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Coverage Report

  1. Project Clover database Thu Jan 15 2026 16:11:02 GMT
  2. Package jalview.workers

File AlignCalcWorker.java

 

Coverage histogram

../../img/srcFileCovDistChart4.png
51% of files have more coverage

Code metrics

8
30
7
1
144
85
12
0.4
4.29
7
1.71

Classes

Class Line # Actions
AlignCalcWorker 39 30 12
0.3777777937.8%
 

Contributing tests

This file is covered by 217 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.workers;
22   
23    import jalview.api.AlignCalcManagerI2;
24    import jalview.api.AlignCalcWorkerI;
25    import jalview.api.AlignViewportI;
26    import jalview.api.AlignmentViewPanel;
27    import jalview.datamodel.AlignmentAnnotation;
28    import jalview.datamodel.AlignmentI;
29    import jalview.datamodel.Annotation;
30   
31    import java.util.List;
32   
33    /**
34    * Base class for alignment calculation workers
35    *
36    * @author jimp
37    *
38    */
 
39    public abstract class AlignCalcWorker implements AlignCalcWorkerI
40    {
41    /**
42    * manager and data source for calculations
43    */
44    protected AlignViewportI alignViewport;
45   
46    protected AlignCalcManagerI2 calcMan;
47   
48    protected AlignmentViewPanel ap;
49   
50    protected List<AlignmentAnnotation> ourAnnots;
51   
 
52  1855 toggle public AlignCalcWorker(AlignViewportI alignViewport,
53    AlignmentViewPanel alignPanel)
54    {
55  1855 this.alignViewport = alignViewport;
56  1855 calcMan = alignViewport.getCalcManager();
57  1855 ap = alignPanel;
58    }
59   
 
60  6 toggle protected void abortAndDestroy()
61    {
62  6 if (calcMan != null)
63    {
64  6 calcMan.cancelWorker(this);
65  0 calcMan.removeWorker(this);
66    }
67  0 alignViewport = null;
68  0 calcMan = null;
69  0 ap = null;
70   
71    }
72   
 
73  100626 toggle @Override
74    public boolean involves(AlignmentAnnotation i)
75    {
76  100626 return ourAnnots != null && ourAnnots.contains(i);
77    }
78   
79    /**
80    * Permanently removes from the alignment all annotation rows managed by this
81    * worker
82    */
 
83  0 toggle @Override
84    public void removeAnnotation()
85    {
86  0 if (ourAnnots != null && alignViewport != null)
87    {
88  0 AlignmentI alignment = alignViewport.getAlignment();
89  0 synchronized (ourAnnots)
90    {
91  0 for (AlignmentAnnotation aa : ourAnnots)
92    {
93  0 alignment.deleteAnnotation(aa, true);
94    }
95    }
96  0 ourAnnots.clear();
97    }
98    }
99   
100    // TODO: allow GUI to query workers associated with annotation to add items to
101    // annotation label panel popup menu
102   
 
103  0 toggle @Override
104    public boolean isDeletable()
105    {
106  0 return false;
107    }
108   
109    /**
110    * Calculate min and max values of annotations and set as graphMin, graphMax
111    * on the AlignmentAnnotation. This is needed because otherwise, well, bad
112    * things happen.
113    *
114    * @param ann
115    * @param anns
116    */
 
117  2 toggle protected void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)
118    {
119    // TODO feels like this belongs inside AlignmentAnnotation!
120  2 float max = Float.MIN_VALUE;
121  2 float min = Float.MAX_VALUE;
122  2 boolean set = false;
123  2 for (Annotation a : anns)
124    {
125  0 if (a != null)
126    {
127  0 set = true;
128  0 float val = a.value;
129  0 max = Math.max(max, val);
130  0 min = Math.min(min, val);
131    }
132    }
133  2 if (set)
134    {
135  0 ann.graphMin = min;
136  0 ann.graphMax = max;
137    }
138    }
139   
 
140  0 toggle public AlignViewportI getAlignViewport()
141    {
142  0 return alignViewport;
143    }
144    }
  • Report generated by OpenClover v 4.4.1 on Thu Jan 15 2026 16:19:00 GMT using coverage data from Thu Jan 15 2026 16:18:50 GMT.
  • OpenClover is free and open-source software.