src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, 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 java.util.*;
  21
  22 import java.awt.*;
  23
  24 import jalview.datamodel.*;
  25
  26 public class ClustalxColourScheme extends ResidueColourScheme // implements
  27 // IParameterizable
  28 {
  29   public static Hashtable colhash = new Hashtable();
  30
  31   Hashtable[] cons;
  32
  33   int[][] cons2;
  34
  35   ConsensusColour[] colours;
  36
  37   ConsensusColour[] ResidueColour;
  38
  39   int size;
  40
  41   Consensus[] conses = new Consensus[32];
  42
  43   Vector colourTable = new Vector();
  44
  45   private boolean includeGaps = true;
  46
  47   {
  48     colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
  49     colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
  50     colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
  51     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
  52     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
  53     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
  54     colhash
  55             .put("MAGENTA",
  56                     new Color((float) 0.8, (float) 0.3, (float) 0.8));
  57     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
  58   }
  59
  60   public ClustalxColourScheme(Vector seqs, int maxWidth)
  61   {
  62     resetClustalX(seqs, maxWidth);
  63   }
  64
  65   public void resetClustalX(Vector seqs, int maxWidth)
  66   {
  67     cons2 = new int[maxWidth][24];
  68     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
  69     // get the current setting of the
  70     // includeGaps param.
  71     int start = 0;
  72
  73     // Initialize the array
  74     for (int j = 0; j < 24; j++)
  75     {
  76       for (int i = 0; i < maxWidth; i++)
  77       {
  78         cons2[i][j] = 0;
  79       }
  80     }
  81
  82     int res;
  83     int i;
  84     int j = 0;
  85     char[] seq;
  86
  87     while (j < seqs.size())
  88     {
  89       seq = ((SequenceI) seqs.elementAt(j)).getSequence();
  90
  91       int end_j = seq.length - 1;
  92
  93       for (i = start; i <= end_j; i++)
  94       {
  95         if ((seq.length - 1) < i)
  96         {
  97           res = 23;
  98         }
  99         else
 100         {
 101           res = ResidueProperties.aaIndex[seq[i]];
 102         }
 103
 104         cons2[i][res]++;
 105       }
 106
 107       j++;
 108     }
 109
 110     this.size = seqs.size();
 111     makeColours();
 112   }
 113
 114   public void makeColours()
 115   {
 116     conses[0] = new Consensus("WLVIMAFCYHP", 60);
 117     conses[1] = new Consensus("WLVIMAFCYHP", 80);
 118     conses[2] = new Consensus("ED", 50);
 119     conses[3] = new Consensus("KR", 60);
 120     conses[4] = new Consensus("G", 50);
 121     conses[5] = new Consensus("N", 50);
 122     conses[6] = new Consensus("QE", 50);
 123     conses[7] = new Consensus("P", 50);
 124     conses[8] = new Consensus("TS", 50);
 125
 126     conses[26] = new Consensus("A", 85);
 127     conses[27] = new Consensus("C", 85);
 128     conses[10] = new Consensus("E", 85);
 129     conses[11] = new Consensus("F", 85);
 130     conses[12] = new Consensus("G", 85);
 131     conses[13] = new Consensus("H", 85);
 132     conses[14] = new Consensus("I", 85);
 133     conses[15] = new Consensus("L", 85);
 134     conses[16] = new Consensus("M", 85);
 135     conses[17] = new Consensus("N", 85);
 136     conses[18] = new Consensus("P", 85);
 137     conses[19] = new Consensus("Q", 85);
 138     conses[20] = new Consensus("R", 85);
 139     conses[21] = new Consensus("S", 85);
 140     conses[22] = new Consensus("T", 85);
 141     conses[23] = new Consensus("V", 85);
 142     conses[24] = new Consensus("W", 85);
 143     conses[25] = new Consensus("Y", 85);
 144     conses[28] = new Consensus("K", 85);
 145     conses[29] = new Consensus("D", 85);
 146
 147     conses[30] = new Consensus("G", 0);
 148     conses[31] = new Consensus("P", 0);
 149
 150     // We now construct the colours
 151     colours = new ConsensusColour[11];
 152
 153     Consensus[] tmp8 = new Consensus[1];
 154     tmp8[0] = conses[30]; // G
 155     colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 156
 157     Consensus[] tmp9 = new Consensus[1];
 158     tmp9[0] = conses[31]; // P
 159     colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 160
 161     Consensus[] tmp10 = new Consensus[1];
 162     tmp10[0] = conses[27]; // C
 163     colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 164
 165     Consensus[] tmp1 = new Consensus[14];
 166     tmp1[0] = conses[0]; // %
 167     tmp1[1] = conses[1]; // #
 168     tmp1[2] = conses[26]; // A
 169     tmp1[3] = conses[27]; // C
 170     tmp1[4] = conses[11]; // F
 171     tmp1[5] = conses[13]; // H
 172     tmp1[6] = conses[14]; // I
 173     tmp1[7] = conses[15]; // L
