src/jalview/schemes/ClustalxColourScheme.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.schemes;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24
  25 import jalview.datamodel.*;
  26
  27 public class ClustalxColourScheme
  28     extends ResidueColourScheme // implements IParameterizable
  29 {
  30   public static Hashtable colhash = new Hashtable();
  31   Hashtable[] cons;
  32   int[][] cons2;
  33   ConsensusColour[] colours;
  34   ConsensusColour[] ResidueColour;
  35   int size;
  36   Consensus[] conses = new Consensus[32];
  37   Vector colourTable = new Vector();
  38   private boolean includeGaps=true;
  39
  40   {
  41     colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));
  42     colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));
  43     colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));
  44     colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3));
  45     colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7));
  46     colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5));
  47     colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8));
  48     colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));
  49   }
  50
  51   public ClustalxColourScheme(Vector seqs, int maxWidth)
  52   {
  53     resetClustalX(seqs, maxWidth);
  54   }
  55
  56   public void resetClustalX(Vector seqs, int maxWidth)
  57   {
  58     cons2 = new int[maxWidth][24];
  59     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to get the current setting of the includeGaps param.
  60     int start = 0;
  61
  62     // Initialize the array
  63     for (int j = 0; j < 24; j++)
  64     {
  65       for (int i = 0; i < maxWidth; i++)
  66       {
  67         cons2[i][j] = 0;
  68       }
  69     }
  70
  71     int res;
  72     int i;
  73     int j = 0;
  74     char[] seq;
  75
  76     while (j < seqs.size())
  77     {
  78       seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
  79
  80       int end_j = seq.length - 1;
  81
  82       for (i = start; i <= end_j; i++)
  83       {
  84         if ( (seq.length - 1) < i)
  85         {
  86           res = 23;
  87         }
  88         else
  89         {
  90           res = ResidueProperties.aaIndex[seq[i]];
  91         }
  92
  93         cons2[i][res]++;
  94       }
  95
  96       j++;
  97     }
  98
  99     this.size = seqs.size();
 100     makeColours();
 101   }
 102
 103   public void makeColours()
 104   {
 105     conses[0] = new Consensus("WLVIMAFCYHP", 60);
 106     conses[1] = new Consensus("WLVIMAFCYHP", 80);
 107     conses[2] = new Consensus("ED", 50);
 108     conses[3] = new Consensus("KR", 60);
 109     conses[4] = new Consensus("G", 50);
 110     conses[5] = new Consensus("N", 50);
 111     conses[6] = new Consensus("QE", 50);
 112     conses[7] = new Consensus("P", 50);
 113     conses[8] = new Consensus("TS", 50);
 114
 115     conses[26] = new Consensus("A", 85);
 116     conses[27] = new Consensus("C", 85);
 117     conses[10] = new Consensus("E", 85);
 118     conses[11] = new Consensus("F", 85);
 119     conses[12] = new Consensus("G", 85);
 120     conses[13] = new Consensus("H", 85);
 121     conses[14] = new Consensus("I", 85);
 122     conses[15] = new Consensus("L", 85);
 123     conses[16] = new Consensus("M", 85);
 124     conses[17] = new Consensus("N", 85);
 125     conses[18] = new Consensus("P", 85);
 126     conses[19] = new Consensus("Q", 85);
 127     conses[20] = new Consensus("R", 85);
 128     conses[21] = new Consensus("S", 85);
 129     conses[22] = new Consensus("T", 85);
 130     conses[23] = new Consensus("V", 85);
 131     conses[24] = new Consensus("W", 85);
 132     conses[25] = new Consensus("Y", 85);
 133     conses[28] = new Consensus("K", 85);
 134     conses[29] = new Consensus("D", 85);
 135
 136     conses[30] = new Consensus("G", 0);
 137     conses[31] = new Consensus("P", 0);
 138
 139     // We now construct the colours
 140     colours = new ConsensusColour[11];
 141
 142     Consensus[] tmp8 = new Consensus[1];
 143     tmp8[0] = conses[30]; //G
 144     colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);
 145
 146     Consensus[] tmp9 = new Consensus[1];
 147     tmp9[0] = conses[31]; //P
 148     colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);
 149
 150     Consensus[] tmp10 = new Consensus[1];
 151     tmp10[0] = conses[27]; //C
 152     colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);
 153
 154     Consensus[] tmp1 = new Consensus[14];
 155     tmp1[0] = conses[0]; //%
 156     tmp1[1] = conses[1]; //#
 157     tmp1[2] = conses[26]; //A
 158     tmp1[3] = conses[27]; //C
 159     tmp1[4] = conses[11]; //F
 160     tmp1[5] = conses[13]; //H
 161     tmp1[6] = conses[14]; //I
