Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AtomSpec	30	34	18	43	0.203703720.4%	Show methods

Class AtomSpec

Class AtomSpec	Line # 30	Total Statements 34	Complexity 18	Uncovered Elements 43	TOTAL Coverage 0.203703720.4%
fromChimeraAtomspec(String) : AtomSpec   fromChimeraAtomspec(String) : AtomSpec	5151	19.019	9.09	29.029	0.0 0.00%
AtomSpec(String,String,int,int)   AtomSpec(String,String,int,int)	104104	4.04	1.01	0.00	1.0 1.0100%
AtomSpec(int,String,int,int)   AtomSpec(int,String,int,int)	120120	4.04	1.01	4.04	0.0 0.00%
getPdbFile() : String   getPdbFile() : String	128128	1.01	1.01	0.00	1.0 1.0100%
getChain() : String   getChain() : String	133133	1.01	1.01	0.00	1.0 1.0100%
getPdbResNum() : int   getPdbResNum() : int	138138	1.01	1.01	0.00	1.0 1.0100%
getAtomIndex() : int   getAtomIndex() : int	143143	1.01	1.01	1.01	0.0 0.00%
getModelNumber() : int   getModelNumber() : int	148148	1.01	1.01	1.01	0.0 0.00%
setPdbFile(String) : void   setPdbFile(String) : void	153153	1.01	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	158158	1.01	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.2037037	jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol	1PASS

 

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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		/**
24		* Java bean representing an atom in a PDB (or similar) structure model or
25		* viewer
26		*
27		* @author gmcarstairs
28		*
29		*/
		20.4% Uncovered Elements: 43 (54) Complexity: 18 Complexity Density: 0.53
30		public class AtomSpec
31		{
32		int modelNo;
33
34		private String pdbFile;
35
36		private String chain;
37
38		private int pdbResNum;
39
40		private int atomIndex;
41
42		/**
43		* Parses a Chimera atomspec e.g. #1:12.A to construct an AtomSpec model (with
44		* null pdb file name)
45		*
46		* @param spec
47		* @return
48		* @throw IllegalArgumentException if the spec cannot be parsed, or represents
49		* more than one residue
50		*/
		0% Uncovered Elements: 29 (29) Complexity: 9 Complexity Density: 0.47
51	0	public static AtomSpec fromChimeraAtomspec(String spec)...
52		{
53	0	int colonPos = spec.indexOf(":");
54	0	if (colonPos == -1)
55		{
56	0	throw new IllegalArgumentException(spec);
57		}
58
59	0	int hashPos = spec.indexOf("#");
60	0	if (hashPos == -1 && colonPos != 0)
61		{
62		// # is missing but something precedes : - reject
63	0	throw new IllegalArgumentException(spec);
64		}
65
66	0	String modelSubmodel = spec.substring(hashPos + 1, colonPos);
67	0	int dotPos = modelSubmodel.indexOf(".");
68	0	int modelId = 0;
69	0	try
70		{
71	0	modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
72		: modelSubmodel.substring(0, dotPos));
73		} catch (NumberFormatException e)
74		{
75		// ignore, default to model 0
76		}
77
78	0	String residueChain = spec.substring(colonPos + 1);
79	0	dotPos = residueChain.indexOf(".");
80	0	int resNum = 0;
81	0	try
82		{
83	0	resNum = Integer.parseInt(dotPos == -1 ? residueChain
84		: residueChain.substring(0, dotPos));
85		} catch (NumberFormatException e)
86		{
87		// could be a range e.g. #1:4-7.B
88	0	throw new IllegalArgumentException(spec);
89		}
90
91	0	String chainId = dotPos == -1 ? "" : residueChain.substring(dotPos + 1);
92
93	0	return new AtomSpec(modelId, chainId, resNum, 0);
94		}
95
96		/**
97		* Constructor
98		*
99		* @param pdbFile
100		* @param chain
101		* @param resNo
102		* @param atomNo
103		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
104	1	public AtomSpec(String pdbFile, String chain, int resNo, int atomNo)...
105		{
106	1	this.pdbFile = pdbFile;
107	1	this.chain = chain;
108	1	this.pdbResNum = resNo;
109	1	this.atomIndex = atomNo;
110		}
111
112		/**
113		* Constructor
114		*
115		* @param modelId
116		* @param chainId
117		* @param resNo
118		* @param atomNo
119		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
120	0	public AtomSpec(int modelId, String chainId, int resNo, int atomNo)...
121		{
122	0	this.modelNo = modelId;
123	0	this.chain = chainId;
124	0	this.pdbResNum = resNo;
125	0	this.atomIndex = atomNo;
126		}
127
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
128	2	public String getPdbFile()...
129		{
130	2	return pdbFile;
131		}
132
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
133	1	public String getChain()...
134		{
135	1	return chain;
136		}
137
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
138	1	public int getPdbResNum()...
139		{
140	1	return pdbResNum;
141		}
142
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
143	0	public int getAtomIndex()...
144		{
145	0	return atomIndex;
146		}
147
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
148	0	public int getModelNumber()...
149		{
150	0	return modelNo;
151		}
152
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
153	0	public void setPdbFile(String file)...
154		{
155	0	pdbFile = file;
156		}
157
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
158	0	@Override...
159		public String toString()
160		{
161	0	return "pdbFile: " + pdbFile + ", chain: " + chain + ", res: "
162		+ pdbResNum + ", atom: " + atomIndex;
163		}
164		}