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Coverage Report

  1. Project Clover database Thu Nov 27 2025 16:51:35 GMT
  2. Package jalview.schemes

File UserColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
13% of files have more coverage

Code metrics

48
100
16
1
360
237
46
0.46
6.25
16
2.88

Classes

Class Line # Actions
UserColourScheme 39 100 46
0.8353658383.5%
 

Contributing tests

This file is covered by 11 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.util.Locale;
24   
25    import jalview.api.AlignViewportI;
26    import jalview.datamodel.AnnotatedCollectionI;
27    import jalview.util.ColorUtils;
28    import jalview.util.StringUtils;
29   
30    import java.awt.Color;
31    import java.util.ArrayList;
32    import java.util.Collections;
33    import java.util.HashMap;
34    import java.util.List;
35    import java.util.Map;
36    import java.util.Map.Entry;
37    import java.util.StringTokenizer;
38   
 
39    public class UserColourScheme extends ResidueColourScheme
40    {
41    /*
42    * lookup (by symbol index) of lower case colours (if configured)
43    */
44    Color[] lowerCaseColours;
45   
46    protected String schemeName;
47   
 
48  5 toggle public UserColourScheme()
49    {
50  5 super(ResidueProperties.aaIndex);
51    }
52   
 
53  8 toggle public UserColourScheme(Color[] newColors)
54    {
55  8 super(ResidueProperties.aaIndex);
56  8 colors = newColors;
57    }
58   
 
59  0 toggle @Override
60    public ColourSchemeI getInstance(AlignViewportI view,
61    AnnotatedCollectionI sg)
62    {
63  0 return new UserColourScheme(this);
64    }
65   
66    /**
67    * Copy constructor
68    *
69    * @return
70    */
 
71  0 toggle protected UserColourScheme(UserColourScheme from)
72    {
73  0 this(from.colors);
74  0 schemeName = from.schemeName;
75  0 if (from.lowerCaseColours != null)
76    {
77  0 lowerCaseColours = new Color[from.lowerCaseColours.length];
78  0 System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
79    from.lowerCaseColours.length);
80    }
81    }
82   
83    /**
84    * Constructor for an animino acid colour scheme. The colour specification may
85    * be one of
86    * <ul>
87    * <li>an AWT colour name e.g. red</li>
88    * <li>an AWT hex rgb colour e.g. ff2288</li>
89    * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
90    * </ul>
91    *
92    * @param colour
93    */
 
94  5 toggle public UserColourScheme(String colour)
95    {
96  5 super(ResidueProperties.aaIndex);
97   
98  5 if (colour.contains("="))
99    {
100    /*
101    * a list of colours per residue(s)
102    */
103  2 parseAppletParameter(colour);
104  2 return;
105    }
106   
107  3 Color col = ColorUtils.parseColourString(colour);
108   
109  3 if (col == null)
110    {
111  1 jalview.bin.Console.outPrintln("Making colour from name: " + colour);
112  1 col = ColorUtils.createColourFromName(colour);
113    }
114   
115  3 setAll(col);
116  3 schemeName = colour;
117    }
118   
119    /**
120    * Sets all symbols to the specified colour
121    *
122    * @param col
123    */
 
124  7 toggle protected void setAll(Color col)
125    {
126  7 if (symbolIndex == null)
127    {
128  0 return;
129    }
130  7 int max = 0;
131  7 for (int index : symbolIndex)
132    {
133  1785 max = Math.max(max, index);
134    }
135  7 colors = new Color[max + 1];
136  175 for (int i = 0; i <= max; i++)
137    {
138  168 colors[i] = col;
139    }
140    }
141   
 
142  0 toggle public Color[] getColours()
143    {
144  0 return colors;
145    }
146   
 
147  0 toggle public Color[] getLowerCaseColours()
148    {
149  0 return lowerCaseColours;
150    }
151   
 
152  3 toggle public void setName(String name)
153    {
154  3 schemeName = name;
155    }
156   
 
157  0 toggle public String getName()
158    {
159  0 return schemeName;
160    }
161   
162    /**
163    * Parse and save residue colours specified as (for example)
164    *
165    * <pre>
166    * D,E=red; K,R,H=0022FF; c=100,50,75
167    * </pre>
168    *
169    * This should be a semi-colon separated list of colours, which may be defined
170    * by colour name, hex value or comma-separated RGB triple. Each colour is
171    * defined for a comma-separated list of amino acid single letter codes. (Note
172    * that this also allows a colour scheme to be defined for ACGT, but not for
173    * U.)
174    *
175    * @param paramValue
176    */
 
