Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignmentAnnotationPojo	28	16	16	6	0.812581.2%	Show methods

Class AlignmentAnnotationPojo

Class AlignmentAnnotationPojo	Line # 28	Total Statements 16	Complexity 16	Uncovered Elements 6	TOTAL Coverage 0.812581.2%
getLabel() : String   getLabel() : String	6969	1.01	1.01	0.00	1.0 1.0100%
setLabel(String) : void   setLabel(String) : void	7474	1.01	1.01	0.00	1.0 1.0100%
getDescription() : String   getDescription() : String	7979	1.01	1.01	0.00	1.0 1.0100%
setDescription(String) : void   setDescription(String) : void	8484	1.01	1.01	0.00	1.0 1.0100%
getAnnotations() : List<AnnotationPojo>   getAnnotations() : List<AnnotationPojo>	8989	1.01	1.01	0.00	1.0 1.0100%
setAnnotations(List<AnnotationPojo>) : void   setAnnotations(List<AnnotationPojo>) : void	9494	1.01	1.01	1.01	0.0 0.00%
getSequenceRef() : String   getSequenceRef() : String	9999	1.01	1.01	0.00	1.0 1.0100%
setSequenceRef(String) : void   setSequenceRef(String) : void	104104	1.01	1.01	1.01	0.0 0.00%
getGraphType() : int   getGraphType() : int	109109	1.01	1.01	0.00	1.0 1.0100%
setGraphType(int) : void   setGraphType(int) : void	114114	1.01	1.01	0.00	1.0 1.0100%
getAnnotationSettings() : AnnotationDisplaySettingPojo   getAnnotationSettings() : AnnotationDisplaySettingPojo	119119	1.01	1.01	0.00	1.0 1.0100%
setAnnotationSettings(AnnotationDisplaySettingPojo) : void   setAnnotationSettings(AnnotationDisplaySettingPojo) : void	124124	1.01	1.01	0.00	1.0 1.0100%
getScore() : double   getScore() : double	130130	1.01	1.01	0.00	1.0 1.0100%
setScore(double) : void   setScore(double) : void	135135	1.01	1.01	1.01	0.0 0.00%
getCalcId() : String   getCalcId() : String	140140	1.01	1.01	0.00	1.0 1.0100%
setCalcId(String) : void   setCalcId(String) : void	145145	1.01	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.8125	jalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNonejalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNone	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.json.binding.biojson.v1;
22
23		import java.util.ArrayList;
24		import java.util.List;
25
26		import com.github.reinert.jjschema.Attributes;
27
		81.2% Uncovered Elements: 6 (32) Complexity: 16 Complexity Density: 1
28		public class AlignmentAnnotationPojo
29		{
30
31		@Attributes(
32		required = false,
33		description = "Label for the alignment annotation")
34		private String label;
35
36		@Attributes(
37		required = false,
38		description = "Description for the alignment annotation")
39		private String description;
40
41		@Attributes(required = false)
42		private List<AnnotationPojo> annotations = new ArrayList<AnnotationPojo>();
43
44		@Attributes(
45		required = false,
46		enums =
47		{ "0", "1", "2" },
48		description = "Determines the rendering for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
49		private int graphType;
50
51		@Attributes(
52		required = false,
53		description = "Reference to the sequence in the alignment<br> if per-sequence annotation")
54		private String sequenceRef;
55
56		@Attributes(
57		required = false,
58		description = "Stores display settings for an annotation")
59		private AnnotationDisplaySettingPojo annotationSettings;
60
61		@Attributes(required = false, description = "Score of the annotation")
62		private double score;
63
64		@Attributes(
65		required = false,
66		description = "The annotation generation source")
67		private String calcId;
68
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
69	2	public String getLabel()...
70		{
71	2	return label;
72		}
73
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
74	2	public void setLabel(String label)...
75		{
76	2	this.label = label;
77		}
78
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
79	2	public String getDescription()...
80		{
81	2	return description;
82		}
83
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
84	2	public void setDescription(String annotationId)...
85		{
86	2	this.description = annotationId;
87		}
88
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
89	72	public List<AnnotationPojo> getAnnotations()...
90		{
91	72	return annotations;
92		}
93
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
94	0	public void setAnnotations(List<AnnotationPojo> annotations)...
95		{
96	0	this.annotations = annotations;
97		}
98
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
99	2	public String getSequenceRef()...
100		{
101	2	return sequenceRef;
102		}
103
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
104	0	public void setSequenceRef(String sequenceRef)...
105		{
106	0	this.sequenceRef = sequenceRef;
107		}
108
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
109	2	public int getGraphType()...
110		{
111	2	return graphType;
112		}
113
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
114	2	public void setGraphType(int graphType)...
115		{
116	2	this.graphType = graphType;
117		}
118
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
119	2	public AnnotationDisplaySettingPojo getAnnotationSettings()...
120		{
121	2	return annotationSettings;
122		}
123
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
124	2	public void setAnnotationSettings(...
125		AnnotationDisplaySettingPojo annotationSettings)
126		{
127	2	this.annotationSettings = annotationSettings;
128		}
129
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
130	2	public double getScore()...
131		{
132	2	return score;
133		}
134
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	public void setScore(double score)...
136		{
137	0	this.score = score;
138		}
139
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
140	2	public String getCalcId()...
141		{
142	2	return calcId;
143		}
144
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
145	2	public void setCalcId(String calcId)...
146		{
147	2	this.calcId = calcId;
148		}
149
150		}