Clover icon

Coverage Report

  1. Project Clover database Mon Nov 11 2024 20:42:03 GMT
  2. Package jalview.datamodel

File VisibleContigsIterator.java

 

Coverage histogram

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

Code metrics

12
31
4
1
114
75
11
0.35
7.75
4
2.75

Classes

Class Line # Actions
VisibleContigsIterator 32 31 11
1.0100%
 

Contributing tests

This file is covered by 47 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.datamodel;
22   
23    import java.util.ArrayList;
24    import java.util.Iterator;
25    import java.util.List;
26   
27    /**
28    * An iterator which iterates over visible regions in a range. Provides a
29    * special "endsAtHidden" indicator to allow callers to determine if the final
30    * visible column is adjacent to a hidden region.
31    */
 
32    public class VisibleContigsIterator implements Iterator<int[]>
33    {
34    private List<int[]> vcontigs = new ArrayList<>();
35   
36    private int currentPosition = 0;
37   
38    private boolean endsAtHidden = false;
39   
 
40  3625 toggle VisibleContigsIterator(int start, int end, List<int[]> hiddenColumns)
41    {
42  3625 if (hiddenColumns != null && hiddenColumns.size() > 0)
43    {
44  1266 int vstart = start;
45  1266 int hideStart;
46  1266 int hideEnd;
47   
48  1266 for (int[] region : hiddenColumns)
49    {
50  2022 endsAtHidden = false;
51  2022 hideStart = region[0];
52  2022 hideEnd = region[1];
53   
54    // navigate to start
55  2022 if (hideEnd < vstart)
56    {
57  637 continue;
58    }
59  1385 if (hideStart > vstart)
60    {
61  884 if (end - 1 > hideStart - 1)
62    {
63  570 int[] contig = new int[] { vstart, hideStart - 1 };
64  570 vcontigs.add(contig);
65  570 endsAtHidden = true;
66    }
67    else
68    {
69  314 int[] contig = new int[] { vstart, end - 1 };
70  314 vcontigs.add(contig);
71    }
72    }
73  1385 vstart = hideEnd + 1;
74   
75    // exit if we're past the end
76  1385 if (vstart >= end)
77    {
78  756 break;
79    }
80    }
81   
82  1266 if (vstart < end)
83    {
84  510 int[] contig = new int[] { vstart, end - 1 };
85  510 vcontigs.add(contig);
86  510 endsAtHidden = false;
87    }
88    }
89    else
90    {
91  2359 int[] contig = new int[] { start, end - 1 };
92  2359 vcontigs.add(contig);
93    }
94    }
95   
 
96  730889 toggle @Override
97    public boolean hasNext()
98    {
99  731263 return (currentPosition < vcontigs.size());
100    }
101   
 
102  3753 toggle @Override
103    public int[] next()
104    {
105  3753 int[] result = vcontigs.get(currentPosition);
106  3753 currentPosition++;
107  3753 return result;
108    }
109   
 
110  730 toggle public boolean endsAtHidden()
111    {
112  730 return endsAtHidden;
113    }
114    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 20:49:40 GMT using coverage data from Mon Nov 11 2024 20:49:29 GMT.
  • OpenClover is free and open-source software.