src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 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.Hashtable;
  29 import java.util.List;
  30 import java.util.Map;
  31 import java.util.Vector;
  32
  33 public class ClustalxColourScheme extends ResidueColourScheme // implements
  34 // IParameterizable
  35 {
  36   public static Hashtable colhash = new Hashtable();
  37
  38   Hashtable[] cons;
  39
  40   int[][] cons2;
  41
  42   ConsensusColour[] colours;
  43
  44   ConsensusColour[] ResidueColour;
  45
  46   int size;
  47
  48   Consensus[] conses = new Consensus[32];
  49
  50   Vector colourTable = new Vector();
  51
  52   private boolean includeGaps = true;
  53
  54   {
  55     colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
  56     colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
  57     colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
  58     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
  59     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
  60     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
  61     colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
  62     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
  63   }
  64
  65   public ClustalxColourScheme(AnnotatedCollectionI alignment,
  66           Map<SequenceI, SequenceCollectionI> hiddenReps)
  67   {
  68     alignmentChanged(alignment, hiddenReps);
  69   }
  70
  71   public void alignmentChanged(AnnotatedCollectionI alignment,
  72           Map<SequenceI, SequenceCollectionI> hiddenReps)
  73   {
  74     int maxWidth = alignment.getWidth();
  75     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
  76     cons2 = new int[maxWidth][24];
  77     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
  78     // get the current setting of the
  79     // includeGaps param.
  80     int start = 0;
  81
  82     // Initialize the array
  83     for (int j = 0; j < 24; j++)
  84     {
  85       for (int i = 0; i < maxWidth; i++)
  86       {
  87         cons2[i][j] = 0;
  88       }
  89     }
  90
  91     int res;
  92     int i;
  93     int j = 0;
  94     char[] seq;
  95
  96     for (SequenceI sq : seqs)
  97     {
  98       seq = sq.getSequence();
  99
 100       int end_j = seq.length - 1;
 101
 102       for (i = start; i <= end_j; i++)
 103       {
 104         if ((seq.length - 1) < i)
 105         {
 106           res = 23;
 107         }
 108         else
 109         {
 110           res = ResidueProperties.aaIndex[seq[i]];
 111         }
 112
 113         cons2[i][res]++;
 114       }
 115
 116       j++;
 117     }
 118
 119     this.size = seqs.size();
 120     makeColours();
 121   }
 122
 123   public void makeColours()
 124   {
 125     conses[0] = new Consensus("WLVIMAFCYHP", 60);
 126     conses[1] = new Consensus("WLVIMAFCYHP", 80);
 127     conses[2] = new Consensus("ED", 50);
 128     conses[3] = new Consensus("KR", 60);
 129     conses[4] = new Consensus("G", 50);
 130     conses[5] = new Consensus("N", 50);
 131     conses[6] = new Consensus("QE", 50);
 132     conses[7] = new Consensus("P", 50);
 133     conses[8] = new Consensus("TS", 50);
 134
 135     conses[26] = new Consensus("A", 85);
 136     conses[27] = new Consensus("C", 85);
 137     conses[10] = new Consensus("E", 85);
 138     conses[11] = new Consensus("F", 85);
 139     conses[12] = new Consensus("G", 85);
 140     conses[13] = new Consensus("H", 85);
 141     conses[14] = new Consensus("I", 85);
 142     conses[15] = new Consensus("L", 85);
 143     conses[16] = new Consensus("M", 85);
 144     conses[17] = new Consensus("N", 85);
 145     conses[18] = new Consensus("P", 85);
 146     conses[19] = new Consensus("Q", 85);
 147     conses[20] = new Consensus("R", 85);
 148     conses[21] = new Consensus("S", 85);
 149     conses[22] = new Consensus("T", 85);
 150     conses[23] = new Consensus("V", 85);
 151     conses[24] = new Consensus("W", 85);
 152     conses[25] = new Consensus("Y", 85);
 153     conses[28] = new Consensus("K", 85);
 154     conses[29] = new Consensus("D", 85);
 155
 156     conses[30] = new Consensus("G", 0);
 157     conses[31] = new Consensus("P", 0);
 158
 159     // We now construct the colours
 160     colours = new ConsensusColour[11];
 161
 162     Consensus[] tmp8 = new Consensus[1];
 163     tmp8[0] = conses[30]; // G
 164     colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 165
 166     Consensus[] tmp9 = new Consensus[1];
 167     tmp9[0] = conses[31]; // P
 168     colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 169
 170     Consensus[] tmp10 = new Consensus[1];
 171     tmp10[0] = conses[27]; // C
 172     colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 173
 174     Consensus[] tmp1 = new Consensus[14];
 175     tmp1[0] = conses[0]; // %
 176     tmp1[1] = conses[1]; // #
 177     tmp1[2] = conses[26]; // A
 178     tmp1[3] = conses[27]; // C
 179     tmp1[4] = conses[11]; // F
 180     tmp1[5] = conses[13]; // H
 181     tmp1[6] = conses[14]; // I
 182     tmp1[7] = conses[15]; // L
 183     tmp1[8] = conses[16]; // M
 184     tmp1[9] = conses[23]; // V
 185     tmp1[10] = conses[24]; // W
