src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 jalview.datamodel.AnnotatedCollectionI;
  21 import jalview.datamodel.SequenceCollectionI;
  22 import jalview.datamodel.SequenceI;
  23
  24 import java.awt.Color;
  25 import java.util.Hashtable;
  26 import java.util.List;
  27 import java.util.Map;
  28 import java.util.Vector;
  29
  30 public class ClustalxColourScheme extends ResidueColourScheme // implements
  31 // IParameterizable
  32 {
  33   public static Hashtable colhash = new Hashtable();
  34
  35   Hashtable[] cons;
  36
  37   int[][] cons2;
  38
  39   ConsensusColour[] colours;
  40
  41   ConsensusColour[] ResidueColour;
  42
  43   int size;
  44
  45   Consensus[] conses = new Consensus[32];
  46
  47   Vector colourTable = new Vector();
  48
  49   private boolean includeGaps = true;
  50
  51   {
  52     colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
  53     colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
  54     colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
  55     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
  56     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
  57     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
  58     colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
  59     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
  60   }
  61
  62   public ClustalxColourScheme(AnnotatedCollectionI alignment,
  63           Map<SequenceI, SequenceCollectionI> hiddenReps)
  64   {
  65     alignmentChanged(alignment, hiddenReps);
  66   }
  67
  68   public void alignmentChanged(AnnotatedCollectionI alignment,
  69           Map<SequenceI, SequenceCollectionI> hiddenReps)
  70   {
  71     int maxWidth = alignment.getWidth();
  72     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
  73     cons2 = new int[maxWidth][24];
  74     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
  75     // get the current setting of the
  76     // includeGaps param.
  77     int start = 0;
  78
  79     // Initialize the array
  80     for (int j = 0; j < 24; j++)
  81     {
  82       for (int i = 0; i < maxWidth; i++)
  83       {
  84         cons2[i][j] = 0;
  85       }
  86     }
  87
  88     int res;
  89     int i;
  90     int j = 0;
  91     char[] seq;
  92
  93     for (SequenceI sq : seqs)
  94     {
  95       seq = sq.getSequence();
  96
  97       int end_j = seq.length - 1;
  98
  99       for (i = start; i <= end_j; i++)
 100       {
 101         if ((seq.length - 1) < i)
 102         {
 103           res = 23;
 104         }
 105         else
 106         {
 107           res = ResidueProperties.aaIndex[seq[i]];
 108         }
 109
 110         cons2[i][res]++;
 111       }
 112
 113       j++;
 114     }
 115
 116     this.size = seqs.size();
 117     makeColours();
 118   }
 119
 120   public void makeColours()
 121   {
 122     conses[0] = new Consensus("WLVIMAFCYHP", 60);
 123     conses[1] = new Consensus("WLVIMAFCYHP", 80);
 124     conses[2] = new Consensus("ED", 50);
 125     conses[3] = new Consensus("KR", 60);
 126     conses[4] = new Consensus("G", 50);
 127     conses[5] = new Consensus("N", 50);
 128     conses[6] = new Consensus("QE", 50);
 129     conses[7] = new Consensus("P", 50);
 130     conses[8] = new Consensus("TS", 50);
 131
 132     conses[26] = new Consensus("A", 85);
 133     conses[27] = new Consensus("C", 85);
 134     conses[10] = new Consensus("E", 85);
 135     conses[11] = new Consensus("F", 85);
 136     conses[12] = new Consensus("G", 85);
 137     conses[13] = new Consensus("H", 85);
 138     conses[14] = new Consensus("I", 85);
 139     conses[15] = new Consensus("L", 85);
 140     conses[16] = new Consensus("M", 85);
 141     conses[17] = new Consensus("N", 85);
 142     conses[18] = new Consensus("P", 85);
 143     conses[19] = new Consensus("Q", 85);
 144     conses[20] = new Consensus("R", 85);
 145     conses[21] = new Consensus("S", 85);
 146     conses[22] = new Consensus("T", 85);
 147     conses[23] = new Consensus("V", 85);
 148     conses[24] = new Consensus("W", 85);
 149     conses[25] = new Consensus("Y", 85);
 150     conses[28] = new Consensus("K", 85);
 151     conses[29] = new Consensus("D", 85);
 152
 153     conses[30] = new Consensus("G", 0);
 154     conses[31] = new Consensus("P", 0);
 155
 156     // We now construct the colours
 157     colours = new ConsensusColour[11];
 158
 159     Consensus[] tmp8 = new Consensus[1];
 160     tmp8[0] = conses[30]; // G
 161     colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 162
 163     Consensus[] tmp9 = new Consensus[1];
 164     tmp9[0] = conses[31]; // P
 165     colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 166
 167     Consensus[] tmp10 = new Consensus[1];
 168     tmp10[0] = conses[27]; // C
 169     colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 170
 171     Consensus[] tmp1 = new Consensus[14];
 172     tmp1[0] = conses[0]; // %
 173     tmp1[1] = conses[1]; // #
 174     tmp1[2] = conses[26]; // A
 175     tmp1[3] = conses[27]; // C