 162     tmp1[7] = conses[15]; //L
 163     tmp1[8] = conses[16]; //M
 164     tmp1[9] = conses[23]; //V
 165     tmp1[10] = conses[24]; //W
 166     tmp1[11] = conses[25]; //Y
 167     tmp1[12] = conses[18]; //P
 168     tmp1[13] = conses[19]; //p
 169     colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
 170
 171     colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
 172
 173     Consensus[] tmp2 = new Consensus[5];
 174     tmp2[0] = conses[8]; //t
 175     tmp2[1] = conses[21]; //S
 176     tmp2[2] = conses[22]; //T
 177     tmp2[3] = conses[0]; //%
 178     tmp2[4] = conses[1]; //#
 179     colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);
 180
 181     Consensus[] tmp3 = new Consensus[3];
 182
 183     tmp3[0] = conses[17]; //N
 184     tmp3[1] = conses[29]; //D
 185     tmp3[2] = conses[5]; //n
 186     colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);
 187
 188     Consensus[] tmp4 = new Consensus[6];
 189     tmp4[0] = conses[6]; // q = QE
 190     tmp4[1] = conses[19]; //Q
 191     tmp4[2] = conses[22]; //E
 192     tmp4[3] = conses[3]; //+
 193     tmp4[4] = conses[28]; //K
 194     tmp4[5] = conses[20]; //R
 195     colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
 196
 197     Consensus[] tmp5 = new Consensus[4];
 198     tmp5[0] = conses[3]; //+
 199     tmp5[1] = conses[28]; //K
 200     tmp5[2] = conses[20]; //R
 201     tmp5[3] = conses[19]; //Q
 202     colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
 203
 204     Consensus[] tmp6 = new Consensus[5];
 205     tmp6[0] = conses[3]; //-
 206     tmp6[1] = conses[29]; //D
 207     tmp6[2] = conses[10]; //E
 208     tmp6[3] = conses[6]; //q
 209     tmp6[4] = conses[19]; //Q
 210     colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
 211
 212     Consensus[] tmp7 = new Consensus[5];
 213     tmp7[0] = conses[3]; //-
 214     tmp7[1] = conses[29]; //D
 215     tmp7[2] = conses[10]; //E
 216     tmp7[3] = conses[17]; //N
 217     tmp7[4] = conses[2]; //DE
 218     colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
 219
 220     // Now attach the ConsensusColours to the residue letters
 221     ResidueColour = new ConsensusColour[20];
 222     ResidueColour[0] = colours[0]; // A
 223     ResidueColour[1] = colours[4]; // R
 224     ResidueColour[2] = colours[2]; // N
 225     ResidueColour[3] = colours[6]; // D
 226     ResidueColour[4] = colours[0]; // C
 227     ResidueColour[5] = colours[3]; // Q
 228     ResidueColour[6] = colours[5]; // E
 229     ResidueColour[7] = colours[7]; // G
 230     ResidueColour[8] = colours[10]; // H
 231     ResidueColour[9] = colours[0]; // I
 232     ResidueColour[10] = colours[0]; // L
 233     ResidueColour[11] = colours[4]; // K
 234     ResidueColour[12] = colours[0]; // M
 235     ResidueColour[13] = colours[0]; // F
 236     ResidueColour[14] = colours[8]; // P
 237     ResidueColour[15] = colours[1]; // S
 238     ResidueColour[16] = colours[1]; // T
 239     ResidueColour[17] = colours[0]; // W
 240     ResidueColour[18] = colours[10]; // Y
 241     ResidueColour[19] = colours[0]; // V
 242   }
 243
 244   public Color findColour(char c)
 245   {
 246     return Color.pink;
 247   }
 248
 249   public Color findColour(char c, int j)
 250   {
 251     Color currentColour;
 252
 253     if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
 254     {
 255       return Color.white;
 256     }
 257
 258     int i = ResidueProperties.aaIndex[c];
 259
 260     currentColour = Color.white;
 261
 262     if (i > 19)
 263     {
 264       return currentColour;
 265     }
 266
 267     for (int k = 0; k < ResidueColour[i].conses.length; k++)
 268     {
 269       if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps))
 270       {
 271         currentColour = ResidueColour[i].c;
 272       }
 273     }
 274
 275     if (i == 4)
 276     {
 277       if (conses[27].isConserved(cons2, j, size, includeGaps))
 278       {
 279         currentColour = (Color) colhash.get("PINK");
 280       }
 281     }
 282
 283     if (conservationColouring)
 284     {
 285       currentColour = applyConservation(currentColour, j);
 286     }
 287
 288     return currentColour;
 289   }
 290
 291   /**
 292    * @return the includeGaps
 293    */
 294   protected boolean isIncludeGaps()
 295   {
 296     return includeGaps;
 297   }
 298
 299   /**
 300    * @param includeGaps the includeGaps to set
 301    */
 302   protected void setIncludeGaps(boolean includeGaps)
 303   {
 304     this.includeGaps = includeGaps;
 305   }
 306 }
 307
 308 class ConsensusColour
 309 {
 310   Consensus[] conses;
 311   Color c;
 312
 313   public ConsensusColour(Color c, Consensus[] conses)
 314   {
 315     this.conses = conses;
 316
 317     //    this.list = list;
 318     this.c = c;
 319   }
 320 }