     ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
  47     PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
  48     YELLOW(0.8f, 0.8f, 0.0f);
  49
  50     final Color colour;
  51
  52     ClustalColour(float r, float g, float b)
  53     {
  54       colour = new Color(r, g, b);
  55     }
  56   }
  57
  58   private class ConsensusColour
  59   {
  60     Consensus[] cons;
  61
  62     Color c;
  63
  64     public ConsensusColour(ClustalColour col, Consensus[] conses)
  65     {
  66       this.cons = conses;
  67       this.c = col.colour;
  68     }
  69   }
  70
  71   private int[][] cons2;
  72
  73   private ConsensusColour[] colours;
  74
  75   private ConsensusColour[] residueColour;
  76
  77   private int size;
  78
  79   private Consensus[] conses = new Consensus[32];
  80
  81   private boolean includeGaps = true;
  82
  83   /**
  84    * Default constructor (required for Class.newInstance())
  85    */
  86   public ClustalxColourScheme()
  87   {
  88
  89   }
  90
  91   public ClustalxColourScheme(AnnotatedCollectionI alignment,
  92           Map<SequenceI, SequenceCollectionI> hiddenReps)
  93   {
  94     alignmentChanged(alignment, hiddenReps);
  95   }
  96
  97   @Override
  98   public void alignmentChanged(AnnotatedCollectionI alignment,
  99           Map<SequenceI, SequenceCollectionI> hiddenReps)
 100   {
 101     int maxWidth = alignment.getWidth();
 102     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
 103     cons2 = new int[maxWidth][24];
 104     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
 105     // get the current setting of the
 106     // includeGaps param.
 107     int res = 0;
 108
 109     for (SequenceI sq : seqs)
 110     {
 111       int end_j = sq.getLength() - 1;
 112       int length = sq.getLength();
 113
 114       for (int i = 0; i <= end_j; i++)
 115       {
 116         if (length - 1 < i)
 117         {
 118           res = 23;
 119         }
 120         else
 121         {
 122           res = ResidueProperties.aaIndex[sq.getCharAt(i)];
 123         }
 124         cons2[i][res]++;
 125       }
 126     }
 127
 128     this.size = seqs.size();
 129     makeColours();
 130   }
 131
 132   void makeColours()
 133   {
 134     conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
 135     conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
 136     conses[2] = new Consensus("ED", FIFTY);
 137     conses[3] = new Consensus("KR", SIXTY);
 138     conses[4] = new Consensus("G", FIFTY);
 139     conses[5] = new Consensus("N", FIFTY);
 140     conses[6] = new Consensus("QE", FIFTY);
 141     conses[7] = new Consensus("P", FIFTY);
 142     conses[8] = new Consensus("TS", FIFTY);
 143
 144     conses[26] = new Consensus("A", EIGHTY_FIVE);
 145     conses[27] = new Consensus("C", EIGHTY_FIVE);
 146     conses[10] = new Consensus("E", EIGHTY_FIVE);
 147     conses[11] = new Consensus("F", EIGHTY_FIVE);
 148     conses[12] = new Consensus("G", EIGHTY_FIVE);
 149     conses[13] = new Consensus("H", EIGHTY_FIVE);
 150     conses[14] = new Consensus("I", EIGHTY_FIVE);
 151     conses[15] = new Consensus("L", EIGHTY_FIVE);
 152     conses[16] = new Consensus("M", EIGHTY_FIVE);
 153     conses[17] = new Consensus("N", EIGHTY_FIVE);
 154     conses[18] = new Consensus("P", EIGHTY_FIVE);
 155     conses[19] = new Consensus("Q", EIGHTY_FIVE);
 156     conses[20] = new Consensus("R", EIGHTY_FIVE);
 157     conses[21] = new Consensus("S", EIGHTY_FIVE);
 158     conses[22] = new Consensus("T", EIGHTY_FIVE);
 159     conses[23] = new Consensus("V", EIGHTY_FIVE);
 160     conses[24] = new Consensus("W", EIGHTY_FIVE);
 161     conses[25] = new Consensus("Y", EIGHTY_FIVE);
 162     conses[28] = new Consensus("K", EIGHTY_FIVE);
 163     conses[29] = new Consensus("D", EIGHTY_FIVE);
 164
 165     conses[30] = new Consensus("G", 0);
 166     conses[31] = new Consensus("P", 0);
 167
 168     // We now construct the colours
 169     colours = new ConsensusColour[11];
 170
 171     Consensus[] tmp8 = new Consensus[1];
 172     tmp8[0] = conses[30]; // G
 173     colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
 174
 175     Consensus[] tmp9 = new Consensus[1];
 176     tmp9[0] = conses[31]; // P
 177     colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
 178
 179     Consensus[] tmp10 = new Consensus[1];
 180     tmp10[0] = conses[27]; // C
 181     colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
 182
 183     Consensus[] tmp1 = new Consensus[14];
 184     tmp1[0] = conses[0]; // %
 185     tmp1[1] = conses[1]; // #
 186     tmp1[2] = conses[26]; // A
 187     tmp1[3] = conses[27]; // C
 188     tmp1[4] = conses[11]; // F
 189     tmp1[5] = conses[13]; // H
 190     tmp1[6] = conses[14]; // I
 191     tmp1[7] = conses[15]; // L
 192     tmp1[8] = conses[16]; // M
 193     tmp1[9] = conses[23]; // V
 194     tmp1[10] = conses[24]; // W
 195     tmp1[11] = conses[25]; // Y
 196     tmp1[12] = conses[18]; // P
 197     tmp1[13] = conses[19]; // p
 198     colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
