JAL-2416 allow space in score matrix name
[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.datamodel.AnnotatedCollectionI;
24 import jalview.datamodel.SequenceCollectionI;
25 import jalview.datamodel.SequenceI;
26 import jalview.util.Comparison;
27
28 import java.awt.Color;
29 import java.util.List;
30 import java.util.Map;
31
32 public class ClustalxColourScheme extends ResidueColourScheme
33 {
34   private static final int EIGHTY_FIVE = 85;
35
36   private static final int FIFTY = 50;
37
38   private static final int EIGHTY = 80;
39
40   private static final int SIXTY = 60;
41
42   enum ClustalColour
43   {
44     RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
45     ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
46     PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
47             0.0f);
48
49     final Color colour;
50
51     ClustalColour(float r, float g, float b)
52     {
53       colour = new Color(r, g, b);
54     }
55   }
56   private class ConsensusColour
57   {
58     Consensus[] cons;
59
60     Color c;
61
62     public ConsensusColour(ClustalColour col, Consensus[] conses)
63     {
64       this.cons = conses;
65       this.c = col.colour;
66     }
67   }
68
69   private int[][] cons2;
70
71   private ConsensusColour[] colours;
72
73   private ConsensusColour[] residueColour;
74
75   private int size;
76
77   private Consensus[] conses = new Consensus[32];
78
79   private boolean includeGaps = true;
80
81   /**
82    * Default constructor (required for Class.newInstance())
83    */
84   public ClustalxColourScheme()
85   {
86
87   }
88
89   public ClustalxColourScheme(AnnotatedCollectionI alignment,
90           Map<SequenceI, SequenceCollectionI> hiddenReps)
91   {
92     alignmentChanged(alignment, hiddenReps);
93   }
94
95   @Override
96   public void alignmentChanged(AnnotatedCollectionI alignment,
97           Map<SequenceI, SequenceCollectionI> hiddenReps)
98   {
99     int maxWidth = alignment.getWidth();
100     List<SequenceI> seqs = alignment.getSequences(hiddenReps);
101     cons2 = new int[maxWidth][24];
102     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
103     // get the current setting of the
104     // includeGaps param.
105     int res = 0;
106
107     for (SequenceI sq : seqs)
108     {
109       char[] seq = sq.getSequence();
110
111       int end_j = seq.length - 1;
112
113       for (int i = 0; i <= end_j; i++)
114       {
115         if ((seq.length - 1) < i)
116         {
117           res = 23;
118         }
119         else
120         {
121           res = ResidueProperties.aaIndex[seq[i]];
122         }
123         cons2[i][res]++;
124       }
125     }
126
127     this.size = seqs.size();
128     makeColours();
129   }
130
131   void makeColours()
132   {
133     conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
134     conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
135     conses[2] = new Consensus("ED", FIFTY);
136     conses[3] = new Consensus("KR", SIXTY);
137     conses[4] = new Consensus("G", FIFTY);
138     conses[5] = new Consensus("N", FIFTY);
139     conses[6] = new Consensus("QE", FIFTY);
140     conses[7] = new Consensus("P", FIFTY);
141     conses[8] = new Consensus("TS", FIFTY);
142
143     conses[26] = new Consensus("A", EIGHTY_FIVE);
144     conses[27] = new Consensus("C", EIGHTY_FIVE);
145     conses[10] = new Consensus("E", EIGHTY_FIVE);
146     conses[11] = new Consensus("F", EIGHTY_FIVE);
147     conses[12] = new Consensus("G", EIGHTY_FIVE);
148     conses[13] = new Consensus("H", EIGHTY_FIVE);
149     conses[14] = new Consensus("I", EIGHTY_FIVE);
150     conses[15] = new Consensus("L", EIGHTY_FIVE);
151     conses[16] = new Consensus("M", EIGHTY_FIVE);
152     conses[17] = new Consensus("N", EIGHTY_FIVE);
153     conses[18] = new Consensus("P", EIGHTY_FIVE);
154     conses[19] = new Consensus("Q", EIGHTY_FIVE);
155     conses[20] = new Consensus("R", EIGHTY_FIVE);
156     conses[21] = new Consensus("S", EIGHTY_FIVE);
157     conses[22] = new Consensus("T", EIGHTY_FIVE);
158     conses[23] = new Consensus("V", EIGHTY_FIVE);
159     conses[24] = new Consensus("W", EIGHTY_FIVE);
160     conses[25] = new Consensus("Y", EIGHTY_FIVE);
161     conses[28] = new Consensus("K", EIGHTY_FIVE);
162     conses[29] = new Consensus("D", EIGHTY_FIVE);
163
164     conses[30] = new Consensus("G", 0);
165     conses[31] = new Consensus("P", 0);
166
167     // We now construct the colours
168     colours = new ConsensusColour[11];
169
170     Consensus[] tmp8 = new Consensus[1];
171     tmp8[0] = conses[30]; // G
172     colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
173
174     Consensus[] tmp9 = new Consensus[1];
