2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemes;
23 import java.awt.Color;
24 import java.util.HashMap;
25 import java.util.List;
28 import jalview.api.AlignViewportI;
29 import jalview.datamodel.AnnotatedCollectionI;
30 import jalview.datamodel.SequenceCollectionI;
31 import jalview.datamodel.SequenceI;
32 import jalview.util.ColorUtils;
33 import jalview.util.Comparison;
35 public class ClustalxColourScheme extends ResidueColourScheme
37 private static final int EIGHTY_FIVE = 85;
39 private static final int FIFTY = 50;
41 private static final int EIGHTY = 80;
43 private static final int SIXTY = 60;
47 RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
48 ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
49 PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
50 YELLOW(0.8f, 0.8f, 0.0f);
54 ClustalColour(float r, float g, float b)
56 colour = new Color(r, g, b);
60 private class ConsensusColour
66 public ConsensusColour(ClustalColour col, Consensus[] conses)
73 private int[][] cons2;
75 private ConsensusColour[] colours;
77 private ConsensusColour[] residueColour;
81 private Consensus[] conses = new Consensus[32];
83 private boolean includeGaps = true;
86 * Default constructor (required for Class.newInstance())
88 public ClustalxColourScheme()
93 public ClustalxColourScheme(AnnotatedCollectionI alignment,
94 Map<SequenceI, SequenceCollectionI> hiddenReps)
96 alignmentChanged(alignment, hiddenReps);
100 public synchronized void alignmentChanged(AnnotatedCollectionI alignment,
101 Map<SequenceI, SequenceCollectionI> hiddenReps)
103 int maxWidth = alignment.getWidth();
104 List<SequenceI> seqs = alignment.getSequences(hiddenReps);
105 cons2 = new int[maxWidth][24];
106 includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
107 // get the current setting of the
108 // includeGaps param.
111 for (SequenceI sq : seqs)
113 int end_j = sq.getLength() - 1;
114 int length = sq.getLength();
116 for (int i = 0; i <= end_j; i++)
124 res = ResidueProperties.aaIndex[sq.getCharAt(i)];
130 this.size = seqs.size();
136 conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
137 conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
138 conses[2] = new Consensus("ED", FIFTY);
139 conses[3] = new Consensus("KR", SIXTY);
140 conses[4] = new Consensus("G", FIFTY);
141 conses[5] = new Consensus("N", FIFTY);
142 conses[6] = new Consensus("QE", FIFTY);
143 conses[7] = new Consensus("P", FIFTY);
144 conses[8] = new Consensus("TS", FIFTY);
146 conses[26] = new Consensus("A", EIGHTY_FIVE);
147 conses[27] = new Consensus("C", EIGHTY_FIVE);
148 conses[10] = new Consensus("E", EIGHTY_FIVE);
149 conses[11] = new Consensus("F", EIGHTY_FIVE);
150 conses[12] = new Consensus("G", EIGHTY_FIVE);
151 conses[13] = new Consensus("H", EIGHTY_FIVE);
152 conses[14] = new Consensus("I", EIGHTY_FIVE);
153 conses[15] = new Consensus("L", EIGHTY_FIVE);
154 conses[16] = new Consensus("M", EIGHTY_FIVE);
155 conses[17] = new Consensus("N", EIGHTY_FIVE);
156 conses[18] = new Consensus("P", EIGHTY_FIVE);
157 conses[19] = new Consensus("Q", EIGHTY_FIVE);
158 conses[20] = new Consensus("R", EIGHTY_FIVE);
159 conses[21] = new Consensus("S", EIGHTY_FIVE);
160 conses[22] = new Consensus("T", EIGHTY_FIVE);
161 conses[23] = new Consensus("V", EIGHTY_FIVE);
162 conses[24] = new Consensus("W", EIGHTY_FIVE);
163 conses[25] = new Consensus("Y", EIGHTY_FIVE);
164 conses[28] = new Consensus("K", EIGHTY_FIVE);
165 conses[29] = new Consensus("D", EIGHTY_FIVE);
167 conses[30] = new Consensus("G", 0);
168 conses[31] = new Consensus("P", 0);
170 // We now construct the colours
171 colours = new ConsensusColour[11];
173 Consensus[] tmp8 = new Consensus[1];
174 tmp8[0] = conses[30]; // G
175 colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
177 Consensus[] tmp9 = new Consensus[1];
178 tmp9[0] = conses[31]; // P
179 colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
181 Consensus[] tmp10 = new Consensus[1];
182 tmp10[0] = conses[27]; // C
183 colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
185 Consensus[] tmp1 = new Consensus[14];
186 tmp1[0] = conses[0]; // %
187 tmp1[1] = conses[1]; // #
188 tmp1[2] = conses[26]; // A
189 tmp1[3] = conses[27]; // C
190 tmp1[4] = conses[11]; // F
191 tmp1[5] = conses[13]; // H
192 tmp1[6] = conses[14]; // I
193 tmp1[7] = conses[15]; // L
194 tmp1[8] = conses[16]; // M
195 tmp1[9] = conses[23]; // V
196 tmp1[10] = conses[24]; // W
197 tmp1[11] = conses[25]; // Y
198 tmp1[12] = conses[18]; // P
199 tmp1[13] = conses[19]; // p
