Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AtomSpecModel	33	24	12	0.00%	Show methods

Class AtomSpecModel

Class AtomSpecModel	Line # 33	Total Statements 24	Complexity 12	TOTAL Coverage 0.00%
AtomSpecModel()   AtomSpecModel()	4343	1.01	1.01	0.0 0.00%
addRange(String,int,int,String) : void   addRange(String,int,int,String) : void	5656	8.08	3.03	0.0 0.00%
getModels() : Iterable<String>   getModels() : Iterable<String>	8383	1.01	1.01	0.0 0.00%
getModelCount() : int   getModelCount() : int	8888	1.01	1.01	0.0 0.00%
getChains(String) : Iterable<String>   getChains(String) : Iterable<String>	9393	1.01	2.02	0.0 0.00%
getRanges(String,String) : List<int[]>   getRanges(String,String) : List<int[]>	107107	12.012	4.04	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.structure;
22
23		import java.util.ArrayList;
24		import java.util.BitSet;
25		import java.util.List;
26		import java.util.Map;
27		import java.util.TreeMap;
28
29		/**
30		* A class to model a set of models, chains and atom range positions
31		*
32		*/
		0% Uncovered Elements: 42 (42) Complexity: 12 Complexity Density: 0.5
33		public class AtomSpecModel
34		{
35		/*
36		* { modelId, {chainCode, List<from-to> ranges} }
37		*/
38		private Map<String, Map<String, BitSet>> atomSpec;
39
40		/**
41		* Constructor
42		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
43	0	public AtomSpecModel()...
44		{
45	0	atomSpec = new TreeMap<>();
46		}
47
48		/**
49		* Adds one contiguous range to this atom spec
50		*
51		* @param model
52		* @param startPos
53		* @param endPos
54		* @param chain
55		*/
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
56	0	public void addRange(String model, int startPos, int endPos, String chain)...
57		{
58		/*
59		* Get/initialize map of data for the colour and model
60		*/
61	0	Map<String, BitSet> modelData = atomSpec.get(model);
62	0	if (modelData == null)
63		{
64	0	atomSpec.put(model, modelData = new TreeMap<>());
65		}
66
67		/*
68		* Get/initialize map of data for colour, model and chain
69		*/
70	0	BitSet chainData = modelData.get(chain);
71	0	if (chainData == null)
72		{
73	0	chainData = new BitSet();
74	0	modelData.put(chain, chainData);
75		}
76
77		/*
78		* Add the start/end positions
79		*/
80	0	chainData.set(startPos, endPos + 1);
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	public Iterable<String> getModels()...
84		{
85	0	return atomSpec.keySet();
86		}
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	public int getModelCount()...
89		{
90	0	return atomSpec.size();
91		}
92
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
93	0	public Iterable<String> getChains(String model)...
94		{
95	0	return atomSpec.containsKey(model) ? atomSpec.get(model).keySet()
96		: null;
97		}
98
99		/**
100		* Returns a (possibly empty) ordered list of contiguous atom ranges for the
101		* given model and chain.
102		*
103		* @param model
104		* @param chain
105		* @return
106		*/
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.33
107	0	public List<int[]> getRanges(String model, String chain)...
108		{
109	0	List<int[]> ranges = new ArrayList<>();
110	0	if (atomSpec.containsKey(model))
111		{
112	0	BitSet bs = atomSpec.get(model).get(chain);
113	0	int start = 0;
114	0	if (bs != null)
115		{
116	0	start = bs.nextSetBit(start);
117	0	int end = 0;
118	0	while (start != -1)
119		{
120	0	end = bs.nextClearBit(start);
121	0	ranges.add(new int[] { start, end - 1 });
122	0	start = bs.nextSetBit(end);
123		}
124		}
125		}
126	0	return ranges;
127		}
128		}