 186     tmp1[11] = conses[25]; // Y
 187     tmp1[12] = conses[18]; // P
 188     tmp1[13] = conses[19]; // p
 189     colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
 190
 191     colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 192
 193     Consensus[] tmp2 = new Consensus[5];
 194     tmp2[0] = conses[8]; // t
 195     tmp2[1] = conses[21]; // S
 196     tmp2[2] = conses[22]; // T
 197     tmp2[3] = conses[0]; // %
 198     tmp2[4] = conses[1]; // #
 199     colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 200
 201     Consensus[] tmp3 = new Consensus[3];
 202
 203     tmp3[0] = conses[17]; // N
 204     tmp3[1] = conses[29]; // D
 205     tmp3[2] = conses[5]; // n
 206     colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 207
 208     Consensus[] tmp4 = new Consensus[6];
 209     tmp4[0] = conses[6]; // q = QE
 210     tmp4[1] = conses[19]; // Q
 211     tmp4[2] = conses[22]; // E
 212     tmp4[3] = conses[3]; // +
 213     tmp4[4] = conses[28]; // K
 214     tmp4[5] = conses[20]; // R
 215     colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 216
 217     Consensus[] tmp5 = new Consensus[4];
 218     tmp5[0] = conses[3]; // +
 219     tmp5[1] = conses[28]; // K
 220     tmp5[2] = conses[20]; // R
 221     tmp5[3] = conses[19]; // Q
 222     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 223
 224     Consensus[] tmp6 = new Consensus[6];
 225     tmp6[0] = conses[3]; // -
 226     tmp6[1] = conses[29]; // D
 227     tmp6[2] = conses[10]; // E
 228     tmp6[3] = conses[6]; // QE
 229     tmp6[4] = conses[19]; // Q
 230     tmp6[5] = conses[2]; // DE
 231     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 232
 233     Consensus[] tmp7 = new Consensus[5];
 234     tmp7[0] = conses[3]; // -
 235     tmp7[1] = conses[29]; // D
 236     tmp7[2] = conses[10]; // E
 237     tmp7[3] = conses[17]; // N
 238     tmp7[4] = conses[2]; // DE
 239     colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 240
 241     // Now attach the ConsensusColours to the residue letters
 242     ResidueColour = new ConsensusColour[20];
 243     ResidueColour[0] = colours[0]; // A
 244     ResidueColour[1] = colours[4]; // R
 245     ResidueColour[2] = colours[2]; // N
 246     ResidueColour[3] = colours[6]; // D
 247     ResidueColour[4] = colours[0]; // C
 248     ResidueColour[5] = colours[3]; // Q
 249     ResidueColour[6] = colours[5]; // E
 250     ResidueColour[7] = colours[7]; // G
 251     ResidueColour[8] = colours[10]; // H
 252     ResidueColour[9] = colours[0]; // I
 253     ResidueColour[10] = colours[0]; // L
 254     ResidueColour[11] = colours[4]; // K
 255     ResidueColour[12] = colours[0]; // M
 256     ResidueColour[13] = colours[0]; // F
 257     ResidueColour[14] = colours[8]; // P
 258     ResidueColour[15] = colours[1]; // S
 259     ResidueColour[16] = colours[1]; // T
 260     ResidueColour[17] = colours[0]; // W
 261     ResidueColour[18] = colours[10]; // Y
 262     ResidueColour[19] = colours[0]; // V
 263   }
 264
 265   @Override
 266   public Color findColour(char c)
 267   {
 268     return Color.pink;
 269   }
 270
 271   @Override
 272   public Color findColour(char c, int j, SequenceI seq)
 273   {
 274     Color currentColour;
 275
 276     if (cons2.length <= j
 277             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 278     {
 279       return Color.white;
 280     }
 281
 282     int i = ResidueProperties.aaIndex[c];
 283
 284     currentColour = Color.white;
 285
 286     if (i > 19)
 287     {
 288       return currentColour;
 289     }
 290
 291     for (int k = 0; k < ResidueColour[i].conses.length; k++)
 292     {
 293       if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
 294               includeGaps))
 295       {
 296         currentColour = ResidueColour[i].c;
 297       }
 298     }
 299
 300     if (i == 4)
 301     {
 302       if (conses[27].isConserved(cons2, j, size, includeGaps))
 303       {
 304         currentColour = (Color) colhash.get("PINK");
 305       }
 306     }
 307
 308     if (conservationColouring)
 309     {
 310       currentColour = applyConservation(currentColour, j);
 311     }
 312
 313     return currentColour;
 314   }
 315
 316   /**
 317    * @return the includeGaps
 318    */
 319   protected boolean isIncludeGaps()
 320   {
 321     return includeGaps;
 322   }
 323
 324   /**
 325    * @param includeGaps
 326    *          the includeGaps to set
 327    */
 328   protected void setIncludeGaps(boolean includeGaps)
 329   {
 330     this.includeGaps = includeGaps;
 331   }
 332
 333   @Override
 334   public ColourSchemeI applyTo(AnnotatedCollectionI sg,
 335           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
 336   {
 337     ClustalxColourScheme css = new ClustalxColourScheme(sg,
 338             hiddenRepSequences);
 339     css.includeGaps = includeGaps;
 340     return css;
 341   }
 342 }
 343
 344 class ConsensusColour
 345 {
 346   Consensus[] conses;
 347
 348   Color c;
 349
 350   public ConsensusColour(Color c, Consensus[] conses)
 351   {
 352     this.conses = conses;
 353
 354     // this.list = list;
 355     this.c = c;
 356   }
 357 }