177  4 toggle void parseAppletParameter(String paramValue)
178    {
179  4 setAll(Color.white);
180   
181  4 StringTokenizer st = new StringTokenizer(paramValue, ";");
182  4 StringTokenizer st2;
183  4 String token = null, colour, residues;
184  4 try
185    {
186  21 while (st.hasMoreElements())
187    {
188  17 token = st.nextToken().trim();
189  17 residues = token.substring(0, token.indexOf("="));
190  17 colour = token.substring(token.indexOf("=") + 1);
191   
192  17 st2 = new StringTokenizer(residues, " ,");
193  45 while (st2.hasMoreTokens())
194    {
195  28 String residue = st2.nextToken();
196   
197  28 int colIndex = ResidueProperties.aaIndex[residue.charAt(0)];
198  28 if (colIndex == -1)
199    {
200  0 continue;
201    }
202   
203  28 if (residue.equalsIgnoreCase("lowerCase"))
204    {
205  1 if (lowerCaseColours == null)
206    {
207  0 lowerCaseColours = new Color[colors.length];
208    }
209  25 for (int i = 0; i < lowerCaseColours.length; i++)
210    {
211  24 if (lowerCaseColours[i] == null)
212    {
213  22 lowerCaseColours[i] = ColorUtils.parseColourString(colour);
214    }
215    }
216   
217  1 continue;
218    }
219   
220  27 if (residue.equals(residue.toLowerCase(Locale.ROOT)))
221    {
222  6 if (lowerCaseColours == null)
223    {
224  4 lowerCaseColours = new Color[colors.length];
225    }
226  6 lowerCaseColours[colIndex] = ColorUtils
227    .parseColourString(colour);
228    }
229    else
230    {
231  21 colors[colIndex] = ColorUtils.parseColourString(colour);
232    }
233    }
234    }
235    } catch (Exception ex)
236    {
237  0 jalview.bin.Console.outPrintln(
238    "Error parsing userDefinedColours:\n" + token + "\n" + ex);
239    }
240   
241    }
242   
 
243  0 toggle public void setLowerCaseColours(Color[] lcolours)
244    {
245  0 lowerCaseColours = lcolours;
246    }
247   
248    /**
249    * Returns the colour for the given residue character. If the residue is
250    * lower-case, and there is a specific colour defined for lower case, that
251    * colour is returned, else the colour for the upper case residue.
252    */
 
253  58 toggle @Override
254    public Color findColour(char c)
255    {
256  58 if ('a' <= c && c <= 'z' && lowerCaseColours != null)
257    {
258  14 Color colour = lowerCaseColours[symbolIndex[c]];
259  14 if (colour != null)
260    {
261  10 return colour;
262    }
263    }
264  48 return super.findColour(c);
265    }
266   
267    /**
268    * Answers the customised name of the colour scheme, if it has one, else "User
269    * Defined"
270    */
 
271  5 toggle @Override
272    public String getSchemeName()
273    {
274  5 if (schemeName != null && schemeName.length() > 0)
275    {
276  1 return schemeName;
277    }
278  4 return ResidueColourScheme.USER_DEFINED;
279    }
280   
281    /**
282    * Generate an applet colour parameter like A,C,D=12ffe9;Q,W=2393fd;w=9178dd
283    *
284    * @return
285    */
 
286  1 toggle public String toAppletParameter()
287    {
288    /*
289    * step 1: build a map from colours to the symbol(s) that have the colour
290    */
291  1 Map<Color, List<String>> colours = new HashMap<>();
292   
293  27 for (char symbol = 'A'; symbol <= 'Z'; symbol++)
294    {
295  26 String residue = String.valueOf(symbol);
296  26 int index = symbolIndex[symbol];
297  26 Color c = colors[index];
298  26 if (c != null && !c.equals(Color.white))
299    {
300  5 if (colours.get(c) == null)
301    {
302  2 colours.put(c, new ArrayList<String>());
303    }
304  5 colours.get(c).add(residue);
305    }
306  26 if (lowerCaseColours != null)
307    {
308  26 c = lowerCaseColours[index];
309  26 if (c != null && !c.equals(Color.white))
310    {
311  1 residue = residue.toLowerCase(Locale.ROOT);
312  1 if (colours.get(c) == null)
313    {
314  1 colours.put(c, new ArrayList<String>());
315    }
316  1 colours.get(c).add(residue);
317    }
318    }
319    }
320   
321    /*
322    * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
323    */
324  1 List<String> residueColours = new ArrayList<>();
325  1 for (Entry<Color, List<String>> cols : colours.entrySet())
326    {
327  3 boolean first = true;
328  3 StringBuilder sb = new StringBuilder();
329  3 for (String residue : cols.getValue())
330    {
331  6 if (!first)
332    {
333  3 sb.append(",");
334    }
335  6 sb.append(residue);
336  6 first = false;
337    }
338  3 sb.append("=");
339    /*
340    * get color as hex value, dropping the alpha (ff) part
341    */
342  3 String hexString = Integer.toHexString(cols.getKey().getRGB())
343    .substring(2);
344  3 sb.append(hexString);
345  3 residueColours.add(sb.toString());
346    }
347   
348    /*
349    * sort and output
350    */
351  1 Collections.sort(residueColours);
352  1 return StringUtils.listToDelimitedString(residueColours, ";");
353    }
354   
 
355  4 toggle @Override
356    public boolean hasGapColour()
357    {
358  4 return (findColour(' ') != null);
359    }
360    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 27 2025 17:01:26 GMT using coverage data from Thu Nov 27 2025 17:01:12 GMT.
  • OpenClover is free and open-source software.