 176     tmp1[4] = conses[11]; // F
 177     tmp1[5] = conses[13]; // H
 178     tmp1[6] = conses[14]; // I
 179     tmp1[7] = conses[15]; // L
 180     tmp1[8] = conses[16]; // M
 181     tmp1[9] = conses[23]; // V
 182     tmp1[10] = conses[24]; // W
 183     tmp1[11] = conses[25]; // Y
 184     tmp1[12] = conses[18]; // P
 185     tmp1[13] = conses[19]; // p
 186     colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
 187
 188     colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 189
 190     Consensus[] tmp2 = new Consensus[5];
 191     tmp2[0] = conses[8]; // t
 192     tmp2[1] = conses[21]; // S
 193     tmp2[2] = conses[22]; // T
 194     tmp2[3] = conses[0]; // %
 195     tmp2[4] = conses[1]; // #
 196     colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 197
 198     Consensus[] tmp3 = new Consensus[3];
 199
 200     tmp3[0] = conses[17]; // N
 201     tmp3[1] = conses[29]; // D
 202     tmp3[2] = conses[5]; // n
 203     colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 204
 205     Consensus[] tmp4 = new Consensus[6];
 206     tmp4[0] = conses[6]; // q = QE
 207     tmp4[1] = conses[19]; // Q
 208     tmp4[2] = conses[22]; // E
 209     tmp4[3] = conses[3]; // +
 210     tmp4[4] = conses[28]; // K
 211     tmp4[5] = conses[20]; // R
 212     colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 213
 214     Consensus[] tmp5 = new Consensus[4];
 215     tmp5[0] = conses[3]; // +
 216     tmp5[1] = conses[28]; // K
 217     tmp5[2] = conses[20]; // R
 218     tmp5[3] = conses[19]; // Q
 219     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 220
 221     Consensus[] tmp6 = new Consensus[6];
 222     tmp6[0] = conses[3]; // -
 223     tmp6[1] = conses[29]; // D
 224     tmp6[2] = conses[10]; // E
 225     tmp6[3] = conses[6]; // QE
 226     tmp6[4] = conses[19]; // Q
 227     tmp6[5] = conses[2]; // DE
 228     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 229
 230     Consensus[] tmp7 = new Consensus[5];
 231     tmp7[0] = conses[3]; // -
 232     tmp7[1] = conses[29]; // D
 233     tmp7[2] = conses[10]; // E
 234     tmp7[3] = conses[17]; // N
 235     tmp7[4] = conses[2]; // DE
 236     colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 237
 238     // Now attach the ConsensusColours to the residue letters
 239     ResidueColour = new ConsensusColour[20];
 240     ResidueColour[0] = colours[0]; // A
 241     ResidueColour[1] = colours[4]; // R
 242     ResidueColour[2] = colours[2]; // N
 243     ResidueColour[3] = colours[6]; // D
 244     ResidueColour[4] = colours[0]; // C
 245     ResidueColour[5] = colours[3]; // Q
 246     ResidueColour[6] = colours[5]; // E
 247     ResidueColour[7] = colours[7]; // G
 248     ResidueColour[8] = colours[10]; // H
 249     ResidueColour[9] = colours[0]; // I
 250     ResidueColour[10] = colours[0]; // L
 251     ResidueColour[11] = colours[4]; // K
 252     ResidueColour[12] = colours[0]; // M
 253     ResidueColour[13] = colours[0]; // F
 254     ResidueColour[14] = colours[8]; // P
 255     ResidueColour[15] = colours[1]; // S
 256     ResidueColour[16] = colours[1]; // T
 257     ResidueColour[17] = colours[0]; // W
 258     ResidueColour[18] = colours[10]; // Y
 259     ResidueColour[19] = colours[0]; // V
 260   }
 261
 262   @Override
 263   public Color findColour(char c)
 264   {
 265     return Color.pink;
 266   }
 267
 268   @Override
 269   public Color findColour(char c, int j, SequenceI seq)
 270   {
 271     Color currentColour;
 272
 273     if (cons2.length <= j
 274             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 275     {
 276       return Color.white;
 277     }
 278
 279     int i = ResidueProperties.aaIndex[c];
 280
 281     currentColour = Color.white;
 282
 283     if (i > 19)
 284     {
 285       return currentColour;
 286     }
 287
 288     for (int k = 0; k < ResidueColour[i].conses.length; k++)
 289     {
 290       if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
 291               includeGaps))
 292       {
 293         currentColour = ResidueColour[i].c;
 294       }
 295     }
 296
 297     if (i == 4)
 298     {
 299       if (conses[27].isConserved(cons2, j, size, includeGaps))
 300       {
 301         currentColour = (Color) colhash.get("PINK");
 302       }
 303     }
 304
 305     if (conservationColouring)
 306     {
 307       currentColour = applyConservation(currentColour, j);
 308     }
 309
 310     return currentColour;
 311   }
 312
 313   /**
 314    * @return the includeGaps
 315    */
 316   protected boolean isIncludeGaps()
 317   {
 318     return includeGaps;
 319   }
 320
 321   /**
 322    * @param includeGaps
 323    *          the includeGaps to set
 324    */
 325   protected void setIncludeGaps(boolean includeGaps)
 326   {
 327     this.includeGaps = includeGaps;
 328   }
 329 }
 330
 331 class ConsensusColour
 332 {
 333   Consensus[] conses;
 334
 335   Color c;
 336
 337   public ConsensusColour(Color c, Consensus[] conses)
 338   {
 339     this.conses = conses;
 340
 341     // this.list = list;
 342     this.c = c;
 343   }
 344 }