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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.schemes

File UserColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

48
100
16
1
358
236
46
0.46
6.25
16
2.88

Classes

Class Line # Actions
UserColourScheme 37 100 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 jalview.api.AlignViewportI;
24    import jalview.datamodel.AnnotatedCollectionI;
25    import jalview.util.ColorUtils;
26    import jalview.util.StringUtils;
27   
28    import java.awt.Color;
29    import java.util.ArrayList;
30    import java.util.Collections;
31    import java.util.HashMap;
32    import java.util.List;
33    import java.util.Map;
34    import java.util.Map.Entry;
35    import java.util.StringTokenizer;
36   
 
37    public class UserColourScheme extends ResidueColourScheme
38    {
39    /*
40    * lookup (by symbol index) of lower case colours (if configured)
41    */
42    Color[] lowerCaseColours;
43   
44    protected String schemeName;
45   
 
46  5 toggle public UserColourScheme()
47    {
48  5 super(ResidueProperties.aaIndex);
49    }
50   
 
51  8 toggle public UserColourScheme(Color[] newColors)
52    {
53  8 super(ResidueProperties.aaIndex);
54  8 colors = newColors;
55    }
56   
 
57  0 toggle @Override
58    public ColourSchemeI getInstance(AlignViewportI view,
59    AnnotatedCollectionI sg)
60    {
61  0 return new UserColourScheme(this);
62    }
63   
64    /**
65    * Copy constructor
66    *
67    * @return
68    */
 
69  0 toggle protected UserColourScheme(UserColourScheme from)
70    {
71  0 this(from.colors);
72  0 schemeName = from.schemeName;
73  0 if (from.lowerCaseColours != null)
74    {
75  0 lowerCaseColours = new Color[from.lowerCaseColours.length];
76  0 System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
77    from.lowerCaseColours.length);
78    }
79    }
80   
81    /**
82    * Constructor for an animino acid colour scheme. The colour specification may
83    * be one of
84    * <ul>
85    * <li>an AWT colour name e.g. red</li>
86    * <li>an AWT hex rgb colour e.g. ff2288</li>
87    * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
88    * </ul>
89    *
90    * @param colour
91    */
 
92  5 toggle public UserColourScheme(String colour)
93    {
94  5 super(ResidueProperties.aaIndex);
95   
96  5 if (colour.contains("="))
97    {
98    /*
99    * a list of colours per residue(s)
100    */
101  2 parseAppletParameter(colour);
102  2 return;
103    }
104   
105  3 Color col = ColorUtils.parseColourString(colour);
106   
107  3 if (col == null)
108    {
109  1 System.out.println("Making colour from name: " + colour);
110  1 col = ColorUtils.createColourFromName(colour);
111    }
112   
113  3 setAll(col);
114  3 schemeName = colour;
115    }
116   
117    /**
118    * Sets all symbols to the specified colour
119    *
120    * @param col
121    */
 
122  7 toggle protected void setAll(Color col)
123    {
124  7 if (symbolIndex == null)
125    {
126  0 return;
127    }
128  7 int max = 0;
129  7 for (int index : symbolIndex)
130    {
131  1785 max = Math.max(max, index);
132    }
133  7 colors = new Color[max + 1];
134  175 for (int i = 0; i <= max; i++)
135    {
136  168 colors[i] = col;
137    }
138    }
139   
 
140  0 toggle public Color[] getColours()
141    {
142  0 return colors;
143    }
144   
 
145  0 toggle public Color[] getLowerCaseColours()
146    {
147  0 return lowerCaseColours;
148    }
149   
 
150  3 toggle public void setName(String name)
151    {
152  3 schemeName = name;
153    }
154   
 
155  0 toggle public String getName()
156    {
157  0 return schemeName;
158    }
159   
160    /**
161    * Parse and save residue colours specified as (for example)
162    *
163    * <pre>
164    * D,E=red; K,R,H=0022FF; c=100,50,75
165    * </pre>
166    *
167    * This should be a semi-colon separated list of colours, which may be defined
168    * by colour name, hex value or comma-separated RGB triple. Each colour is
169    * defined for a comma-separated list of amino acid single letter codes. (Note
170    * that this also allows a colour scheme to be defined for ACGT, but not for
171    * U.)
172    *
173    * @param paramValue
174    */
 