 199
 200     colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
 201
 202     Consensus[] tmp2 = new Consensus[5];
 203     tmp2[0] = conses[8]; // t
 204     tmp2[1] = conses[21]; // S
 205     tmp2[2] = conses[22]; // T
 206     tmp2[3] = conses[0]; // %
 207     tmp2[4] = conses[1]; // #
 208     colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
 209
 210     Consensus[] tmp3 = new Consensus[3];
 211
 212     tmp3[0] = conses[17]; // N
 213     tmp3[1] = conses[29]; // D
 214     tmp3[2] = conses[5]; // n
 215     colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
 216
 217     Consensus[] tmp4 = new Consensus[6];
 218     tmp4[0] = conses[6]; // q = QE
 219     tmp4[1] = conses[19]; // Q
 220     tmp4[2] = conses[22]; // E
 221     tmp4[3] = conses[3]; // +
 222     tmp4[4] = conses[28]; // K
 223     tmp4[5] = conses[20]; // R
 224     colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
 225
 226     Consensus[] tmp5 = new Consensus[4];
 227     tmp5[0] = conses[3]; // +
 228     tmp5[1] = conses[28]; // K
 229     tmp5[2] = conses[20]; // R
 230     tmp5[3] = conses[19]; // Q
 231     colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
 232
 233     Consensus[] tmp6 = new Consensus[6];
 234     tmp6[0] = conses[3]; // -
 235     tmp6[1] = conses[29]; // D
 236     tmp6[2] = conses[10]; // E
 237     tmp6[3] = conses[6]; // QE
 238     tmp6[4] = conses[19]; // Q
 239     tmp6[5] = conses[2]; // DE
 240     colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
 241
 242     Consensus[] tmp7 = new Consensus[5];
 243     tmp7[0] = conses[3]; // -
 244     tmp7[1] = conses[29]; // D
 245     tmp7[2] = conses[10]; // E
 246     tmp7[3] = conses[17]; // N
 247     tmp7[4] = conses[2]; // DE
 248     colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
 249
 250     // Now attach the ConsensusColours to the residue letters
 251     residueColour = new ConsensusColour[20];
 252     residueColour[0] = colours[0]; // A
 253     residueColour[1] = colours[4]; // R
 254     residueColour[2] = colours[2]; // N
 255     residueColour[3] = colours[6]; // D
 256     residueColour[4] = colours[0]; // C
 257     residueColour[5] = colours[3]; // Q
 258     residueColour[6] = colours[5]; // E
 259     residueColour[7] = colours[7]; // G
 260     residueColour[8] = colours[10]; // H
 261     residueColour[9] = colours[0]; // I
 262     residueColour[10] = colours[0]; // L
 263     residueColour[11] = colours[4]; // K
 264     residueColour[12] = colours[0]; // M
 265     residueColour[13] = colours[0]; // F
 266     residueColour[14] = colours[8]; // P
 267     residueColour[15] = colours[1]; // S
 268     residueColour[16] = colours[1]; // T
 269     residueColour[17] = colours[0]; // W
 270     residueColour[18] = colours[10]; // Y
 271     residueColour[19] = colours[0]; // V
 272   }
 273
 274   @Override
 275   public Color findColour(char c)
 276   {
 277     return Color.pink;
 278   }
 279
 280   @Override
 281   protected Color findColour(char c, int j, SequenceI seq)
 282   {
 283     // TODO why the test for includeGaps here?
 284     if (cons2.length <= j || Comparison.isGap(c)
 285     /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
 286     {
 287       return Color.white;
 288     }
 289
 290     int i = ResidueProperties.aaIndex[c];
 291
 292     Color colour = Color.white;
 293
 294     if (i > 19)
 295     {
 296       return colour;
 297     }
 298
 299     for (int k = 0; k < residueColour[i].cons.length; k++)
 300     {
 301       if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
 302       {
 303         colour = residueColour[i].c;
 304       }
 305     }
 306
 307     if (i == 4)
 308     {
 309       /*
 310        * override to colour C pink if >85% conserved
 311        */
 312       if (conses[27].isConserved(cons2, j, size, includeGaps))
 313       {
 314         colour = ClustalColour.PINK.colour;
 315       }
 316     }
 317
 318     return colour;
 319   }
 320
 321   /**
 322    * @return the includeGaps
 323    */
 324   protected boolean isIncludeGaps()
 325   {
 326     return includeGaps;
 327   }
 328
 329   /**
 330    * @param includeGaps
 331    *          the includeGaps to set
 332    */
 333   protected void setIncludeGaps(boolean includeGaps)
 334   {
 335     this.includeGaps = includeGaps;
 336   }
 337
 338   @Override
 339   public ColourSchemeI getInstance(AlignViewportI view,
 340           AnnotatedCollectionI sg)
 341   {
 342     ClustalxColourScheme css = new ClustalxColourScheme(sg,
 343             view == null ? null : view.getHiddenRepSequences());
 344     css.includeGaps = includeGaps;
 345     return css;
 346   }
 347
 348   @Override
 349   public boolean isPeptideSpecific()
 350   {
 351     return true;
 352   }
 353
 354   @Override
 355   public String getSchemeName()
 356   {
 357     return JalviewColourScheme.Clustal.toString();
 358   }
 359
 360   @Override
 361   public boolean isSimple()
 362   {
 363     return false;
 364   }
 365 }