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Coverage Report

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

File ColourSchemeProperty.java

 

Coverage histogram

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

Code metrics

12
20
4
1
158
58
11
0.55
5
4
2.75

Classes

Class Line # Actions
ColourSchemeProperty 41 20 11
0.7575%
 

Contributing tests

This file is covered by 121 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   
27    import java.awt.Color;
28   
29    /**
30    * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
31    * intelligently with mapping unknown names to user defined colourschemes (that
32    * exist or can be created from the string representation of the colourscheme
33    * name - either a hex RGB triplet or a named colour under java.awt.color ). The
34    * values of the colourscheme constants is important for callers of
35    * getColourName(int i), since it can be used to enumerate the set of built in
36    * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
37    *
38    * @author $author$
39    * @version $Revision$
40    */
 
41    public class ColourSchemeProperty
42    {
43   
44    /**
45    * Returns a colour scheme for the given name, with which the given data may
46    * be coloured. The name is not case-sensitive, and may be one of
47    * <ul>
48    * <li>any currently registered colour scheme; Jalview by default
49    * provides</li>
50    * <ul>
51    * <li>Clustal</li>
52    * <li>Blosum62</li>
53    * <li>% Identity</li>
54    * <li>Hydrophobic</li>
55    * <li>Zappo</li>
56    * <li>Taylor</li>
57    * <li>Helix Propensity</li>
58    * <li>Strand Propensity</li>
59    * <li>Turn Propensity</li>
60    * <li>Buried Index</li>
61    * <li>Nucleotide</li>
62    * <li>Purine/Pyrimidine</li>
63    * <li>T-Coffee Scores</li>
64    * <li>RNA Helices</li>
65    * </ul>
66    * <li>the name of a programmatically added colour scheme</li>
67    * <li>an AWT colour name e.g. red</li>
68    * <li>an AWT hex rgb colour e.g. ff2288</li>
69    * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
70    * </ul>
71    *
72    * If none of these formats is matched, the string is converted to a colour
73    * using a hashing algorithm. For name "None", returns null.
74    *
75    * @param forData
76    * @param name
77    * @return
78    */
 
79  412 toggle public static ColourSchemeI getColourScheme(AlignViewportI view,
80    AnnotatedCollectionI forData,
81    String name)
82    {
83  412 if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
84    {
85  366 return null;
86   
87    }
88   
89    /*
90    * if this is the name of a registered colour scheme, just
91    * create a new instance of it
92    */
93  46 ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
94    view,
95    forData, null);
96  46 if (scheme != null)
97    {
98  44 return scheme;
99    }
100   
101    /*
102    * try to parse the string as a residues colour scheme
103    * e.g. A=red;T,G=blue etc
104    * else parse the name as a colour specification
105    * e.g. "red" or "ff00ed",
106    * or failing that hash the name to a colour
107    */
108  2 UserColourScheme ucs = new UserColourScheme(name);
109  2 return ucs;
110    }
111   
112    public static Color rnaHelices[] = null;
113   
 
114  3 toggle public static void initRnaHelicesShading(int n)
115    {
116  3 int j = 0;
117  3 if (rnaHelices == null)
118    {
119  3 rnaHelices = new Color[n + 1];
120    }
121  0 else if (rnaHelices != null && rnaHelices.length <= n)
122    {
123  0 Color[] t = new Color[n + 1];
124  0 System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
125  0 j = rnaHelices.length;
126  0 rnaHelices = t;
127    }
128    else
129    {
130  0 return;
131    }
132    // Generate random colors and store
133  6 for (; j <= n; j++)
134    {
135  3 rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
136    }
137    }
138   
139    /**
140    * delete the existing cached RNA helices colours
141    */
 
142  9 toggle public static void resetRnaHelicesShading()
143    {
144  9 rnaHelices = null;
145    }
146   
147    /**
148    * Returns the name of the colour scheme (or "None" if it is null)
149    *
150    * @param cs
151    * @return
152    */
 
153  63 toggle public static String getColourName(ColourSchemeI cs)
154    {
155  63 return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
156    }
157   
158    }
  • 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.