 174     tmp1[8] = conses[16]; // M
 175     tmp1[9] = conses[23]; // V
 176     tmp1[10] = conses[24]; // W
 177     tmp1[11] = conses[25]; // Y
 178     tmp1[12] = conses[18]; // P
 179     tmp1[13] = conses[19]; // p
 180     colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
 181
 182     colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 183
 184     Consensus[] tmp2 = new Consensus[5];
 185     tmp2[0] = conses[8]; // t
 186     tmp2[1] = conses[21]; // S
 187     tmp2[2] = conses[22]; // T
 188     tmp2[3] = conses[0]; // %
 189     tmp2[4] = conses[1]; // #
 190     colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 191
 192     Consensus[] tmp3 = new Consensus[3];
 193
 194     tmp3[0] = conses[17]; // N
 195     tmp3[1] = conses[29]; // D
 196     tmp3[2] = conses[5]; // n
 197     colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 198
 199     Consensus[] tmp4 = new Consensus[6];
 200     tmp4[0] = conses[6]; // q = QE
 201     tmp4[1] = conses[19]; // Q
 202     tmp4[2] = conses[22]; // E
 203     tmp4[3] = conses[3]; // +
 204     tmp4[4] = conses[28]; // K
 205     tmp4[5] = conses[20]; // R
 206     colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 207
 208     Consensus[] tmp5 = new Consensus[4];
 209     tmp5[0] = conses[3]; // +
 210     tmp5[1] = conses[28]; // K
 211     tmp5[2] = conses[20]; // R
 212     tmp5[3] = conses[19]; // Q
 213     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 214
 215     Consensus[] tmp6 = new Consensus[6];
 216     tmp6[0] = conses[3]; // -
 217     tmp6[1] = conses[29]; // D
 218     tmp6[2] = conses[10]; // E
 219     tmp6[3] = conses[6]; //  QE
 220     tmp6[4] = conses[19]; // Q
 221     tmp6[5] = conses[2]; // DE
 222     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 223
 224     Consensus[] tmp7 = new Consensus[5];
 225     tmp7[0] = conses[3]; // -
 226     tmp7[1] = conses[29]; // D
 227     tmp7[2] = conses[10]; // E
 228     tmp7[3] = conses[17]; // N
 229     tmp7[4] = conses[2]; // DE
 230     colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 231
 232     // Now attach the ConsensusColours to the residue letters
 233     ResidueColour = new ConsensusColour[20];
 234     ResidueColour[0] = colours[0]; // A
 235     ResidueColour[1] = colours[4]; // R
 236     ResidueColour[2] = colours[2]; // N
 237     ResidueColour[3] = colours[6]; // D
 238     ResidueColour[4] = colours[0]; // C
 239     ResidueColour[5] = colours[3]; // Q
 240     ResidueColour[6] = colours[5]; // E
 241     ResidueColour[7] = colours[7]; // G
 242     ResidueColour[8] = colours[10]; // H
 243     ResidueColour[9] = colours[0]; // I
 244     ResidueColour[10] = colours[0]; // L
 245     ResidueColour[11] = colours[4]; // K
 246     ResidueColour[12] = colours[0]; // M
 247     ResidueColour[13] = colours[0]; // F
 248     ResidueColour[14] = colours[8]; // P
 249     ResidueColour[15] = colours[1]; // S
 250     ResidueColour[16] = colours[1]; // T
 251     ResidueColour[17] = colours[0]; // W
 252     ResidueColour[18] = colours[10]; // Y
 253     ResidueColour[19] = colours[0]; // V
 254   }
 255
 256   public Color findColour(char c)
 257   {
 258     return Color.pink;
 259   }
 260
 261   public Color findColour(char c, int j)
 262   {
 263     Color currentColour;
 264
 265     if (cons2.length <= j
 266             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 267     {
 268       return Color.white;
 269     }
 270
 271     int i = ResidueProperties.aaIndex[c];
 272
 273     currentColour = Color.white;
 274
 275     if (i > 19)
 276     {
 277       return currentColour;
 278     }
 279
 280     for (int k = 0; k < ResidueColour[i].conses.length; k++)
 281     {
 282       if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
 283               includeGaps))
 284       {
 285         currentColour = ResidueColour[i].c;
 286       }
 287     }
 288
 289     if (i == 4)
 290     {
 291       if (conses[27].isConserved(cons2, j, size, includeGaps))
 292       {
 293         currentColour = (Color) colhash.get("PINK");
 294       }
 295     }
 296
 297     if (conservationColouring)
 298     {
 299       currentColour = applyConservation(currentColour, j);
 300     }
 301
 302     return currentColour;
 303   }
 304
 305   /**
 306    * @return the includeGaps
 307    */
 308   protected boolean isIncludeGaps()
 309   {
 310     return includeGaps;
 311   }
 312
 313   /**
 314    * @param includeGaps
 315    *          the includeGaps to set
 316    */
 317   protected void setIncludeGaps(boolean includeGaps)
 318   {
 319     this.includeGaps = includeGaps;
 320   }
 321 }
 322
 323 class ConsensusColour
 324 {
 325   Consensus[] conses;
 326
 327   Color c;
 328
 329   public ConsensusColour(Color c, Consensus[] conses)
 330   {
 331     this.conses = conses;
 332
 333     // this.list = list;
 334     this.c = c;
 335   }
 336 }