Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
VisibleContigsIterator	32	31	11	0.00%	Show methods

Class VisibleContigsIterator

Class VisibleContigsIterator	Line # 32	Total Statements 31	Complexity 11	TOTAL Coverage 0.00%
VisibleContigsIterator(int,int,List<int[]>)   VisibleContigsIterator(int,int,List<int[]>)	4040	26.026	8.08	0.0 0.00%
hasNext() : boolean   hasNext() : boolean	9696	1.01	1.01	0.0 0.00%
next() : int[]   next() : int[]	102102	3.03	1.01	0.0 0.00%
endsAtHidden() : boolean   endsAtHidden() : boolean	110110	1.01	1.01	0.0 0.00%

 

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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		*/
		0% Uncovered Elements: 47 (47) Complexity: 11 Complexity Density: 0.35
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
		0% Uncovered Elements: 38 (38) Complexity: 8 Complexity Density: 0.31
40	0	VisibleContigsIterator(int start, int end, List<int[]> hiddenColumns)...
41		{
42	0	if (hiddenColumns != null && hiddenColumns.size() > 0)
43		{
44	0	int vstart = start;
45	0	int hideStart;
46	0	int hideEnd;
47
48	0	for (int[] region : hiddenColumns)
49		{
50	0	endsAtHidden = false;
51	0	hideStart = region[0];
52	0	hideEnd = region[1];
53
54		// navigate to start
55	0	if (hideEnd < vstart)
56		{
57	0	continue;
58		}
59	0	if (hideStart > vstart)
60		{
61	0	if (end - 1 > hideStart - 1)
62		{
63	0	int[] contig = new int[] { vstart, hideStart - 1 };
64	0	vcontigs.add(contig);
65	0	endsAtHidden = true;
66		}
67		else
68		{
69	0	int[] contig = new int[] { vstart, end - 1 };
70	0	vcontigs.add(contig);
71		}
72		}
73	0	vstart = hideEnd + 1;
74
75		// exit if we're past the end
76	0	if (vstart >= end)
77		{
78	0	break;
79		}
80		}
81
82	0	if (vstart < end)
83		{
84	0	int[] contig = new int[] { vstart, end - 1 };
85	0	vcontigs.add(contig);
86	0	endsAtHidden = false;
87		}
88		}
89		else
90		{
91	0	int[] contig = new int[] { start, end - 1 };
92	0	vcontigs.add(contig);
93		}
94		}
95
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
96	0	@Override...
97		public boolean hasNext()
98		{
99	0	return (currentPosition < vcontigs.size());
100		}
101
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
102	0	@Override...
103		public int[] next()
104		{
105	0	int[] result = vcontigs.get(currentPosition);
106	0	currentPosition++;
107	0	return result;
108		}
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	public boolean endsAtHidden()...
111		{
112	0	return endsAtHidden;
113		}
114		}