175     tmp9[0] = conses[31]; // P
176     colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
177
178     Consensus[] tmp10 = new Consensus[1];
179     tmp10[0] = conses[27]; // C
180     colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
181
182     Consensus[] tmp1 = new Consensus[14];
183     tmp1[0] = conses[0]; // %
184     tmp1[1] = conses[1]; // #
185     tmp1[2] = conses[26]; // A
186     tmp1[3] = conses[27]; // C
187     tmp1[4] = conses[11]; // F
188     tmp1[5] = conses[13]; // H
189     tmp1[6] = conses[14]; // I
190     tmp1[7] = conses[15]; // L
191     tmp1[8] = conses[16]; // M
192     tmp1[9] = conses[23]; // V
193     tmp1[10] = conses[24]; // W
194     tmp1[11] = conses[25]; // Y
195     tmp1[12] = conses[18]; // P
196     tmp1[13] = conses[19]; // p
197     colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
198
199     colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
200
201     Consensus[] tmp2 = new Consensus[5];
202     tmp2[0] = conses[8]; // t
203     tmp2[1] = conses[21]; // S
204     tmp2[2] = conses[22]; // T
205     tmp2[3] = conses[0]; // %
206     tmp2[4] = conses[1]; // #
207     colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
208
209     Consensus[] tmp3 = new Consensus[3];
210
211     tmp3[0] = conses[17]; // N
212     tmp3[1] = conses[29]; // D
213     tmp3[2] = conses[5]; // n
214     colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
215
216     Consensus[] tmp4 = new Consensus[6];
217     tmp4[0] = conses[6]; // q = QE
218     tmp4[1] = conses[19]; // Q
219     tmp4[2] = conses[22]; // E
220     tmp4[3] = conses[3]; // +
221     tmp4[4] = conses[28]; // K
222     tmp4[5] = conses[20]; // R
223     colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
224
225     Consensus[] tmp5 = new Consensus[4];
226     tmp5[0] = conses[3]; // +
227     tmp5[1] = conses[28]; // K
228     tmp5[2] = conses[20]; // R
229     tmp5[3] = conses[19]; // Q
230     colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
231
232     Consensus[] tmp6 = new Consensus[6];
233     tmp6[0] = conses[3]; // -
234     tmp6[1] = conses[29]; // D
235     tmp6[2] = conses[10]; // E
236     tmp6[3] = conses[6]; // QE
237     tmp6[4] = conses[19]; // Q
238     tmp6[5] = conses[2]; // DE
239     colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
240
241     Consensus[] tmp7 = new Consensus[5];
242     tmp7[0] = conses[3]; // -
243     tmp7[1] = conses[29]; // D
244     tmp7[2] = conses[10]; // E
245     tmp7[3] = conses[17]; // N
246     tmp7[4] = conses[2]; // DE
247     colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
248
249     // Now attach the ConsensusColours to the residue letters
250     residueColour = new ConsensusColour[20];
251     residueColour[0] = colours[0]; // A
252     residueColour[1] = colours[4]; // R
253     residueColour[2] = colours[2]; // N
254     residueColour[3] = colours[6]; // D
255     residueColour[4] = colours[0]; // C
256     residueColour[5] = colours[3]; // Q
257     residueColour[6] = colours[5]; // E
258     residueColour[7] = colours[7]; // G
259     residueColour[8] = colours[10]; // H
260     residueColour[9] = colours[0]; // I
261     residueColour[10] = colours[0]; // L
262     residueColour[11] = colours[4]; // K
263     residueColour[12] = colours[0]; // M
264     residueColour[13] = colours[0]; // F
265     residueColour[14] = colours[8]; // P
266     residueColour[15] = colours[1]; // S
267     residueColour[16] = colours[1]; // T
268     residueColour[17] = colours[0]; // W
269     residueColour[18] = colours[10]; // Y
270     residueColour[19] = colours[0]; // V
271   }
272
273   @Override
274   public Color findColour(char c)
275   {
276     return Color.pink;
277   }
278
279   @Override
280   protected Color findColour(char c, int j, SequenceI seq)
281   {
282     // TODO why the test for includeGaps here?
283     if (cons2.length <= j || Comparison.isGap(c)
284     /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
285     {
286       return Color.white;
287     }
288
289     int i = ResidueProperties.aaIndex[c];
290
291     Color colour = Color.white;
292
293     if (i > 19)
294     {
295       return colour;
296     }
297
298     for (int k = 0; k < residueColour[i].cons.length; k++)
299     {
300       if (residueColour[i].cons[k].isConserved(cons2, j, size,
301               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(AnnotatedCollectionI sg,
340           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
341   {
342     ClustalxColourScheme css = new ClustalxColourScheme(sg,
343             hiddenRepSequences);
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 }