Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequencePoint	29	12	8	0.2272727322.7%	Show methods

Class SequencePoint

Class SequencePoint	Line # 29	Total Statements 12	Complexity 8	TOTAL Coverage 0.2272727322.7%
SequencePoint(SequenceI,Point)   SequencePoint(SequenceI,Point)	4747	2.02	1.01	1.0 1.0100%
SequencePoint(SequenceI,float[])   SequencePoint(SequenceI,float[])	6262	1.01	1.01	0.0 0.00%
getSequence() : SequenceI   getSequence() : SequenceI	6767	1.01	1.01	1.0 1.0100%
translate(float,float,float) : void   translate(float,float,float) : void	7777	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	8585	1.01	1.01	0.0 0.00%
getDisplayName() : String   getDisplayName() : String	9191	6.06	3.03	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22727273	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	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.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		*/
		22.7% Uncovered Elements: 17 (22) Complexity: 8 Complexity Density: 0.67
29		public class SequencePoint extends AnnotationMapping
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		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
47	30	public SequencePoint(SequenceI sequence, Point pt)...
48		{
49	30	this.sequence = sequence;
50	30	this.coord = pt;
51		}
52
53
54		/**
55		* Constructor given a sequence and an array of x, y, z coordinate positions
56		*
57		* @param sequence
58		* @param coords
59		* @throws ArrayIndexOutOfBoundsException
60		* if array length is less than 3
61		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	public SequencePoint(SequenceI sequence, float[] coords)...
63		{
64	0	this(sequence, new Point(coords[0], coords[1], coords[2]));
65		}
66
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
67	60	public SequenceI getSequence()...
68		{
69	60	return sequence;
70		}
71
72		/**
73		* Applies a translation to the (x, y, z) coordinates
74		*
75		* @param centre
76		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	public void translate(float x, float y, float z)...
78		{
79	0	coord = new Point(coord.x + x, coord.y + y, coord.z + z);
80		}
81
82		/**
83		* string representation for ease of inspection in debugging or logging only
84		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
85	0	@Override...
86		public String toString()
87		{
88	0	return sequence.getName() + " " + coord.toString();
89		}
90
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
91	0	public String getDisplayName()...
92		{
93	0	String displayName = sequence.getName();
94
95	0	if (hasLabel())
96		{
97	0	displayName = displayName + "|" + label;
98		}
99
100	0	if (hasAnnotationDetails())
101		{
102	0	displayName = displayName + "|" + annotationDetails;
103		}
104
105	0	return displayName;
106		}
107
108		}