Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StartRegionIterator	31	24	10	0.777777877.8%	Show methods

Class StartRegionIterator

Class StartRegionIterator	Line # 31	Total Statements 24	Complexity 10	TOTAL Coverage 0.777777877.8%
StartRegionIterator(int,int,List<int[]>)   StartRegionIterator(int,int,List<int[]>)	5656	1.01	1.01	0.0 0.00%
StartRegionIterator(HiddenCursorPosition,int,int,List<int[]>)   StartRegionIterator(HiddenCursorPosition,int,int,List<int[]>)	7474	19.019	7.07	0.7777778 0.777777877.8%
hasNext() : boolean   hasNext() : boolean	124124	1.01	1.01	1.0 1.0100%
next() : Integer   next() : Integer	135135	3.03	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.7777778	jalview.datamodel.HiddenColumnsTest.testBoundedStartIteratorjalview.datamodel.HiddenColumnsTest.testBoundedStartIterator	1PASS
	0.6944444	jalview.analysis.AnnotationSorterTest.testSort_timingSemisortedjalview.analysis.AnnotationSorterTest.testSort_timingSemisorted	1PASS
	0.6944444	jalview.structures.models.AAStructureBindingModelTest.testBuildColoursMapjalview.structures.models.AAStructureBindingModelTest.testBuildColoursMap	1PASS
	0.6944444	jalview.analysis.AnnotationSorterTest.testSort_timingPresortedjalview.analysis.AnnotationSorterTest.testSort_timingPresorted	1PASS

 

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 start positions of hidden column
29		* regions in a range.
30		*/
		77.8% Uncovered Elements: 8 (36) Complexity: 10 Complexity Density: 0.42
31		public class StartRegionIterator implements Iterator<Integer>
32		{
33		// start position to iterate from
34		private int start;
35
36		// end position to iterate to
37		private int end;
38
39		// current index in hiddenColumns
40		private int currentPosition = 0;
41
42		// local copy or reference to hiddenColumns
43		private List<Integer> positions = null;
44
45		/**
46		* Construct an iterator over hiddenColums bounded at [lowerBound,upperBound]
47		*
48		* @param lowerBound
49		* lower bound to iterate from
50		* @param upperBound
51		* upper bound to iterate to
52		* @param useCopyCols
53		* whether to make a local copy of hiddenColumns for iteration (set
54		* to true if calling from outwith the HiddenColumns class)
55		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	StartRegionIterator(int lowerBound, int upperBound,...
57		List<int[]> hiddenColumns)
58		{
59	0	this(null, lowerBound, upperBound, hiddenColumns);
60		}
61
62		/**
63		* Construct an iterator over hiddenColums bounded at [lowerBound,upperBound]
64		*
65		* @param pos
66		* a hidden cursor position to start from - may be null
67		* @param lowerBound
68		* lower bound to iterate from - will be ignored if pos != null
69		* @param upperBound
70		* upper bound to iterate to
71		* @param hiddenColumns
72		* the hidden columns collection to use
73		*/
		77.8% Uncovered Elements: 6 (27) Complexity: 7 Complexity Density: 0.37
74	14	StartRegionIterator(HiddenCursorPosition pos, int lowerBound,...
75		int upperBound, List<int[]> hiddenColumns)
76		{
77	14	start = lowerBound;
78	14	end = upperBound;
79
80	14	if (hiddenColumns != null)
81		{
82	14	positions = new ArrayList<>(hiddenColumns.size());
83
84		// navigate to start, keeping count of hidden columns
85	14	int i = 0;
86	14	int hiddenSoFar = 0;
87
88	14	if (pos != null)
89		{
90		// use the cursor position provided
91	13	i = pos.getRegionIndex();
92	13	hiddenSoFar = pos.getHiddenSoFar();
93		}
94		else
95		{
96		// navigate to start
97	1	while ((i < hiddenColumns.size())
98		&& (hiddenColumns.get(i)[0] < start + hiddenSoFar))
99		{
100	0	int[] region = hiddenColumns.get(i);
101	0	hiddenSoFar += region[1] - region[0] + 1;
102	0	i++;
103		}
104		}
105
106		// iterate from start to end, adding start positions of each
107		// hidden region. Positions are visible columns count, not absolute
108	30	while (i < hiddenColumns.size()
109		&& (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
110		{
111	16	int[] region = hiddenColumns.get(i);
112	16	positions.add(region[0] - hiddenSoFar);
113	16	hiddenSoFar += region[1] - region[0] + 1;
114	16	i++;
115		}
116		}
117		else
118		{
119	0	positions = new ArrayList<>();
120		}
121
122		}
123
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
124	28	@Override...
125		public boolean hasNext()
126		{
127	28	return (currentPosition < positions.size());
128		}
129
130		/**
131		* Get next hidden region start position
132		*
133		* @return the start position in *visible* coordinates
134		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
135	16	@Override...
136		public Integer next()
137		{
138	16	int result = positions.get(currentPosition);
139	16	currentPosition++;
140	16	return result;
141		}
142		}