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Coverage Report

  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.schemes

File ClustalxColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
20% of files have more coverage

Code metrics

28
198
15
3
436
335
32
0.16
13.2
5
2.13

Classes

Class Line # Actions
ClustalxColourScheme 35 195 30
0.762711976.3%
ClustalxColourScheme.ClustalColour 45 1 1
1.0100%
ClustalxColourScheme.ConsensusColour 60 2 1
1.0100%
 

Contributing tests

This file is covered by 188 tests. .

Source view

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 java.awt.Color;
24    import java.util.HashMap;
25    import java.util.List;
26    import java.util.Map;
27   
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;
34   
 
35    public class ClustalxColourScheme extends ResidueColourScheme
36    {
37    private static final int EIGHTY_FIVE = 85;
38   
39    private static final int FIFTY = 50;
40   
41    private static final int EIGHTY = 80;
42   
43    private static final int SIXTY = 60;
44   
 
45    enum ClustalColour
46    {
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);
51   
52    final Color colour;
53   
 
54  8 toggle ClustalColour(float r, float g, float b)
55    {
56  8 colour = new Color(r, g, b);
57    }
58    }
59   
 
60    private class ConsensusColour
61    {
62    Consensus[] cons;
63   
64    Color c;
65   
 
66  187 toggle public ConsensusColour(ClustalColour col, Consensus[] conses)
67    {
68  187 this.cons = conses;
69  187 this.c = col.colour;
70    }
71    }
72   
73    private int[][] cons2;
74   
75    private ConsensusColour[] colours;
76   
77    private ConsensusColour[] residueColour;
78   
79    private int size;
80   
81    private Consensus[] conses = new Consensus[32];
82   
83    private boolean includeGaps = true;
84   
85    /**
86    * Default constructor (required for Class.newInstance())
87    */
 
88  51 toggle public ClustalxColourScheme()
89    {
90   
91    }
92   
 
93  13 toggle public ClustalxColourScheme(AnnotatedCollectionI alignment,
94    Map<SequenceI, SequenceCollectionI> hiddenReps)
95    {
96  13 alignmentChanged(alignment, hiddenReps);
97    }
98   
 
99  17 toggle @Override
100    public synchronized void alignmentChanged(AnnotatedCollectionI alignment,
101    Map<SequenceI, SequenceCollectionI> hiddenReps)
102    {
103  17 int maxWidth = alignment.getWidth();
104  17 List<SequenceI> seqs = alignment.getSequences(hiddenReps);
105  17 cons2 = new int[maxWidth][24];
106  17 includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
107    // get the current setting of the
108    // includeGaps param.
109  17 int res = 0;
110   
111  17 for (SequenceI sq : seqs)
112    {
113  90 int end_j = sq.getLength() - 1;
114  90 int length = sq.getLength();
115   
116  10905 for (int i = 0; i <= end_j; i++)
117    {
118  10815 if (length - 1 < i)
119    {
120  0 res = 23;
121    }
122    else
123    {
124  10815 res = ResidueProperties.aaIndex[sq.getCharAt(i)];
125    }
126  10815 cons2[i][res]++;
127    }
128    }
129   
130  17 this.size = seqs.size();
131  17 makeColours();
132    }
133   
 
