JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
[jalview.git] / src / jalview / schemes / ClustalxColourScheme.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3  * Copyright (C) $$Year-Rel$$ 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
10  * of the License, or (at your option) any later version.
11  *  
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.
16  * 
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.
20  */
21 package jalview.schemes;
22
23 import jalview.api.AlignViewportI;
24 import jalview.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.SequenceCollectionI;
26 import jalview.datamodel.SequenceI;
27 import jalview.util.Comparison;
28
29 import java.awt.Color;
30 import java.util.List;
31 import java.util.Map;
32
33 public class ClustalxColourScheme extends ResidueColourScheme
34 {
35   private static final int EIGHTY_FIVE = 85;
36
37   private static final int FIFTY = 50;
38
39   private static final int EIGHTY = 80;
40
41   private static final int SIXTY = 60;
42
43   enum ClustalColour
44   {
45     RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
46     ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
47     PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
48     YELLOW(0.8f, 0.8f, 0.0f);
49
50     final Color colour;
51
52     ClustalColour(float r, float g, float b)
53     {
54       colour = new Color(r, g, b);
55     }
56   }
57
58   private class ConsensusColour
59   {
60     Consensus[] cons;
61
62     Color c;
63
64     public ConsensusColour(ClustalColour col, Consensus[] conses)
65     {
66       this.cons = conses;
67       this.c = col.colour;
68     }
69   }
70
71   private int[][] cons2;
72
73   private ConsensusColour[] colours;
74
75   private ConsensusColour[] residueColour;
76
77   private int size;
78
79   private Consensus[] conses = new Consensus[32];
80
81   private boolean includeGaps = true;
82
83   /**
84    * Default constructor (required for Class.newInstance())
85    */
86   public ClustalxColourScheme()
87   {
88
89   }
90
91   public ClustalxColourScheme(AnnotatedCollectionI alignment,
92           Map<SequenceI, SequenceCollectionI> hiddenReps)
93   {
94     alignmentChanged(alignment, hiddenReps);
95   }
96
97   @Override
98   public void alignmentChanged(AnnotatedCollectionI alignment,
99           Map<SequenceI, SequenceCollectionI> hiddenReps)
100   {
101     int maxWidth = alignment.getWidth();
102     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
103     cons2 = new int[maxWidth][24];
104     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
105     // get the current setting of the
106     // includeGaps param.
107     int res = 0;
108
109     for (SequenceI sq : seqs)
110     {
111       int end_j = sq.getLength() - 1;
112       int length = sq.getLength();
113
114       for (int i = 0; i <= end_j; i++)
115       {
116         if (length - 1 < i)
117         {
118           res = 23;
119         }
120         else
121         {
122           res = ResidueProperties.aaIndex[sq.getCharAt(i)];
123         }
124         cons2[i][res]++;
125       }
126     }
127
128     this.size = seqs.size();
129     makeColours();
130   }
131
132   void makeColours()
133   {
134     conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
135     conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
136     conses[2] = new Consensus("ED", FIFTY);
137     conses[3] = new Consensus("KR", SIXTY);
138     conses[4] = new Consensus("G", FIFTY);
139     conses[5] = new Consensus("N", FIFTY);
140     conses[6] = new Consensus("QE", FIFTY);
141     conses[7] = new Consensus("P", FIFTY);
142     conses[8] = new Consensus("TS", FIFTY);
143
144     conses[26] = new Consensus("A", EIGHTY_FIVE);
145     conses[27] = new Consensus("C", EIGHTY_FIVE);
146     conses[10] = new Consensus("E", EIGHTY_FIVE);
147     conses[11] = new Consensus("F", EIGHTY_FIVE);
148     conses[12] = new Consensus("G", EIGHTY_FIVE);
149     conses[13] = new Consensus("H", EIGHTY_FIVE);
150     conses[14] = new Consensus("I", EIGHTY_FIVE);
151     conses[15] = new Consensus("L", EIGHTY_FIVE);
152     conses[16] = new Consensus("M", EIGHTY_FIVE);
153     conses[17] = new Consensus("N", EIGHTY_FIVE);
154     conses[18] = new Consensus("P", EIGHTY_FIVE);
155     conses[19] = new Consensus("Q", EIGHTY_FIVE);
156     conses[20] = new Consensus("R", EIGHTY_FIVE);
157     conses[21] = new Consensus("S", EIGHTY_FIVE);
158     conses[22] = new Consensus("T", EIGHTY_FIVE);
159     conses[23] = new Consensus("V", EIGHTY_FIVE);
160     conses[24] = new Consensus("W", EIGHTY_FIVE);
161     conses[25] = new Consensus("Y", EIGHTY_FIVE);
162     conses[28] = new Consensus("K", EIGHTY_FIVE);
163     conses[29] = new Consensus("D", EIGHTY_FIVE);
164
165     conses[30] = new Consensus("G", 0);
166     conses[31] = new Consensus("P", 0);
167
168     // We now construct the colours
169     colours = new ConsensusColour[11];
170
171     Consensus[] tmp8 = new Consensus[1];
172     tmp8[0] = conses[30]; // G
173     colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
174
175     Consensus[] tmp9 = new Consensus[1];
176     tmp9[0] = conses[31]; // P
177     colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
178
179     Consensus[] tmp10 = new Consensus[1];
180     tmp10[0] = conses[27]; // C
181     colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
182
183     Consensus[] tmp1 = new Consensus[14];
