Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AtomSpecModel	52	45	16	3	0.958904195.9%	Show methods

Class AtomSpecModel

Class AtomSpecModel	Line # 52	Total Statements 45	Complexity 16	Uncovered Elements 3	TOTAL Coverage 0.958904195.9%
AtomSpecModel()   AtomSpecModel()	5959	1.01	1.01	0.00	1.0 1.0100%
addRange(int,int,int,String) : void   addRange(int,int,int,String) : void	7272	8.08	3.03	0.00	1.0 1.0100%
getAtomSpec() : String   getAtomSpec() : String	105105	28.028	8.08	3.03	0.9285714 0.928571492.9%
appendRange(StringBuilder,int,int,String,boolean) : void   appendRange(StringBuilder,int,int,String,boolean) : void	180180	8.08	4.04	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.9589041	jalview.ext.rbvi.chimera.AtomSpecModelTest.testGetAtomSpecjalview.ext.rbvi.chimera.AtomSpecModelTest.testGetAtomSpec	1PASS
	0.9315069	jalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildColourCommandsjalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildColourCommands	1PASS
	0.8356164	jalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildSetAttributeCommandsjalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildSetAttributeCommands	1PASS
	0.8082192	jalview.ext.rbvi.chimera.ChimeraCommandsTest.testGetColourBySequenceCommands_hiddenColumnsjalview.ext.rbvi.chimera.ChimeraCommandsTest.testGetColourBySequenceCommands_hiddenColumns	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.ext.rbvi.chimera;
22
23		import jalview.util.IntRangeComparator;
24
25		import java.util.ArrayList;
26		import java.util.Collections;
27		import java.util.Iterator;
28		import java.util.List;
29		import java.util.Map;
30		import java.util.TreeMap;
31
32		/**
33		* A class to model a Chimera atomspec pattern, for example
34		*
35		* <pre>
36		* #0:15.A,28.A,54.A,63.A,70-72.A,83-84.A,97-98.A|#1:2.A,6.A,11.A,13-14.A,70.A,82.A,96-97.A
37		* </pre>
38		*
39		* where
40		* <ul>
41		* <li>#0 is a model number</li>
42		* <li>15 or 70-72 is a residue number, or range of residue numbers</li>
43		* <li>.A is a chain identifier</li>
44		* <li>residue ranges are separated by comma</li>
45		* <li>atomspecs for distinct models are separated by | (or)</li>
46		* </ul>
47		*
48		* <pre>
49		* &#64;see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
50		* </pre>
51		*/
		95.9% Uncovered Elements: 3 (73) Complexity: 16 Complexity Density: 0.36
52		public class AtomSpecModel
53		{
54		private Map<Integer, Map<String, List<int[]>>> atomSpec;
55
56		/**
57		* Constructor
58		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
59	12	public AtomSpecModel()...
60		{
61	12	atomSpec = new TreeMap<Integer, Map<String, List<int[]>>>();
62		}
63
64		/**
65		* Adds one contiguous range to this atom spec
66		*
67		* @param model
68		* @param startPos
69		* @param endPos
70		* @param chain
71		*/
		100% Uncovered Elements: 0 (12) Complexity: 3 Complexity Density: 0.38
72	34	public void addRange(int model, int startPos, int endPos, String chain)...
73		{
74		/*
75		* Get/initialize map of data for the colour and model
76		*/
77	34	Map<String, List<int[]>> modelData = atomSpec.get(model);
78	34	if (modelData == null)
79		{
80	19	atomSpec.put(model, modelData = new TreeMap<String, List<int[]>>());
81		}
82
83		/*
84		* Get/initialize map of data for colour, model and chain
85		*/
86	34	List<int[]> chainData = modelData.get(chain);
87	34	if (chainData == null)
88		{
89	24	chainData = new ArrayList<int[]>();
90	24	modelData.put(chain, chainData);
91		}
92
93		/*
94		* Add the start/end positions
95		*/
96	34	chainData.add(new int[] { startPos, endPos });
97		// TODO add intelligently, using a RangeList class
98		}
99
100		/**
101		* Returns the range(s) formatted as a Chimera atomspec
102		*
103		* @return
104		*/
		92.9% Uncovered Elements: 3 (42) Complexity: 8 Complexity Density: 0.29
105	25	public String getAtomSpec()...
106		{
107	25	StringBuilder sb = new StringBuilder(128);
108	25	boolean firstModel = true;
109	25	for (Integer model : atomSpec.keySet())
110		{
111	37	if (!firstModel)
112		{
113	13	sb.append("|");
114		}
115	37	firstModel = false;
116	37	sb.append("#").append(model).append(":");
117
118	37	boolean firstPositionForModel = true;
119	37	final Map<String, List<int[]>> modelData = atomSpec.get(model);
120
121	37	for (String chain : modelData.keySet())
122		{
123	54	chain = " ".equals(chain) ? chain : chain.trim();
124
125	54	List<int[]> rangeList = modelData.get(chain);
126
127		/*
128		* sort ranges into ascending start position order
129		*/
130	54	Collections.sort(rangeList, IntRangeComparator.ASCENDING);
131
132	54	int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
133	54	int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
134
135	54	Iterator<int[]> iterator = rangeList.iterator();
136	142	while (iterator.hasNext())
137		{
138	88	int[] range = iterator.next();
139	88	if (range[0] <= end + 1)
140		{
141		/*
142		* range overlaps or is contiguous with the last one
143		* - so just extend the end position, and carry on
144		* (unless this is the last in the list)
145		*/
146	77	end = Math.max(end, range[1]);
147		}
148		else
149		{
150		/*
151		* we have a break so append the last range
152		*/
153	11	appendRange(sb, start, end, chain, firstPositionForModel);
154	11	firstPositionForModel = false;
155	11	start = range[0];
156	11	end = range[1];
157		}
158		}
159
160		/*
161		* and append the last range
162		*/
163	54	if (!rangeList.isEmpty())
164		{
165	54	appendRange(sb, start, end, chain, firstPositionForModel);
166	54	firstPositionForModel = false;
167		}
168		}
169		}
170	25	return sb.toString();
171		}
172
173		/**
174		* @param sb
175		* @param start
176		* @param end
177		* @param chain
178		* @param firstPositionForModel
179		*/
		100% Uncovered Elements: 0 (14) Complexity: 4 Complexity Density: 0.5
180	65	protected void appendRange(StringBuilder sb, int start, int end,...
181		String chain, boolean firstPositionForModel)
182		{
183	65	if (!firstPositionForModel)
184		{
185	28	sb.append(",");
186		}
187	65	if (end == start)
188		{
189	16	sb.append(start);
190		}
191		else
192		{
193	49	sb.append(start).append("-").append(end);
194		}
195
196	65	sb.append(".");
197	65	if (!" ".equals(chain)) {
198	64	sb.append(chain);
199		}
200		}
201		}