134  17 toggle void makeColours()
135    {
136  17 conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
137  17 conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
138  17 conses[2] = new Consensus("ED", FIFTY);
139  17 conses[3] = new Consensus("KR", SIXTY);
140  17 conses[4] = new Consensus("G", FIFTY);
141  17 conses[5] = new Consensus("N", FIFTY);
142  17 conses[6] = new Consensus("QE", FIFTY);
143  17 conses[7] = new Consensus("P", FIFTY);
144  17 conses[8] = new Consensus("TS", FIFTY);
145   
146  17 conses[26] = new Consensus("A", EIGHTY_FIVE);
147  17 conses[27] = new Consensus("C", EIGHTY_FIVE);
148  17 conses[10] = new Consensus("E", EIGHTY_FIVE);
149  17 conses[11] = new Consensus("F", EIGHTY_FIVE);
150  17 conses[12] = new Consensus("G", EIGHTY_FIVE);
151  17 conses[13] = new Consensus("H", EIGHTY_FIVE);
152  17 conses[14] = new Consensus("I", EIGHTY_FIVE);
153  17 conses[15] = new Consensus("L", EIGHTY_FIVE);
154  17 conses[16] = new Consensus("M", EIGHTY_FIVE);
155  17 conses[17] = new Consensus("N", EIGHTY_FIVE);
156  17 conses[18] = new Consensus("P", EIGHTY_FIVE);
157  17 conses[19] = new Consensus("Q", EIGHTY_FIVE);
158  17 conses[20] = new Consensus("R", EIGHTY_FIVE);
159  17 conses[21] = new Consensus("S", EIGHTY_FIVE);
160  17 conses[22] = new Consensus("T", EIGHTY_FIVE);
161  17 conses[23] = new Consensus("V", EIGHTY_FIVE);
162  17 conses[24] = new Consensus("W", EIGHTY_FIVE);
163  17 conses[25] = new Consensus("Y", EIGHTY_FIVE);
164  17 conses[28] = new Consensus("K", EIGHTY_FIVE);
165  17 conses[29] = new Consensus("D", EIGHTY_FIVE);
166   
167  17 conses[30] = new Consensus("G", 0);
168  17 conses[31] = new Consensus("P", 0);
169   
170    // We now construct the colours
171  17 colours = new ConsensusColour[11];
172   
173  17 Consensus[] tmp8 = new Consensus[1];
174  17 tmp8[0] = conses[30]; // G
175  17 colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
176   
177  17 Consensus[] tmp9 = new Consensus[1];
178  17 tmp9[0] = conses[31]; // P
179  17 colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
180   
181  17 Consensus[] tmp10 = new Consensus[1];
182  17 tmp10[0] = conses[27]; // C
183  17 colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
184   
185  17 Consensus[] tmp1 = new Consensus[14];
186  17 tmp1[0] = conses[0]; // %
187  17 tmp1[1] = conses[1]; // #
188  17 tmp1[2] = conses[26]; // A
189  17 tmp1[3] = conses[27]; // C
190  17 tmp1[4] = conses[11]; // F
191  17 tmp1[5] = conses[13]; // H
192  17 tmp1[6] = conses[14]; // I
193  17 tmp1[7] = conses[15]; // L
194  17 tmp1[8] = conses[16]; // M
195  17 tmp1[9] = conses[23]; // V
196  17 tmp1[10] = conses[24]; // W
197  17 tmp1[11] = conses[25]; // Y
198  17 tmp1[12] = conses[18]; // P
199  17 tmp1[13] = conses[19]; // p
200  17 colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
201   
202  17 colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
203   
204  17 Consensus[] tmp2 = new Consensus[5];
205  17 tmp2[0] = conses[8]; // t
206  17 tmp2[1] = conses[21]; // S
207  17 tmp2[2] = conses[22]; // T
208  17 tmp2[3] = conses[0]; // %
209  17 tmp2[4] = conses[1]; // #
210  17 colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
211   
212  17 Consensus[] tmp3 = new Consensus[3];
213   
214  17 tmp3[0] = conses[17]; // N
215  17 tmp3[1] = conses[29]; // D
216  17 tmp3[2] = conses[5]; // n
217  17 colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
218   
219  17 Consensus[] tmp4 = new Consensus[6];
220  17 tmp4[0] = conses[6]; // q = QE
221  17 tmp4[1] = conses[19]; // Q
222  17 tmp4[2] = conses[22]; // E
223  17 tmp4[3] = conses[3]; // +
224  17 tmp4[4] = conses[28]; // K
225  17 tmp4[5] = conses[20]; // R
226  17 colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
227   
228  17 Consensus[] tmp5 = new Consensus[4];
229  17 tmp5[0] = conses[3]; // +
230  17 tmp5[1] = conses[28]; // K
231  17 tmp5[2] = conses[20]; // R
232  17 tmp5[3] = conses[19]; // Q
233  17 colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
234   
235  17 Consensus[] tmp6 = new Consensus[6];
236  17 tmp6[0] = conses[3]; // -
237  17 tmp6[1] = conses[29]; // D
238  17 tmp6[2] = conses[10]; // E
239  17 tmp6[3] = conses[6]; // QE
240  17 tmp6[4] = conses[19]; // Q
241  17 tmp6[5] = conses[2]; // DE
242  17 colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
243   
244  17 Consensus[] tmp7 = new Consensus[5];
245  17 tmp7[0] = conses[3]; // -
246  17 tmp7[1] = conses[29]; // D
247  17 tmp7[2] = conses[10]; // E
248  17 tmp7[3] = conses[17]; // N
249  17 tmp7[4] = conses[2]; // DE
250  17 colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
251   
252    // Now attach the ConsensusColours to the residue letters
253  17 residueColour = new ConsensusColour[20];
254  17 residueColour[0] = colours[0]; // A
255  17 residueColour[1] = colours[4]; // R
256  17 residueColour[2] = colours[2]; // N
257  17 residueColour[3] = colours[6]; // D
258  17 residueColour[4] = colours[0]; // C
259  17 residueColour[5] = colours[3]; // Q
260  17 residueColour[6] = colours[5]; // E
261  17 residueColour[7] = colours[7]; // G
262  17 residueColour[8] = colours[10]; // H
263  17 residueColour[9] = colours[0]; // I
264  17 residueColour[10] = colours[0]; // L
265  17 residueColour[11] = colours[4]; // K
266  17 residueColour[12] = colours[0]; // M
267  17 residueColour[13] = colours[0]; // F
268  17 residueColour[14] = colours[8]; // P
269  17 residueColour[15] = colours[1]; // S
270  17 residueColour[16] = colours[1]; // T
271  17 residueColour[17] = colours[0]; // W
272  17 residueColour[18] = colours[10]; // Y
273  17 residueColour[19] = colours[0]; // V
274    }
275   
 