184     tmp1[0] = conses[0]; // %
185     tmp1[1] = conses[1]; // #
186     tmp1[2] = conses[26]; // A
187     tmp1[3] = conses[27]; // C
188     tmp1[4] = conses[11]; // F
189     tmp1[5] = conses[13]; // H
190     tmp1[6] = conses[14]; // I
191     tmp1[7] = conses[15]; // L
192     tmp1[8] = conses[16]; // M
193     tmp1[9] = conses[23]; // V
194     tmp1[10] = conses[24]; // W
195     tmp1[11] = conses[25]; // Y
196     tmp1[12] = conses[18]; // P
197     tmp1[13] = conses[19]; // p
198     colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
199
200     colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
201
202     Consensus[] tmp2 = new Consensus[5];
203     tmp2[0] = conses[8]; // t
204     tmp2[1] = conses[21]; // S
205     tmp2[2] = conses[22]; // T
206     tmp2[3] = conses[0]; // %
207     tmp2[4] = conses[1]; // #
208     colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
209
210     Consensus[] tmp3 = new Consensus[3];
211
212     tmp3[0] = conses[17]; // N
213     tmp3[1] = conses[29]; // D
214     tmp3[2] = conses[5]; // n
215     colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
216
217     Consensus[] tmp4 = new Consensus[6];
218     tmp4[0] = conses[6]; // q = QE
219     tmp4[1] = conses[19]; // Q
220     tmp4[2] = conses[22]; // E
221     tmp4[3] = conses[3]; // +
222     tmp4[4] = conses[28]; // K
223     tmp4[5] = conses[20]; // R
224     colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
225
226     Consensus[] tmp5 = new Consensus[4];
227     tmp5[0] = conses[3]; // +
228     tmp5[1] = conses[28]; // K
229     tmp5[2] = conses[20]; // R
230     tmp5[3] = conses[19]; // Q
231     colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
232
233     Consensus[] tmp6 = new Consensus[6];
234     tmp6[0] = conses[3]; // -
235     tmp6[1] = conses[29]; // D
236     tmp6[2] = conses[10]; // E
237     tmp6[3] = conses[6]; // QE
238     tmp6[4] = conses[19]; // Q
239     tmp6[5] = conses[2]; // DE
240     colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
241
242     Consensus[] tmp7 = new Consensus[5];
243     tmp7[0] = conses[3]; // -
244     tmp7[1] = conses[29]; // D
245     tmp7[2] = conses[10]; // E
246     tmp7[3] = conses[17]; // N
247     tmp7[4] = conses[2]; // DE
248     colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
249
250     // Now attach the ConsensusColours to the residue letters
251     residueColour = new ConsensusColour[20];
252     residueColour[0] = colours[0]; // A
253     residueColour[1] = colours[4]; // R
254     residueColour[2] = colours[2]; // N
255     residueColour[3] = colours[6]; // D
256     residueColour[4] = colours[0]; // C
257     residueColour[5] = colours[3]; // Q
258     residueColour[6] = colours[5]; // E
259     residueColour[7] = colours[7]; // G
260     residueColour[8] = colours[10]; // H
261     residueColour[9] = colours[0]; // I
262     residueColour[10] = colours[0]; // L
263     residueColour[11] = colours[4]; // K
264     residueColour[12] = colours[0]; // M
265     residueColour[13] = colours[0]; // F
266     residueColour[14] = colours[8]; // P
267     residueColour[15] = colours[1]; // S
268     residueColour[16] = colours[1]; // T
269     residueColour[17] = colours[0]; // W
270     residueColour[18] = colours[10]; // Y
271     residueColour[19] = colours[0]; // V
272   }
273
274   @Override
275   public Color findColour(char c)
276   {
277     return Color.pink;
278   }
279
280   @Override
281   protected Color findColour(char c, int j, SequenceI seq)
282   {
283     // TODO why the test for includeGaps here?
284     if (cons2.length <= j || Comparison.isGap(c)
285     /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
286     {
287       return Color.white;
288     }
289
290     int i = ResidueProperties.aaIndex[c];
291
292     Color colour = Color.white;
293
294     if (i > 19)
295     {
296       return colour;
297     }
298
299     for (int k = 0; k < residueColour[i].cons.length; k++)
300     {
301       if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
302       {
303         colour = residueColour[i].c;
304       }
305     }
306
307     if (i == 4)
308     {
309       /*
310        * override to colour C pink if >85% conserved
311        */
312       if (conses[27].isConserved(cons2, j, size, includeGaps))
313       {
314         colour = ClustalColour.PINK.colour;
315       }
316     }
317
318     return colour;
319   }
320
321   /**
322    * @return the includeGaps
323    */
324   protected boolean isIncludeGaps()
325   {
326     return includeGaps;
327   }
328
329   /**
330    * @param includeGaps
331    *          the includeGaps to set
332    */
333   protected void setIncludeGaps(boolean includeGaps)
334   {
335     this.includeGaps = includeGaps;
336   }
337
338   @Override
339   public ColourSchemeI getInstance(AlignViewportI view,
340           AnnotatedCollectionI sg)
341   {
342     ClustalxColourScheme css = new ClustalxColourScheme(sg,
343             view == null ? null : view.getHiddenRepSequences());
344     css.includeGaps = includeGaps;
345     return css;
346   }
347
348   @Override
349   public boolean isPeptideSpecific()
350   {
351     return true;
352   }
353
354   @Override
355   public String getSchemeName()
356   {
357     return JalviewColourScheme.Clustal.toString();
358   }
359
360   @Override
361   public boolean isSimple()
362   {
363     return false;
364   }
365 }