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 java.awt.Color;
  24 import java.util.HashMap;
  25 import java.util.List;
  26 import java.util.Map;
  27
  28 import jalview.api.AlignViewportI;
  29 import jalview.datamodel.AnnotatedCollectionI;
  30 import jalview.datamodel.SequenceCollectionI;
  31 import jalview.datamodel.SequenceI;
  32 import jalview.util.ColorUtils;
  33 import jalview.util.Comparison;
  34
  35 public class ClustalxColourScheme extends ResidueColourScheme
  36 {
  37   private static final int EIGHTY_FIVE = 85;
  38
  39   private static final int FIFTY = 50;
  40
  41   private static final int EIGHTY = 80;
  42
  43   private static final int SIXTY = 60;
  44
  45   enum ClustalColour
  46   {
  47     RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
  48     ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
  49     PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
  50     YELLOW(0.8f, 0.8f, 0.0f);
  51
  52     final Color colour;
  53
  54     ClustalColour(float r, float g, float b)
  55     {
  56       colour = new Color(r, g, b);
  57     }
  58   }
  59
  60   private class ConsensusColour
  61   {
  62     Consensus[] cons;
  63
  64     Color c;
  65
  66     public ConsensusColour(ClustalColour col, Consensus[] conses)
  67     {
  68       this.cons = conses;
  69       this.c = col.colour;
  70     }
  71   }
  72
  73   private int[][] cons2;
  74
  75   private ConsensusColour[] colours;
  76
  77   private ConsensusColour[] residueColour;
  78
  79   private int size;
  80
  81   private Consensus[] conses = new Consensus[32];
  82
  83   private boolean includeGaps = true;
  84
  85   /**
  86    * Default constructor (required for Class.newInstance())
  87    */
  88   public ClustalxColourScheme()
  89   {
  90
  91   }
  92
  93   public ClustalxColourScheme(AnnotatedCollectionI alignment,
  94           Map<SequenceI, SequenceCollectionI> hiddenReps)
  95   {
  96     alignmentChanged(alignment, hiddenReps);
  97   }
  98
  99   @Override
 100   public synchronized void alignmentChanged(AnnotatedCollectionI alignment,
 101           Map<SequenceI, SequenceCollectionI> hiddenReps)
 102   {
 103     int maxWidth = alignment.getWidth();
 104     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
 105     cons2 = new int[maxWidth][24];
 106     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
 107     // get the current setting of the
 108     // includeGaps param.
 109     int res = 0;
 110
 111     for (SequenceI sq : seqs)
 112     {
 113       int end_j = sq.getLength() - 1;
 114       int length = sq.getLength();
 115
 116       for (int i = 0; i <= end_j; i++)
 117       {
 118         if (length - 1 < i)
 119         {
 120           res = 23;
 121         }
 122         else
 123         {
 124           res = ResidueProperties.aaIndex[sq.getCharAt(i)];
 125         }
 126         cons2[i][res]++;
 127       }
 128     }
 129
 130     this.size = seqs.size();
 131     makeColours();
 132   }
 133
 134   void makeColours()
 135   {
 136     conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
 137     conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
 138     conses[2] = new Consensus("ED", FIFTY);
 139     conses[3] = new Consensus("KR", SIXTY);
 140     conses[4] = new Consensus("G", FIFTY);
 141     conses[5] = new Consensus("N", FIFTY);
 142     conses[6] = new Consensus("QE", FIFTY);
 143     conses[7] = new Consensus("P", FIFTY);
 144     conses[8] = new Consensus("TS", FIFTY);
 145
 146     conses[26] = new Consensus("A", EIGHTY_FIVE);
 147     conses[27] = new Consensus("C", EIGHTY_FIVE);
 148     conses[10] = new Consensus("E", EIGHTY_FIVE);
 149     conses[11] = new Consensus("F", EIGHTY_FIVE);
 150     conses[12] = new Consensus("G", EIGHTY_FIVE);
 151     conses[13] = new Consensus("H", EIGHTY_FIVE);
 152     conses[14] = new Consensus("I", EIGHTY_FIVE);
 153     conses[15] = new Consensus("L", EIGHTY_FIVE);
 154     conses[16] = new Consensus("M", EIGHTY_FIVE);
 155     conses[17] = new Consensus("N", EIGHTY_FIVE);
 156     conses[18] = new Consensus("P", EIGHTY_FIVE);
 157     conses[19] = new Consensus("Q", EIGHTY_FIVE);
 158     conses[20] = new Consensus("R", EIGHTY_FIVE);
 159     conses[21] = new Consensus("S", EIGHTY_FIVE);
 160     conses[22] = new Consensus("T", EIGHTY_FIVE);
 161     conses[23] = new Consensus("V", EIGHTY_FIVE);
 162     conses[24] = new Consensus("W", EIGHTY_FIVE);
 163     conses[25] = new Consensus("Y", EIGHTY_FIVE);
