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Coverage Report

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

File ColourSchemes.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
27% of files have more coverage

Code metrics

12
28
9
1
198
92
17
0.61
3.11
9
1.89

Classes

Class Line # Actions
ColourSchemes 31 28 17
0.693877669.4%
 

Contributing tests

This file is covered by 103 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.datamodel.SequenceCollectionI;
26    import jalview.datamodel.SequenceI;
27   
28    import java.util.LinkedHashMap;
29    import java.util.Map;
30   
 
31    public class ColourSchemes
32    {
33    /*
34    * singleton instance of this class
35    */
36    private static ColourSchemes instance = new ColourSchemes();
37   
38    /*
39    * a map from scheme name (lower-cased) to an instance of it
40    */
41    private Map<String, ColourSchemeI> schemes;
42   
43    /**
44    * Returns the singleton instance of this class
45    *
46    * @return
47    */
 
48  332 toggle public static ColourSchemes getInstance()
49    {
50  332 return instance;
51    }
52   
 
53  18 toggle private ColourSchemes()
54    {
55  18 loadColourSchemes();
56    }
57   
58    /**
59    * Loads an instance of each standard or user-defined colour scheme
60    *
61    * @return
62    */
 
63  18 toggle void loadColourSchemes()
64    {
65    /*
66    * store in an order-preserving map, so items can be added to menus
67    * in the order in which they are 'discovered'
68    */
69  18 schemes = new LinkedHashMap<>();
70   
71  18 for (JalviewColourScheme cs : JalviewColourScheme.values())
72    {
73  270 try
74    {
75  270 registerColourScheme(
76    cs.getSchemeClass().getDeclaredConstructor().newInstance());
77    } catch (InstantiationException | IllegalAccessException e)
78    {
79  0 System.err.println("Error instantiating colour scheme for "
80    + cs.toString() + " " + e.getMessage());
81  0 e.printStackTrace();
82    } catch (ReflectiveOperationException roe)
83    {
84  0 roe.printStackTrace();
85    }
86    }
87    }
88   
89    /**
90    * Registers a colour scheme
91    *
92    * @param cs
93    */
 
94  272 toggle public void registerColourScheme(ColourSchemeI cs)
95    {
96  272 String name = cs.getSchemeName();
97  272 if (name == null)
98    {
99  0 System.err.println("ColourScheme name may not be null");
100  0 return;
101    }
102   
103    /*
104    * name is lower-case for non-case-sensitive lookup
105    * (name in the colour keeps its true case)
106    */
107  272 String lower = name.toLowerCase();
108  272 if (schemes.containsKey(lower))
109    {
110  0 System.err
111    .println("Warning: overwriting colour scheme named " + name);
112    }
113  272 schemes.put(lower, cs);
114    }
115   
116    /**
117    * Removes a colour scheme by name
118    *
119    * @param name
120    */
 
121  0 toggle public void removeColourScheme(String name)
122    {
123  0 if (name != null)
124    {
125  0 schemes.remove(name.toLowerCase());
126    }
127    }
128   
129    /**
130    * Returns an instance of the colour scheme with which the given view may be
131    * coloured
132    *
133    * @param name
134    * name of the colour scheme
135    * @param viewport
136    * @param forData
137    * the data to be coloured
138    * @param optional
139    * map from hidden representative sequences to the sequences they
140    * represent
141    * @return
142    */
 
143  81 toggle public ColourSchemeI getColourScheme(String name,
144    AlignViewportI viewport, AnnotatedCollectionI forData,
145    Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
146    {
147  81 if (name == null)
148    {
149  0 return null;
150    }
151  81 ColourSchemeI cs = schemes.get(name.toLowerCase());
152  81 return cs == null ? null
153    : cs.getInstance(viewport, forData);
154    }
155   
156    /**
157    * Returns an instance of the colour scheme with which the given view may be
158    * coloured
159    *
160    * @param name
161    * name of the colour scheme
162    * @param forData
163    * the data to be coloured
164    * @return
165    */
 
166  17 toggle public ColourSchemeI getColourScheme(String name,
167    AnnotatedCollectionI forData)
168    {
169  17 return getColourScheme(name, null, forData, null);
170    }
171   
172    /**
173    * Returns an iterable set of the colour schemes, in the order in which they
174    * were added
175    *
176    * @return
177    */
 
178  262 toggle public Iterable<ColourSchemeI> getColourSchemes()
179    {
180  262 return schemes.values();
181    }
182   
183    /**
184    * Answers true if there is a scheme with the given name, else false. The test
185    * is not case-sensitive.
186    *
187    * @param name
188    * @return
189    */
 
190  7 toggle public boolean nameExists(String name)
191    {
192  7 if (name == null)
193    {
194  1 return false;
195    }
196  6 return schemes.containsKey(name.toLowerCase());
197    }
198    }
  • 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.