276  0 toggle @Override
277    public Color findColour(char c)
278    {
279  0 return Color.pink;
280    }
281   
 
282  19 toggle @Override
283    protected synchronized Color findColour(char c, int j, SequenceI seq)
284    {
285    // TODO why the test for includeGaps here?
286  19 if (cons2.length <= j || Comparison.isGap(c)
287    /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
288    {
289  0 return Color.white;
290    }
291   
292  19 int i = ResidueProperties.aaIndex[c];
293   
294  19 Color colour = Color.white;
295   
296  19 if (i > 19)
297    {
298  0 return colour;
299    }
300   
301  170 for (int k = 0; k < residueColour[i].cons.length; k++)
302    {
303  151 if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
304    {
305  22 colour = residueColour[i].c;
306    }
307    }
308   
309  19 if (i == 4)
310    {
311    /*
312    * override to colour C pink if >85% conserved
313    */
314  3 if (conses[27].isConserved(cons2, j, size, includeGaps))
315    {
316  1 colour = ClustalColour.PINK.colour;
317    }
318    }
319   
320  19 return colour;
321    }
322   
323    /**
324    * @return the includeGaps
325    */
 
326  17 toggle protected boolean isIncludeGaps()
327    {
328  17 return includeGaps;
329    }
330   
331    /**
332    * @param includeGaps
333    * the includeGaps to set
334    */
 
335  2 toggle protected void setIncludeGaps(boolean includeGaps)
336    {
337  2 this.includeGaps = includeGaps;
338    }
339   
 
340  7 toggle @Override
341    public ColourSchemeI getInstance(AlignViewportI view,
342    AnnotatedCollectionI sg)
343    {
344  7 ClustalxColourScheme css = new ClustalxColourScheme(sg,
345  7 view == null ? null : view.getHiddenRepSequences());
346  7 css.includeGaps = includeGaps;
347  7 return css;
348    }
349   
 
350  844 toggle @Override
351    public boolean isPeptideSpecific()
352    {
353  844 return true;
354    }
355   
 
356  566 toggle @Override
357    public String getSchemeName()
358    {
359  566 return JalviewColourScheme.Clustal.toString();
360    }
361   
 
362  47 toggle @Override
363    public boolean isSimple()
364    {
365  47 return false;
366    }
367   
 
368  0 toggle public String toRuleRep()
369    {
370  0 makeColours();
371  0 HashMap<String, String> cols = new HashMap();
372  0 for (String res : ResidueProperties.aa)
373    {
374  0 StringBuilder sb = new StringBuilder();
375   
376  0 int rnum = ResidueProperties.aaIndex[res.charAt(0)];
377  0 if (rnum < 0 || rnum >= residueColour.length)
378    {
379  0 continue;
380    }
381   
382  0 ConsensusColour cc = residueColour[rnum];
383  0 if (cc == null)
384    {
385  0 continue;
386    }
387    // sb.append("Residue "+res+" ("+rnum+")");
388    // sb.append("\t");
389  0 sb.append(cc.c.toString());
390  0 double f = 0;
391  0 sb.append("\t");
392  0 for (Consensus cons : cc.cons)
393    {
394  0 if (cons.threshold == 0 || f != cons.threshold)
395    {
396  0 if (f != 0)
397    {
398   
399  0 sb.append("}, {");
400    }
401    else
402    {
403  0 sb.append("{");
404    }
405  0 sb.append(cons.threshold);
406  0 sb.append(",");
407  0 f = cons.threshold;
408    }
409    else
410    {
411  0 sb.append(",");
412    }
413  0 sb.append(cons.maskstr);
414    }
415  0 sb.append("}");
416  0 String clxrep = sb.toString();
417  0 String xres = cols.get(clxrep);
418  0 if (xres == null)
419    {
420  0 xres = "";
421    }
422  0 xres += res;
423  0 cols.put(clxrep, xres);
424    }
425  0 StringBuilder sb = new StringBuilder();
426  0 for (String clxrep : cols.keySet())
427    {
428  0 sb.append(cols.get(clxrep));
429  0 sb.append("\t");
430  0 sb.append(clxrep);
431  0 sb.append("\n");
432   
433    }
434  0 return sb.toString();
435    }
436    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.