Clover icon

Coverage Report

  1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.schemes

File ColourSchemeProperty.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
21% of files have more coverage

Code metrics

12
20
4
1
156
56
11
0.55
5
4
2.75

Classes

Class Line # Actions
ColourSchemeProperty 41 20 11
0.7575%
 

Contributing tests

This file is covered by 208 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  657 toggle public static ColourSchemeI getColourScheme(AlignViewportI view,
80    AnnotatedCollectionI forData, String name)
81    {
82  657 if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
83    {
84  592 return null;
85   
86    }
87   
88    /*
89    * if this is the name of a registered colour scheme, just
90    * create a new instance of it
91    */
92  65 ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
93    view, forData, null);
94  65 if (scheme != null)
95    {
96  63 return scheme;
97    }
98   
99    /*
100    * try to parse the string as a residues colour scheme
101    * e.g. A=red;T,G=blue etc
102    * else parse the name as a colour specification
103    * e.g. "red" or "ff00ed",
104    * or failing that hash the name to a colour
105    */
106  2 UserColourScheme ucs = new UserColourScheme(name);
107  2 return ucs;
108    }
109   
110    public static Color rnaHelices[] = null;
111   
 
112  3 toggle public static void initRnaHelicesShading(int n)
113    {
114  3 int j = 0;
115  3 if (rnaHelices == null)
116    {
117  3 rnaHelices = new Color[n + 1];
118    }
119  0 else if (rnaHelices != null && rnaHelices.length <= n)
120    {
121  0 Color[] t = new Color[n + 1];
122  0 System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
123  0 j = rnaHelices.length;
124  0 rnaHelices = t;
125    }
126    else
127    {
128  0 return;
129    }
130    // Generate random colors and store
131  6 for (; j <= n; j++)
132    {
133  3 rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
134    }
135    }
136   
137    /**
138    * delete the existing cached RNA helices colours
139    */
 
140  9 toggle public static void resetRnaHelicesShading()
141    {
142  9 rnaHelices = null;
143    }
144   
145    /**
146    * Returns the name of the colour scheme (or "None" if it is null)
147    *
148    * @param cs
149    * @return
150    */
 
151  86 toggle public static String getColourName(ColourSchemeI cs)
152    {
153  86 return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
154    }
155   
156    }
  • Report generated by OpenClover v 4.4.1 on Fri Dec 6 2024 13:54:25 GMT using coverage data from Fri Dec 6 2024 13:54:13 GMT.
  • OpenClover is free and open-source software.