Clover icon

Coverage Report

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

File IdColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart5.png
43% of files have more coverage

Code metrics

4
10
9
1
108
60
11
1.1
1.11
9
1.22

Classes

Class Line # Actions
IdColourScheme 38 10 11
0.4782608747.8%
 

Contributing tests

This file is covered by 185 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.awt.Color;
29    import java.util.Map;
30   
31    /**
32    * shade sequences using the colour shown in the ID panel. Useful to map
33    * sequence groupings onto residue data (eg tree subgroups visualised on
34    * structures or overview window)
35    *
36    * @author jprocter
37    */
 
38    public class IdColourScheme implements ColourSchemeI
39    {
40    AlignViewportI view = null;
41   
 
42  50 toggle public IdColourScheme()
43    {
44   
45    }
46   
 
47  1 toggle public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)
48    {
49  1 this.view = view;
50    }
51   
 
52  564 toggle @Override
53    public String getSchemeName()
54    {
55  564 return JalviewColourScheme.IdColour.toString();
56    }
57   
58    /**
59    * Returns a new instance of this colour scheme with which the given data may
60    * be coloured
61    */
 
62  1 toggle @Override
63    public ColourSchemeI getInstance(AlignViewportI view,
64    AnnotatedCollectionI coll)
65    {
66  1 return new IdColourScheme(view, coll);
67    }
68   
 
69  0 toggle @Override
70    public void alignmentChanged(AnnotatedCollectionI alignment,
71    Map<SequenceI, SequenceCollectionI> hiddenReps)
72    {
73    }
74   
 
75  0 toggle @Override
76    public Color findColour(char symbol, int position, SequenceI seq,
77    String consensusResidue, float pid)
78    {
79    // rather than testing if coll is a sequence group, and if so looking at
80    // ((SequenceGroup)coll).idColour
81    // we always return the sequence ID colour, in case the user has customised
82    // the displayed Id colour by right-clicking an internal node in the tree.
83  0 if (view == null)
84    {
85  0 return Color.WHITE;
86    }
87  0 Color col = view.getSequenceColour(seq);
88  0 return Color.WHITE.equals(col) ? Color.WHITE : col.darker();
89    }
90   
 
91  0 toggle @Override
92    public boolean hasGapColour()
93    {
94  0 return false;
95    }
96   
 
97  462 toggle @Override
98    public boolean isApplicableTo(AnnotatedCollectionI ac)
99    {
100  462 return true;
101    }
102   
 
103  47 toggle @Override
104    public boolean isSimple()
105    {
106  47 return false;
107    }
108    }
  • 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.