src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.schemes;
  20
  21 import jalview.datamodel.AnnotatedCollectionI;
  22 import jalview.datamodel.SequenceCollectionI;
  23 import jalview.datamodel.SequenceI;
  24
  25 import java.awt.Color;
  26 import java.util.Hashtable;
  27 import java.util.List;
  28 import java.util.Map;
  29 import java.util.Vector;
  30
  31 public class ClustalxColourScheme extends ResidueColourScheme // implements
  32 // IParameterizable
  33 {
  34   public static Hashtable colhash = new Hashtable();
  35
  36   Hashtable[] cons;
  37
  38   int[][] cons2;
  39
  40   ConsensusColour[] colours;
  41
  42   ConsensusColour[] ResidueColour;
  43
  44   int size;
  45
  46   Consensus[] conses = new Consensus[32];
  47
  48   Vector colourTable = new Vector();
  49
  50   private boolean includeGaps = true;
  51
  52   {
  53     colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
  54     colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
  55     colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
  56     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
  57     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
  58     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
  59     colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
  60     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
  61   }
  62
  63   public ClustalxColourScheme(AnnotatedCollectionI alignment,
  64           Map<SequenceI, SequenceCollectionI> hiddenReps)
  65   {
  66     alignmentChanged(alignment, hiddenReps);
  67   }
  68
  69   public void alignmentChanged(AnnotatedCollectionI alignment,
  70           Map<SequenceI, SequenceCollectionI> hiddenReps)
  71   {
  72     int maxWidth = alignment.getWidth();
  73     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
  74     cons2 = new int[maxWidth][24];
  75     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
  76     // get the current setting of the
  77     // includeGaps param.
  78     int start = 0;
  79
  80     // Initialize the array
  81     for (int j = 0; j < 24; j++)
  82     {
  83       for (int i = 0; i < maxWidth; i++)
  84       {
  85         cons2[i][j] = 0;
  86       }
  87     }
  88
  89     int res;
  90     int i;
  91     int j = 0;
  92     char[] seq;
  93
  94     for (SequenceI sq : seqs)
  95     {
  96       seq = sq.getSequence();
  97
  98       int end_j = seq.length - 1;
  99
 100       for (i = start; i <= end_j; i++)
 101       {
 102         if ((seq.length - 1) < i)
 103         {
 104           res = 23;
 105         }
 106         else
 107         {
 108           res = ResidueProperties.aaIndex[seq[i]];
 109         }
 110
 111         cons2[i][res]++;
 112       }
 113
 114       j++;
 115     }
 116
 117     this.size = seqs.size();
 118     makeColours();
 119   }
 120
 121   public void makeColours()
 122   {
 123     conses[0] = new Consensus("WLVIMAFCYHP", 60);
 124     conses[1] = new Consensus("WLVIMAFCYHP", 80);
 125     conses[2] = new Consensus("ED", 50);
 126     conses[3] = new Consensus("KR", 60);
 127     conses[4] = new Consensus("G", 50);
 128     conses[5] = new Consensus("N", 50);
 129     conses[6] = new Consensus("QE", 50);
 130     conses[7] = new Consensus("P", 50);
 131     conses[8] = new Consensus("TS", 50);
 132
 133     conses[26] = new Consensus("A", 85);
 134     conses[27] = new Consensus("C", 85);
 135     conses[10] = new Consensus("E", 85);
 136     conses[11] = new Consensus("F", 85);
 137     conses[12] = new Consensus("G", 85);
 138     conses[13] = new Consensus("H", 85);
 139     conses[14] = new Consensus("I", 85);
 140     conses[15] = new Consensus("L", 85);
 141     conses[16] = new Consensus("M", 85);
 142     conses[17] = new Consensus("N", 85);
 143     conses[18] = new Consensus("P", 85);
 144     conses[19] = new Consensus("Q", 85);
 145     conses[20] = new Consensus("R", 85);
 146     conses[21] = new Consensus("S", 85);
 147     conses[22] = new Consensus("T", 85);
 148     conses[23] = new Consensus("V", 85);
 149     conses[24] = new Consensus("W", 85);
 150     conses[25] = new Consensus("Y", 85);
 151     conses[28] = new Consensus("K", 85);
 152     conses[29] = new Consensus("D", 85);
 153
 154     conses[30] = new Consensus("G", 0);
 155     conses[31] = new Consensus("P", 0);
 156
 157     // We now construct the colours
 158     colours = new ConsensusColour[11];
 159
 160     Consensus[] tmp8 = new Consensus[1];
 161     tmp8[0] = conses[30]; // G
 162     colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 163
 164     Consensus[] tmp9 = new Consensus[1];
 165     tmp9[0] = conses[31]; // P
 166     colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 167
 168     Consensus[] tmp10 = new Consensus[1];
 169     tmp10[0] = conses[27]; // C
 170     colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 171
 172     Consensus[] tmp1 = new Consensus[14];
 173     tmp1[0] = conses[0]; // %
 174     tmp1[1] = conses[1]; // #
 175     tmp1[2] = conses[26]; // A
 176     tmp1[3] = conses[27]; // C
