Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Atom	27	28	8	0.00%	Show methods

Class Atom

Class Atom	Line # 27	Total Statements 28	Complexity 8	TOTAL Coverage 0.00%
Atom(String)   Atom(String)	7171	19.019	3.03	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	112112	6.06	4.04	0.0 0.00%
Atom(float,float,float)   Atom(float,float,float)	130130	3.03	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 mc_view;
22
23		import jalview.schemes.ResidueProperties;
24
25		import java.awt.Color;
26
		0% Uncovered Elements: 39 (39) Complexity: 8 Complexity Density: 0.29
27		public class Atom
28		{
29		public float x;
30
31		public float y;
32
33		public float z;
34
35		public int number;
36
37		public String name;
38
39		public String resName;
40
41		public int resNumber;
42
43		public char insCode = ' ';
44
45		public String resNumIns = null;
46
47		public int type;
48
49		Color color = Color.lightGray;
50
51		public String chain;
52
53		/**
54		* this is a temporary value - designed to store the position in sequence that
55		* this atom corresponds to after aligning the chain to a SequenceI object. Do
56		* not rely on its value being correct when visualizing sequence colourings on
57		* the structure - use the StructureSelectionManager's mapping instead.
58		*/
59		public int alignmentMapping = -1;
60
61		public int atomIndex;
62
63		public float occupancy = 0;
64
65		public float tfactor = 0;
66
67		// need these if we ever want to export Atom data
68		// public boolean tfacset=true,occset=true;
69		public boolean isSelected = false;
70
		0% Uncovered Elements: 23 (23) Complexity: 3 Complexity Density: 0.16
71	0	public Atom(String str)...
72		{
73	0	atomIndex = Integer.parseInt(str.substring(6, 11).trim());
74
75	0	name = str.substring(12, 15).trim();
76
77	0	resName = str.substring(17, 20);
78		// JAL-1828 treat MSE Selenomethionine as MET (etc)
79	0	resName = ResidueProperties.getCanonicalAminoAcid(resName);
80
81	0	chain = str.substring(21, 22);
82
83	0	resNumber = Integer.parseInt(str.substring(22, 26).trim());
84	0	resNumIns = str.substring(22, 27).trim();
85	0	insCode = str.substring(26, 27).charAt(0);
86	0	this.x = (new Float(str.substring(30, 38).trim()).floatValue());
87	0	this.y = (new Float(str.substring(38, 46).trim()).floatValue());
88	0	this.z = (new Float(str.substring(47, 55).trim()).floatValue());
89		// optional entries - see JAL-730
90	0	String tm = str.substring(54, 60).trim();
91	0	if (tm.length() > 0)
92		{
93	0	occupancy = (new Float(tm)).floatValue();
94		}
95		else
96		{
97	0	occupancy = 1f; // default occupancy
98		// see note above: occset=false;
99		}
100	0	tm = str.substring(60, 66).trim();
101	0	if (tm.length() > 0)
102		{
103	0	tfactor = (new Float(tm).floatValue());
104		}
105		else
106		{
107	0	tfactor = 1f;
108		// see note above: tfacset=false;
109		}
110		}
111
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
112	0	@Override...
113		public boolean equals(Object that)
114		{
115	0	if (this == that || that == null)
116		{
117	0	return true;
118		}
119	0	if (that instanceof Atom)
120		{
121	0	Atom other = (Atom) that;
122	0	return other.resName.equals(this.resName)
123		&& other.resNumber == this.resNumber
124		&& other.resNumIns.equals(this.resNumIns)
125		&& other.chain.equals(this.chain);
126		}
127	0	return false;
128		}
129
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
130	0	public Atom(float x, float y, float z)...
131		{
132	0	this.x = x;
133	0	this.y = y;
134	0	this.z = z;
135		}
136		}