 164     conses[28] = new Consensus("K", EIGHTY_FIVE);
 165     conses[29] = new Consensus("D", EIGHTY_FIVE);
 166
 167     conses[30] = new Consensus("G", 0);
 168     conses[31] = new Consensus("P", 0);
 169
 170     // We now construct the colours
 171     colours = new ConsensusColour[11];
 172
 173     Consensus[] tmp8 = new Consensus[1];
 174     tmp8[0] = conses[30]; // G
 175     colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
 176
 177     Consensus[] tmp9 = new Consensus[1];
 178     tmp9[0] = conses[31]; // P
 179     colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
 180
 181     Consensus[] tmp10 = new Consensus[1];
 182     tmp10[0] = conses[27]; // C
 183     colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
 184
 185     Consensus[] tmp1 = new Consensus[14];
 186     tmp1[0] = conses[0]; // %
 187     tmp1[1] = conses[1]; // #
 188     tmp1[2] = conses[26]; // A
 189     tmp1[3] = conses[27]; // C
 190     tmp1[4] = conses[11]; // F
 191     tmp1[5] = conses[13]; // H
 192     tmp1[6] = conses[14]; // I
 193     tmp1[7] = conses[15]; // L
 194     tmp1[8] = conses[16]; // M
 195     tmp1[9] = conses[23]; // V
 196     tmp1[10] = conses[24]; // W
 197     tmp1[11] = conses[25]; // Y
 198     tmp1[12] = conses[18]; // P
 199     tmp1[13] = conses[19]; // p
 200     colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
 201
 202     colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
 203
 204     Consensus[] tmp2 = new Consensus[5];
 205     tmp2[0] = conses[8]; // t
 206     tmp2[1] = conses[21]; // S
 207     tmp2[2] = conses[22]; // T
 208     tmp2[3] = conses[0]; // %
 209     tmp2[4] = conses[1]; // #
 210     colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
 211
 212     Consensus[] tmp3 = new Consensus[3];
 213
 214     tmp3[0] = conses[17]; // N
 215     tmp3[1] = conses[29]; // D
 216     tmp3[2] = conses[5]; // n
 217     colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
 218
 219     Consensus[] tmp4 = new Consensus[6];
 220     tmp4[0] = conses[6]; // q = QE
 221     tmp4[1] = conses[19]; // Q
 222     tmp4[2] = conses[22]; // E
 223     tmp4[3] = conses[3]; // +
 224     tmp4[4] = conses[28]; // K
 225     tmp4[5] = conses[20]; // R
 226     colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
 227
 228     Consensus[] tmp5 = new Consensus[4];
 229     tmp5[0] = conses[3]; // +
 230     tmp5[1] = conses[28]; // K
 231     tmp5[2] = conses[20]; // R
 232     tmp5[3] = conses[19]; // Q
 233     colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
 234
 235     Consensus[] tmp6 = new Consensus[6];
 236     tmp6[0] = conses[3]; // -
 237     tmp6[1] = conses[29]; // D
 238     tmp6[2] = conses[10]; // E
 239     tmp6[3] = conses[6]; // QE
 240     tmp6[4] = conses[19]; // Q
 241     tmp6[5] = conses[2]; // DE
 242     colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
 243
 244     Consensus[] tmp7 = new Consensus[5];
 245     tmp7[0] = conses[3]; // -
 246     tmp7[1] = conses[29]; // D
 247     tmp7[2] = conses[10]; // E
 248     tmp7[3] = conses[17]; // N
 249     tmp7[4] = conses[2]; // DE
 250     colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
 251
 252     // Now attach the ConsensusColours to the residue letters
 253     residueColour = new ConsensusColour[20];
 254     residueColour[0] = colours[0]; // A
 255     residueColour[1] = colours[4]; // R
 256     residueColour[2] = colours[2]; // N
 257     residueColour[3] = colours[6]; // D
 258     residueColour[4] = colours[0]; // C
 259     residueColour[5] = colours[3]; // Q
 260     residueColour[6] = colours[5]; // E
 261     residueColour[7] = colours[7]; // G
 262     residueColour[8] = colours[10]; // H
 263     residueColour[9] = colours[0]; // I
 264     residueColour[10] = colours[0]; // L
 265     residueColour[11] = colours[4]; // K
 266     residueColour[12] = colours[0]; // M
 267     residueColour[13] = colours[0]; // F
 268     residueColour[14] = colours[8]; // P
 269     residueColour[15] = colours[1]; // S
 270     residueColour[16] = colours[1]; // T
 271     residueColour[17] = colours[0]; // W
 272     residueColour[18] = colours[10]; // Y
 273     residueColour[19] = colours[0]; // V
 274   }
 275
 276   @Override
 277   public Color findColour(char c)
 278   {
 279     return Color.pink;
 280   }
 281
 282   @Override
 283   protected synchronized Color findColour(char c, int j, SequenceI seq)
 284   {
 285     // TODO why the test for includeGaps here?
