src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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, Map<SequenceI, SequenceCollectionI> hiddenReps)
  63   {
  64     alignmentChanged(alignment,hiddenReps);
  65   }
  66   public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps) {
  67     int maxWidth=alignment.getWidth();
  68     List<SequenceI> seqs=alignment.getSequences(hiddenReps);
  69     cons2 = new int[maxWidth][24];
  70     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
  71     // get the current setting of the
  72     // includeGaps param.
  73     int start = 0;
  74
  75     // Initialize the array
  76     for (int j = 0; j < 24; j++)
  77     {
  78       for (int i = 0; i < maxWidth; i++)
  79       {
  80         cons2[i][j] = 0;
  81       }
  82     }
  83
  84     int res;
  85     int i;
  86     int j = 0;
  87     char[] seq;
  88
  89     for (SequenceI sq: seqs)
  90     {
  91       seq = sq.getSequence();
  92
  93       int end_j = seq.length - 1;
  94
  95       for (i = start; i <= end_j; i++)
  96       {
  97         if ((seq.length - 1) < i)
  98         {
  99           res = 23;
 100         }
 101         else
 102         {
 103           res = ResidueProperties.aaIndex[seq[i]];
 104         }
 105
 106         cons2[i][res]++;
 107       }
 108
 109       j++;
 110     }
 111
 112     this.size = seqs.size();
 113     makeColours();
 114   }
 115
 116   public void makeColours()
 117   {
 118     conses[0] = new Consensus("WLVIMAFCYHP", 60);
 119     conses[1] = new Consensus("WLVIMAFCYHP", 80);
 120     conses[2] = new Consensus("ED", 50);
 121     conses[3] = new Consensus("KR", 60);
 122     conses[4] = new Consensus("G", 50);
 123     conses[5] = new Consensus("N", 50);
 124     conses[6] = new Consensus("QE", 50);
 125     conses[7] = new Consensus("P", 50);
 126     conses[8] = new Consensus("TS", 50);
 127
 128     conses[26] = new Consensus("A", 85);
 129     conses[27] = new Consensus("C", 85);
 130     conses[10] = new Consensus("E", 85);
 131     conses[11] = new Consensus("F", 85);
 132     conses[12] = new Consensus("G", 85);
 133     conses[13] = new Consensus("H", 85);
 134     conses[14] = new Consensus("I", 85);
 135     conses[15] = new Consensus("L", 85);
 136     conses[16] = new Consensus("M", 85);
 137     conses[17] = new Consensus("N", 85);
 138     conses[18] = new Consensus("P", 85);
 139     conses[19] = new Consensus("Q", 85);
 140     conses[20] = new Consensus("R", 85);
 141     conses[21] = new Consensus("S", 85);
 142     conses[22] = new Consensus("T", 85);
 143     conses[23] = new Consensus("V", 85);
 144     conses[24] = new Consensus("W", 85);
 145     conses[25] = new Consensus("Y", 85);
 146     conses[28] = new Consensus("K", 85);
 147     conses[29] = new Consensus("D", 85);
 148
 149     conses[30] = new Consensus("G", 0);
 150     conses[31] = new Consensus("P", 0);
 151
 152     // We now construct the colours
 153     colours = new ConsensusColour[11];
 154
 155     Consensus[] tmp8 = new Consensus[1];
 156     tmp8[0] = conses[30]; // G
 157     colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 158
 159     Consensus[] tmp9 = new Consensus[1];
 160     tmp9[0] = conses[31]; // P
 161     colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 162
 163     Consensus[] tmp10 = new Consensus[1];
 164     tmp10[0] = conses[27]; // C
 165     colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 166
 167     Consensus[] tmp1 = new Consensus[14];
 168     tmp1[0] = conses[0]; // %
 169     tmp1[1] = conses[1]; // #
 170     tmp1[2] = conses[26]; // A
 171     tmp1[3] = conses[27]; // C
 172     tmp1[4] = conses[11]; // F
 173     tmp1[5] = conses[13]; // H
 174     tmp1[6] = conses[14]; // I
 175     tmp1[7] = conses[15]; // L
 176     tmp1[8] = conses[16]; // M
 177     tmp1[9] = conses[23]; // V
 178     tmp1[10] = conses[24]; // W
 179     tmp1[11] = conses[25]; // Y
 180     tmp1[12] = conses[18]; // P
 181     tmp1[13] = conses[19]; // p
 182     colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
 183
 184     colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 185
 186     Consensus[] tmp2 = new Consensus[5];
 187     tmp2[0] = conses[8]; // t
 188     tmp2[1] = conses[21]; // S
 189     tmp2[2] = conses[22]; // T
 190     tmp2[3] = conses[0]; // %
 191     tmp2[4] = conses[1]; // #