200 colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
202 colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
204 Consensus[] tmp2 = new Consensus[5];
205 tmp2[0] = conses[8]; // t
206 tmp2[1] = conses[21]; // S
207 tmp2[2] = conses[22]; // T
208 tmp2[3] = conses[0]; // %
209 tmp2[4] = conses[1]; // #
210 colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
212 Consensus[] tmp3 = new Consensus[3];
214 tmp3[0] = conses[17]; // N
215 tmp3[1] = conses[29]; // D
216 tmp3[2] = conses[5]; // n
217 colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
219 Consensus[] tmp4 = new Consensus[6];
220 tmp4[0] = conses[6]; // q = QE
221 tmp4[1] = conses[19]; // Q
222 tmp4[2] = conses[22]; // E
223 tmp4[3] = conses[3]; // +
224 tmp4[4] = conses[28]; // K
225 tmp4[5] = conses[20]; // R
226 colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
228 Consensus[] tmp5 = new Consensus[4];
229 tmp5[0] = conses[3]; // +
230 tmp5[1] = conses[28]; // K
231 tmp5[2] = conses[20]; // R
232 tmp5[3] = conses[19]; // Q
233 colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
235 Consensus[] tmp6 = new Consensus[6];
236 tmp6[0] = conses[3]; // -
237 tmp6[1] = conses[29]; // D
238 tmp6[2] = conses[10]; // E
239 tmp6[3] = conses[6]; // QE
240 tmp6[4] = conses[19]; // Q
241 tmp6[5] = conses[2]; // DE
242 colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
244 Consensus[] tmp7 = new Consensus[5];
245 tmp7[0] = conses[3]; // -
246 tmp7[1] = conses[29]; // D
247 tmp7[2] = conses[10]; // E
248 tmp7[3] = conses[17]; // N
249 tmp7[4] = conses[2]; // DE
250 colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
252 // Now attach the ConsensusColours to the residue letters
253 residueColour = new ConsensusColour[20];
254 residueColour[0] = colours[0]; // A
255 residueColour[1] = colours[4]; // R
256 residueColour[2] = colours[2]; // N
257 residueColour[3] = colours[6]; // D
258 residueColour[4] = colours[0]; // C
259 residueColour[5] = colours[3]; // Q
260 residueColour[6] = colours[5]; // E
261 residueColour[7] = colours[7]; // G
262 residueColour[8] = colours[10]; // H
263 residueColour[9] = colours[0]; // I
264 residueColour[10] = colours[0]; // L
265 residueColour[11] = colours[4]; // K
266 residueColour[12] = colours[0]; // M
267 residueColour[13] = colours[0]; // F
268 residueColour[14] = colours[8]; // P
269 residueColour[15] = colours[1]; // S
270 residueColour[16] = colours[1]; // T
271 residueColour[17] = colours[0]; // W
272 residueColour[18] = colours[10]; // Y
273 residueColour[19] = colours[0]; // V
277 public Color findColour(char c)
283 protected synchronized Color findColour(char c, int j, SequenceI seq)
285 // TODO why the test for includeGaps here?
286 if (cons2.length <= j || Comparison.isGap(c)
287 /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
292 int i = ResidueProperties.aaIndex[c];
294 Color colour = Color.white;
301 for (int k = 0; k < residueColour[i].cons.length; k++)
303 if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
305 colour = residueColour[i].c;
312 * override to colour C pink if >85% conserved
314 if (conses[27].isConserved(cons2, j, size, includeGaps))
316 colour = ClustalColour.PINK.colour;
324 * @return the includeGaps
326 protected boolean isIncludeGaps()
333 * the includeGaps to set
335 protected void setIncludeGaps(boolean includeGaps)
337 this.includeGaps = includeGaps;
341 public ColourSchemeI getInstance(AlignViewportI view,
342 AnnotatedCollectionI sg)
344 ClustalxColourScheme css = new ClustalxColourScheme(sg,
345 view == null ? null : view.getHiddenRepSequences());
346 css.includeGaps = includeGaps;
351 public boolean isPeptideSpecific()
357 public String getSchemeName()
359 return JalviewColourScheme.Clustal.toString();
363 public boolean isSimple()
367 public String toRuleRep()
370 HashMap<String, String> cols=new HashMap();
371 for (String res:ResidueProperties.aa) {
372 StringBuilder sb = new StringBuilder();
374 int rnum=ResidueProperties.aaIndex[res.charAt(0)];
375 if (rnum<0 || rnum>=residueColour.length)
380 ConsensusColour cc = residueColour[rnum];
385 //sb.append("Residue "+res+" ("+rnum+")");
387 sb.append(cc.c.toString());
390 for (Consensus cons: cc.cons) {
391 if (cons.threshold==0 || f!=cons.threshold)
400 sb.append(cons.threshold);
406 sb.append(cons.maskstr);
409 String clxrep=sb.toString();
410 String xres = cols.get(clxrep);
411 if (xres==null) { xres = "";}
413 cols.put(clxrep, xres);
415 StringBuilder sb = new StringBuilder();
416 for (String clxrep:cols.keySet())
418 sb.append(cols.get(clxrep));
424 return sb.toString();