Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequencePoint	29	6	5	0.00%	Show methods

Class SequencePoint

Class SequencePoint	Line # 29	Total Statements 6	Complexity 5	TOTAL Coverage 0.00%
SequencePoint(SequenceI,Point)   SequencePoint(SequenceI,Point)	4747	2.02	1.01	0.0 0.00%
SequencePoint(SequenceI,float[])   SequencePoint(SequenceI,float[])	6161	1.01	1.01	0.0 0.00%
getSequence() : SequenceI   getSequence() : SequenceI	6666	1.01	1.01	0.0 0.00%
translate(float,float,float) : void   translate(float,float,float) : void	7676	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	8484	1.01	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 jalview.datamodel;
22
23		/**
24		* A bean that models a set of (x, y, z) values and a reference to a sequence.
25		* As used in Principal Component Analysis, the (x, y, z) values are the
26		* sequence's score for the currently selected first, second and third
27		* dimensions of the PCA.
28		*/
		0% Uncovered Elements: 11 (11) Complexity: 5 Complexity Density: 0.83
29		public class SequencePoint
30		{
31		/*
32		* Associated alignment sequence, or dummy sequence object
33		*/
34		private final SequenceI sequence;
35
36		/*
37		* x, y, z values
38		*/
39		public Point coord;
40
41		/**
42		* Constructor
43		*
44		* @param sequence
45		* @param coord
46		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
47	0	public SequencePoint(SequenceI sequence, Point pt)...
48		{
49	0	this.sequence = sequence;
50	0	this.coord = pt;
51		}
52
53		/**
54		* Constructor given a sequence and an array of x, y, z coordinate positions
55		*
56		* @param sequence
57		* @param coords
58		* @throws ArrayIndexOutOfBoundsException
59		* if array length is less than 3
60		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	public SequencePoint(SequenceI sequence, float[] coords)...
62		{
63	0	this(sequence, new Point(coords[0], coords[1], coords[2]));
64		}
65
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	public SequenceI getSequence()...
67		{
68	0	return sequence;
69		}
70
71		/**
72		* Applies a translation to the (x, y, z) coordinates
73		*
74		* @param centre
75		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	public void translate(float x, float y, float z)...
77		{
78	0	coord = new Point(coord.x + x, coord.y + y, coord.z + z);
79		}
80
81		/**
82		* string representation for ease of inspection in debugging or logging only
83		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
84	0	@Override...
85		public String toString()
86		{
87	0	return sequence.getName() + " " + coord.toString();
88		}
89		}