175  4 toggle void parseAppletParameter(String paramValue)
176    {
177  4 setAll(Color.white);
178   
179  4 StringTokenizer st = new StringTokenizer(paramValue, ";");
180  4 StringTokenizer st2;
181  4 String token = null, colour, residues;
182  4 try
183    {
184  21 while (st.hasMoreElements())
185    {
186  17 token = st.nextToken().trim();
187  17 residues = token.substring(0, token.indexOf("="));
188  17 colour = token.substring(token.indexOf("=") + 1);
189   
190  17 st2 = new StringTokenizer(residues, " ,");
191  45 while (st2.hasMoreTokens())
192    {
193  28 String residue = st2.nextToken();
194   
195  28 int colIndex = ResidueProperties.aaIndex[residue.charAt(0)];
196  28 if (colIndex == -1)
197    {
198  0 continue;
199    }
200   
201  28 if (residue.equalsIgnoreCase("lowerCase"))
202    {
203  1 if (lowerCaseColours == null)
204    {
205  0 lowerCaseColours = new Color[colors.length];
206    }
207  25 for (int i = 0; i < lowerCaseColours.length; i++)
208    {
209  24 if (lowerCaseColours[i] == null)
210    {
211  22 lowerCaseColours[i] = ColorUtils.parseColourString(colour);
212    }
213    }
214   
215  1 continue;
216    }
217   
218  27 if (residue.equals(residue.toLowerCase()))
219    {
220  6 if (lowerCaseColours == null)
221    {
222  4 lowerCaseColours = new Color[colors.length];
223    }
224  6 lowerCaseColours[colIndex] = ColorUtils
225    .parseColourString(colour);
226    }
227    else
228    {
229  21 colors[colIndex] = ColorUtils.parseColourString(colour);
230    }
231    }
232    }
233    } catch (Exception ex)
234    {
235  0 System.out.println(
236    "Error parsing userDefinedColours:\n" + token + "\n" + ex);
237    }
238   
239    }
240   
 
241  0 toggle public void setLowerCaseColours(Color[] lcolours)
242    {
243  0 lowerCaseColours = lcolours;
244    }
245   
246    /**
247    * Returns the colour for the given residue character. If the residue is
248    * lower-case, and there is a specific colour defined for lower case, that
249    * colour is returned, else the colour for the upper case residue.
250    */
 
251  58 toggle @Override
252    public Color findColour(char c)
253    {
254  58 if ('a' <= c && c <= 'z' && lowerCaseColours != null)
255    {
256  14 Color colour = lowerCaseColours[symbolIndex[c]];
257  14 if (colour != null)
258    {
259  10 return colour;
260    }
261    }
262  48 return super.findColour(c);
263    }
264   
265    /**
266    * Answers the customised name of the colour scheme, if it has one, else "User
267    * Defined"
268    */
 
269  5 toggle @Override
270    public String getSchemeName()
271    {
272  5 if (schemeName != null && schemeName.length() > 0)
273    {
274  1 return schemeName;
275    }
276  4 return ResidueColourScheme.USER_DEFINED;
277    }
278   
279    /**
280    * Generate an applet colour parameter like A,C,D=12ffe9;Q,W=2393fd;w=9178dd
281    *
282    * @return
283    */
 
284  1 toggle public String toAppletParameter()
285    {
286    /*
287    * step 1: build a map from colours to the symbol(s) that have the colour
288    */
289  1 Map<Color, List<String>> colours = new HashMap<>();
290   
291  27 for (char symbol = 'A'; symbol <= 'Z'; symbol++)
292    {
293  26 String residue = String.valueOf(symbol);
294  26 int index = symbolIndex[symbol];
295  26 Color c = colors[index];
296  26 if (c != null && !c.equals(Color.white))
297    {
298  5 if (colours.get(c) == null)
299    {
300  2 colours.put(c, new ArrayList<String>());
301    }
302  5 colours.get(c).add(residue);
303    }
304  26 if (lowerCaseColours != null)
305    {
306  26 c = lowerCaseColours[index];
307  26 if (c != null && !c.equals(Color.white))
308    {
309  1 residue = residue.toLowerCase();
310  1 if (colours.get(c) == null)
311    {
312  1 colours.put(c, new ArrayList<String>());
313    }
314  1 colours.get(c).add(residue);
315    }
316    }
317    }
318   
319    /*
320    * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
321    */
322  1 List<String> residueColours = new ArrayList<>();
323  1 for (Entry<Color, List<String>> cols : colours.entrySet())
324    {
325  3 boolean first = true;
326  3 StringBuilder sb = new StringBuilder();
327  3 for (String residue : cols.getValue())
328    {
329  6 if (!first)
330    {
331  3 sb.append(",");
332    }
333  6 sb.append(residue);
334  6 first = false;
335    }
336  3 sb.append("=");
337    /*
338    * get color as hex value, dropping the alpha (ff) part
339    */
340  3 String hexString = Integer.toHexString(cols.getKey().getRGB())
341    .substring(2);
342  3 sb.append(hexString);
343  3 residueColours.add(sb.toString());
344    }
345   
346    /*
347    * sort and output
348    */
349  1 Collections.sort(residueColours);
350  1 return StringUtils.listToDelimitedString(residueColours, ";");
351    }
352   
 
353  4 toggle @Override
354    public boolean hasGapColour()
355    {
356  4 return (findColour(' ') != null);
357    }
358    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.