 177     tmp1[4] = conses[11]; // F
 178     tmp1[5] = conses[13]; // H
 179     tmp1[6] = conses[14]; // I
 180     tmp1[7] = conses[15]; // L
 181     tmp1[8] = conses[16]; // M
 182     tmp1[9] = conses[23]; // V
 183     tmp1[10] = conses[24]; // W
 184     tmp1[11] = conses[25]; // Y
 185     tmp1[12] = conses[18]; // P
 186     tmp1[13] = conses[19]; // p
 187     colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
 188
 189     colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 190
 191     Consensus[] tmp2 = new Consensus[5];
 192     tmp2[0] = conses[8]; // t
 193     tmp2[1] = conses[21]; // S
 194     tmp2[2] = conses[22]; // T
 195     tmp2[3] = conses[0]; // %
 196     tmp2[4] = conses[1]; // #
 197     colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 198
 199     Consensus[] tmp3 = new Consensus[3];
 200
 201     tmp3[0] = conses[17]; // N
 202     tmp3[1] = conses[29]; // D
 203     tmp3[2] = conses[5]; // n
 204     colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 205
 206     Consensus[] tmp4 = new Consensus[6];
 207     tmp4[0] = conses[6]; // q = QE
 208     tmp4[1] = conses[19]; // Q
 209     tmp4[2] = conses[22]; // E
 210     tmp4[3] = conses[3]; // +
 211     tmp4[4] = conses[28]; // K
 212     tmp4[5] = conses[20]; // R
 213     colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 214
 215     Consensus[] tmp5 = new Consensus[4];
 216     tmp5[0] = conses[3]; // +
 217     tmp5[1] = conses[28]; // K
 218     tmp5[2] = conses[20]; // R
 219     tmp5[3] = conses[19]; // Q
 220     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 221
 222     Consensus[] tmp6 = new Consensus[6];
 223     tmp6[0] = conses[3]; // -
 224     tmp6[1] = conses[29]; // D
 225     tmp6[2] = conses[10]; // E
 226     tmp6[3] = conses[6]; // QE
 227     tmp6[4] = conses[19]; // Q
 228     tmp6[5] = conses[2]; // DE
 229     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 230
 231     Consensus[] tmp7 = new Consensus[5];
 232     tmp7[0] = conses[3]; // -
 233     tmp7[1] = conses[29]; // D
 234     tmp7[2] = conses[10]; // E
 235     tmp7[3] = conses[17]; // N
 236     tmp7[4] = conses[2]; // DE
 237     colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 238
 239     // Now attach the ConsensusColours to the residue letters
 240     ResidueColour = new ConsensusColour[20];
 241     ResidueColour[0] = colours[0]; // A
 242     ResidueColour[1] = colours[4]; // R
 243     ResidueColour[2] = colours[2]; // N
 244     ResidueColour[3] = colours[6]; // D
 245     ResidueColour[4] = colours[0]; // C
 246     ResidueColour[5] = colours[3]; // Q
 247     ResidueColour[6] = colours[5]; // E
 248     ResidueColour[7] = colours[7]; // G
 249     ResidueColour[8] = colours[10]; // H
 250     ResidueColour[9] = colours[0]; // I
 251     ResidueColour[10] = colours[0]; // L
 252     ResidueColour[11] = colours[4]; // K
 253     ResidueColour[12] = colours[0]; // M
 254     ResidueColour[13] = colours[0]; // F
 255     ResidueColour[14] = colours[8]; // P
 256     ResidueColour[15] = colours[1]; // S
 257     ResidueColour[16] = colours[1]; // T
 258     ResidueColour[17] = colours[0]; // W
 259     ResidueColour[18] = colours[10]; // Y
 260     ResidueColour[19] = colours[0]; // V
 261   }
 262
 263   @Override
 264   public Color findColour(char c)
 265   {
 266     return Color.pink;
 267   }
 268
 269   @Override
 270   public Color findColour(char c, int j, SequenceI seq)
 271   {
 272     Color currentColour;
 273
 274     if (cons2.length <= j
 275             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 276     {
 277       return Color.white;
 278     }
 279
 280     int i = ResidueProperties.aaIndex[c];
 281
 282     currentColour = Color.white;
 283
 284     if (i > 19)
 285     {
 286       return currentColour;
 287     }
 288
 289     for (int k = 0; k < ResidueColour[i].conses.length; k++)
 290     {
 291       if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
 292               includeGaps))
 293       {
 294         currentColour = ResidueColour[i].c;
 295       }
 296     }
 297
 298     if (i == 4)
 299     {
 300       if (conses[27].isConserved(cons2, j, size, includeGaps))
 301       {
 302         currentColour = (Color) colhash.get("PINK");
 303       }
 304     }
 305
 306     if (conservationColouring)
 307     {
 308       currentColour = applyConservation(currentColour, j);
 309     }
 310
 311     return currentColour;
 312   }
 313
 314   /**
 315    * @return the includeGaps
 316    */
 317   protected boolean isIncludeGaps()
 318   {
 319     return includeGaps;
 320   }
 321
 322   /**
 323    * @param includeGaps
 324    *          the includeGaps to set
 325    */
 326   protected void setIncludeGaps(boolean includeGaps)
 327   {
 328     this.includeGaps = includeGaps;
 329   }
 330 }
 331
 332 class ConsensusColour
 333 {
 334   Consensus[] conses;
 335
 336   Color c;
 337
 338   public ConsensusColour(Color c, Consensus[] conses)
 339   {
 340     this.conses = conses;
 341
 342     // this.list = list;
 343     this.c = c;
 344   }
 345 }