 286     if (cons2.length <= j || Comparison.isGap(c)
 287     /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
 288     {
 289       return Color.white;
 290     }
 291
 292     int i = ResidueProperties.aaIndex[c];
 293
 294     Color colour = Color.white;
 295
 296     if (i > 19)
 297     {
 298       return colour;
 299     }
 300
 301     for (int k = 0; k < residueColour[i].cons.length; k++)
 302     {
 303       if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
 304       {
 305         colour = residueColour[i].c;
 306       }
 307     }
 308
 309     if (i == 4)
 310     {
 311       /*
 312        * override to colour C pink if >85% conserved
 313        */
 314       if (conses[27].isConserved(cons2, j, size, includeGaps))
 315       {
 316         colour = ClustalColour.PINK.colour;
 317       }
 318     }
 319
 320     return colour;
 321   }
 322
 323   /**
 324    * @return the includeGaps
 325    */
 326   protected boolean isIncludeGaps()
 327   {
 328     return includeGaps;
 329   }
 330
 331   /**
 332    * @param includeGaps
 333    *          the includeGaps to set
 334    */
 335   protected void setIncludeGaps(boolean includeGaps)
 336   {
 337     this.includeGaps = includeGaps;
 338   }
 339
 340   @Override
 341   public ColourSchemeI getInstance(AlignViewportI view,
 342           AnnotatedCollectionI sg)
 343   {
 344     ClustalxColourScheme css = new ClustalxColourScheme(sg,
 345             view == null ? null : view.getHiddenRepSequences());
 346     css.includeGaps = includeGaps;
 347     return css;
 348   }
 349
 350   @Override
 351   public boolean isPeptideSpecific()
 352   {
 353     return true;
 354   }
 355
 356   @Override
 357   public String getSchemeName()
 358   {
 359     return JalviewColourScheme.Clustal.toString();
 360   }
 361
 362   @Override
 363   public boolean isSimple()
 364   {
 365     return false;
 366   }
 367   public String toRuleRep()
 368   {
 369     makeColours();
 370     HashMap<String, String> cols=new HashMap();
 371     for (String res:ResidueProperties.aa) {
 372       StringBuilder sb = new StringBuilder();
 373
 374       int rnum=ResidueProperties.aaIndex[res.charAt(0)];
 375       if (rnum<0 || rnum>=residueColour.length)
 376       {
 377         continue;
 378       }
 379
 380       ConsensusColour cc = residueColour[rnum];
 381       if (cc==null)
 382       {
 383         continue;
 384       }
 385       //sb.append("Residue "+res+" ("+rnum+")");
 386       //sb.append("\t");
 387       sb.append(cc.c.toString());
 388       double f=0;
 389       sb.append("\t");
 390       for (Consensus cons: cc.cons) {
 391         if (cons.threshold==0 || f!=cons.threshold)
 392         {
 393           if (f!=0)
 394           {
 395
 396               sb.append("}, {");
 397           } else {
 398           sb.append("{");
 399           }
 400         sb.append(cons.threshold);
 401         sb.append(",");
 402         f=cons.threshold;
 403         } else {
 404           sb.append(",");
 405         }
 406         sb.append(cons.maskstr);
 407       }
 408       sb.append("}");
 409       String clxrep=sb.toString();
 410       String xres = cols.get(clxrep);
 411       if (xres==null) { xres = "";}
 412       xres+=res;
 413       cols.put(clxrep, xres);
 414     }
 415     StringBuilder sb = new StringBuilder();
 416     for (String clxrep:cols.keySet())
 417     {
 418       sb.append(cols.get(clxrep));
 419       sb.append("\t");
 420       sb.append(clxrep);
 421       sb.append("\n");
 422
 423     }
 424     return sb.toString();
 425   }
 426 }