2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
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.
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.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.schemes;
24 import jalview.datamodel.*;
26 public class ClustalxColourScheme extends ResidueColourScheme // implements
29 public static Hashtable colhash = new Hashtable();
35 ConsensusColour[] colours;
37 ConsensusColour[] ResidueColour;
41 Consensus[] conses = new Consensus[32];
43 Vector colourTable = new Vector();
45 private boolean includeGaps = true;
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));
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));
60 public ClustalxColourScheme(Vector seqs, int maxWidth)
62 resetClustalX(seqs, maxWidth);
65 public void resetClustalX(Vector seqs, int maxWidth)
67 cons2 = new int[maxWidth][24];
68 includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
69 // get the current setting of the
73 // Initialize the array
74 for (int j = 0; j < 24; j++)
76 for (int i = 0; i < maxWidth; i++)
87 while (j < seqs.size())
89 seq = ((SequenceI) seqs.elementAt(j)).getSequence();
91 int end_j = seq.length - 1;
93 for (i = start; i <= end_j; i++)
95 if ((seq.length - 1) < i)
101 res = ResidueProperties.aaIndex[seq[i]];
110 this.size = seqs.size();
114 public void makeColours()
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);
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);
147 conses[30] = new Consensus("G", 0);
148 conses[31] = new Consensus("P", 0);
150 // We now construct the colours
151 colours = new ConsensusColour[11];
153 Consensus[] tmp8 = new Consensus[1];
154 tmp8[0] = conses[30]; // G
155 colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
157 Consensus[] tmp9 = new Consensus[1];
158 tmp9[0] = conses[31]; // P
159 colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
161 Consensus[] tmp10 = new Consensus[1];
162 tmp10[0] = conses[27]; // C
163 colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
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);
182 colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
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);
192 Consensus[] tmp3 = new Consensus[3];
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);
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);
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);
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);
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);
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
256 public Color findColour(char c)
261 public Color findColour(char c, int j)
265 if (cons2.length <= j
266 || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
271 int i = ResidueProperties.aaIndex[c];
273 currentColour = Color.white;
277 return currentColour;
280 for (int k = 0; k < ResidueColour[i].conses.length; k++)
282 if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
285 currentColour = ResidueColour[i].c;
291 if (conses[27].isConserved(cons2, j, size, includeGaps))
293 currentColour = (Color) colhash.get("PINK");
297 if (conservationColouring)
299 currentColour = applyConservation(currentColour, j);
302 return currentColour;
306 * @return the includeGaps
308 protected boolean isIncludeGaps()
315 * the includeGaps to set
317 protected void setIncludeGaps(boolean includeGaps)
319 this.includeGaps = includeGaps;
323 class ConsensusColour
329 public ConsensusColour(Color c, Consensus[] conses)
331 this.conses = conses;