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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:56:54 GMT
  2. Package jalview.schemes

File PIDColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

10
15
5
1
105
60
12
0.8
3
5
2.4

Classes

Class Line # Actions
PIDColourScheme 31 15 12
0.9333333493.3%
 

Contributing tests

This file is covered by 193 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.SequenceGroup;
26    import jalview.datamodel.SequenceI;
27    import jalview.util.Comparison;
28   
29    import java.awt.Color;
30   
 
31    public class PIDColourScheme extends ResidueColourScheme
32    {
33    private static final Color[] pidColours = { new Color(100, 100, 255),
34    new Color(153, 153, 255), new Color(204, 204, 255), };
35   
36    private static final float[] thresholds = { 80, 60, 40, };
37   
38    SequenceGroup group;
39   
 
40  67 toggle public PIDColourScheme()
41    {
42    }
43   
 
44  14 toggle @Override
45    public Color findColour(char c, int j, SequenceI seq,
46    String consensusResidue, float pid)
47    {
48    /*
49    * compare as upper case; note consensusResidue is
50    * always computed as uppercase
51    */
52  14 if ('a' <= c && c <= 'z')
53    {
54  1 c -= ('a' - 'A');
55    }
56   
57  14 if (consensusResidue == null || Comparison.isGap(c))
58    {
59  0 return Color.white;
60    }
61   
62  14 Color colour = Color.white;
63   
64    /*
65    * test whether this is the consensus (or joint consensus) residue
66    */
67  14 boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
68  14 if (matchesConsensus)
69    {
70  31 for (int i = 0; i < thresholds.length; i++)
71    {
72  29 if (pid > thresholds[i])
73    {
74  11 colour = pidColours[i];
75  11 break;
76    }
77    }
78    }
79   
80  14 return colour;
81    }
82   
 
83  564 toggle @Override
84    public String getSchemeName()
85    {
86  564 return JalviewColourScheme.PID.toString();
87    }
88   
89    /**
90    * Returns a new instance of this colour scheme with which the given data may
91    * be coloured
92    */
 
93  3 toggle @Override
94    public ColourSchemeI getInstance(AlignViewportI view,
95    AnnotatedCollectionI coll)
96    {
97  3 return new PIDColourScheme();
98    }
99   
 
100  47 toggle @Override
101    public boolean isSimple()
102    {
103  47 return false;
104    }
105    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 18 2024 10:04:05 GMT using coverage data from Mon Nov 18 2024 10:03:47 GMT.
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