 192     colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 193
 194     Consensus[] tmp3 = new Consensus[3];
 195
 196     tmp3[0] = conses[17]; // N
 197     tmp3[1] = conses[29]; // D
 198     tmp3[2] = conses[5]; // n
 199     colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 200
 201     Consensus[] tmp4 = new Consensus[6];
 202     tmp4[0] = conses[6]; // q = QE
 203     tmp4[1] = conses[19]; // Q
 204     tmp4[2] = conses[22]; // E
 205     tmp4[3] = conses[3]; // +
 206     tmp4[4] = conses[28]; // K
 207     tmp4[5] = conses[20]; // R
 208     colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 209
 210     Consensus[] tmp5 = new Consensus[4];
 211     tmp5[0] = conses[3]; // +
 212     tmp5[1] = conses[28]; // K
 213     tmp5[2] = conses[20]; // R
 214     tmp5[3] = conses[19]; // Q
 215     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 216
 217     Consensus[] tmp6 = new Consensus[6];
 218     tmp6[0] = conses[3]; // -
 219     tmp6[1] = conses[29]; // D
 220     tmp6[2] = conses[10]; // E
 221     tmp6[3] = conses[6]; // QE
 222     tmp6[4] = conses[19]; // Q
 223     tmp6[5] = conses[2]; // DE
 224     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 225
 226     Consensus[] tmp7 = new Consensus[5];
 227     tmp7[0] = conses[3]; // -
 228     tmp7[1] = conses[29]; // D
 229     tmp7[2] = conses[10]; // E
 230     tmp7[3] = conses[17]; // N
 231     tmp7[4] = conses[2]; // DE
 232     colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 233
 234     // Now attach the ConsensusColours to the residue letters
 235     ResidueColour = new ConsensusColour[20];
 236     ResidueColour[0] = colours[0]; // A
 237     ResidueColour[1] = colours[4]; // R
 238     ResidueColour[2] = colours[2]; // N
 239     ResidueColour[3] = colours[6]; // D
 240     ResidueColour[4] = colours[0]; // C
 241     ResidueColour[5] = colours[3]; // Q
 242     ResidueColour[6] = colours[5]; // E
 243     ResidueColour[7] = colours[7]; // G
 244     ResidueColour[8] = colours[10]; // H
 245     ResidueColour[9] = colours[0]; // I
 246     ResidueColour[10] = colours[0]; // L
 247     ResidueColour[11] = colours[4]; // K
 248     ResidueColour[12] = colours[0]; // M
 249     ResidueColour[13] = colours[0]; // F
 250     ResidueColour[14] = colours[8]; // P
 251     ResidueColour[15] = colours[1]; // S
 252     ResidueColour[16] = colours[1]; // T
 253     ResidueColour[17] = colours[0]; // W
 254     ResidueColour[18] = colours[10]; // Y
 255     ResidueColour[19] = colours[0]; // V
 256   }
 257
 258   @Override
 259   public Color findColour(char c)
 260   {
 261     return Color.pink;
 262   }
 263
 264   @Override
 265   public Color findColour(char c, int j, SequenceI seq)
 266   {
 267     Color currentColour;
 268
 269     if (cons2.length <= j
 270             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 271     {
 272       return Color.white;
 273     }
 274
 275     int i = ResidueProperties.aaIndex[c];
 276
 277     currentColour = Color.white;
 278
 279     if (i > 19)
 280     {
 281       return currentColour;
 282     }
 283
 284     for (int k = 0; k < ResidueColour[i].conses.length; k++)
 285     {
 286       if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
 287               includeGaps))
 288       {
 289         currentColour = ResidueColour[i].c;
 290       }
 291     }
 292
 293     if (i == 4)
 294     {
 295       if (conses[27].isConserved(cons2, j, size, includeGaps))
 296       {
 297         currentColour = (Color) colhash.get("PINK");
 298       }
 299     }
 300
 301     if (conservationColouring)
 302     {
 303       currentColour = applyConservation(currentColour, j);
 304     }
 305
 306     return currentColour;
 307   }
 308
 309   /**
 310    * @return the includeGaps
 311    */
 312   protected boolean isIncludeGaps()
 313   {
 314     return includeGaps;
 315   }
 316
 317   /**
 318    * @param includeGaps
 319    *          the includeGaps to set
 320    */
 321   protected void setIncludeGaps(boolean includeGaps)
 322   {
 323     this.includeGaps = includeGaps;
 324   }
 325 }
 326
 327 class ConsensusColour
 328 {
 329   Consensus[] conses;
 330
 331   Color c;
 332
 333   public ConsensusColour(Color c, Consensus[] conses)
 334   {
 335     this.conses = conses;
 336
 337     // this.list = list;
 338     this.c = c;
 339   }
 340 }