Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentPojo	33	14	15	0.724137972.4%	Show methods

Class AlignmentPojo

Class AlignmentPojo	Line # 33	Total Statements 14	Complexity 15	TOTAL Coverage 0.724137972.4%
AlignmentPojo()   AlignmentPojo()	8484	0.00	1.01	-1.0 -1.0 -
getSeqs() : List<SequencePojo>   getSeqs() : List<SequencePojo>	8888	1.01	1.01	1.0 1.0100%
setSeqs(ArrayList<SequencePojo>) : void   setSeqs(ArrayList<SequencePojo>) : void	9393	1.01	1.01	0.0 0.00%
getAppSettings() : Map<String, Object>   getAppSettings() : Map<String, Object>	9898	1.01	1.01	1.0 1.0100%
setAppSettings(Map<String, Object>) : void   setAppSettings(Map<String, Object>) : void	103103	1.01	1.01	0.0 0.00%
getAlignAnnotation() : List<AlignmentAnnotationPojo>   getAlignAnnotation() : List<AlignmentAnnotationPojo>	108108	1.01	1.01	1.0 1.0100%
setAlignAnnotation(List<AlignmentAnnotationPojo>) : void   setAlignAnnotation(List<AlignmentAnnotationPojo>) : void	113113	1.01	1.01	1.0 1.0100%
getSeqGroups() : List<SequenceGrpPojo>   getSeqGroups() : List<SequenceGrpPojo>	119119	1.01	1.01	1.0 1.0100%
setSeqGroups(List<SequenceGrpPojo>) : void   setSeqGroups(List<SequenceGrpPojo>) : void	124124	1.01	1.01	0.0 0.00%
getSeqFeatures() : List<SequenceFeaturesPojo>   getSeqFeatures() : List<SequenceFeaturesPojo>	129129	1.01	1.01	1.0 1.0100%
setSeqFeatures(List<SequenceFeaturesPojo>) : void   setSeqFeatures(List<SequenceFeaturesPojo>) : void	134134	1.01	1.01	1.0 1.0100%
getSvid() : String   getSvid() : String	139139	1.01	1.01	1.0 1.0100%
setGlobalColorScheme(String) : void   setGlobalColorScheme(String) : void	144144	1.01	1.01	1.0 1.0100%
getColourScheme() : String   getColourScheme() : String	149149	1.01	1.01	1.0 1.0100%
setColourScheme(String) : void   setColourScheme(String) : void	154154	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.7241379	jalview.io.JSONFileTest.testGrpParsed_colourNonejalview.io.JSONFileTest.testGrpParsed_colourNone	1PASS
	0.7241379	jalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNonejalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNone	1PASS
	0.7241379	jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip	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.HashMap;
25		import java.util.List;
26		import java.util.Map;
27
28		import com.github.reinert.jjschema.Attributes;
29
30		@Attributes(
31		title = "BioJSON",
32		description = "A specification for the representation and exchange of bioinformatics data")
		72.4% Uncovered Elements: 8 (29) Complexity: 15 Complexity Density: 1.07
33		public class AlignmentPojo
34		{
35		@Attributes(
36		required = true,
37		description = "Serial version identifier for <b>BioJSON</b> schema")
38		private String svid = "1.0";
39
40		@Attributes(
41		required = true,
42		minItems = 1,
43		description = "An array of Sequences which makes up the Alignment")
44		private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
45
46		@Attributes(
47		required = false,
48		minItems = 0,
49		exclusiveMaximum = true,
50		description = "Alignment annotations stores symbols and graphs usually rendered </br>"
51		+ "below the alignment and often reflect properties of the alignment </br>as a whole.")
52		private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
53
54		@Attributes(
55		required = false,
56		minItems = 0,
57		description = "A sequence group is a rectangular region of an alignment <br>bounded by startRes and endRes positions in the alignment <br>coordinate system for a set of sequences")
58		private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
59
60		@Attributes(
61		required = false,
62		minItems = 0,
63		description = "Sequence features are properties of the individual sequences, <br>they do not change with the alignment, but are shown mapped<br> on to specific residues within the alignment")
64		private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
65
66		@Attributes(
67		required = false,
68		enums =
69		{ "None", "User Defined", "Clustal", "Zappo", "Taylor", "Nucleotide",
70		"Pyrimidine", "Purine", "Turn", "Helix", "Strand", "Buried",
71		"Hydro", "T-Coffee Scores", "RNA Interaction type", "Blosum62",
72		"RNA Helices", "% Identity" },
73		description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the alignment")
74		private String colourScheme;
75
76		@Attributes(
77		required = true,
78		maxItems = 0,
79		description = "AppSettings stores key=value pairs of custom application specific <br>"
80		+ "settings (i.e visualisation settings, etc) for different applications<br>"
81		+ "that consume or generate BioJSON")
82		Map<String, Object> appSettings = new HashMap<String, Object>();
83
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
84	8	public AlignmentPojo()...
85		{
86		}
87
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
88	68	public List<SequencePojo> getSeqs()...
89		{
90	68	return seqs;
91		}
92
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
93	0	public void setSeqs(ArrayList<SequencePojo> seqs)...
94		{
95	0	this.seqs = seqs;
96		}
97
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
98	50	public Map<String, Object> getAppSettings()...
99		{
100	50	return appSettings;
101		}
102
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
103	0	public void setAppSettings(Map<String, Object> appSettings)...
104		{
105	0	this.appSettings = appSettings;
106		}
107
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
108	8	public List<AlignmentAnnotationPojo> getAlignAnnotation()...
109		{
110	8	return alignAnnotation;
111		}
112
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
113	8	public void setAlignAnnotation(...
114		List<AlignmentAnnotationPojo> alignAnnotation)
115		{
116	8	this.alignAnnotation = alignAnnotation;
117		}
118
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
119	14	public List<SequenceGrpPojo> getSeqGroups()...
120		{
121	14	return seqGroups;
122		}
123
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
124	0	public void setSeqGroups(List<SequenceGrpPojo> seqGroups)...
125		{
126	0	this.seqGroups = seqGroups;
127		}
128
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
129	8	public List<SequenceFeaturesPojo> getSeqFeatures()...
130		{
131	8	return seqFeatures;
132		}
133
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
134	8	public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)...
135		{
136	8	this.seqFeatures = seqFeatures;
137		}
138
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
139	8	public String getSvid()...
140		{
141	8	return svid;
142		}
143
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
144	8	public void setGlobalColorScheme(String globalColorScheme)...
145		{
146	8	this.appSettings.put("globalColorScheme", globalColorScheme);
147		}
148
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
149	8	public String getColourScheme()...
150		{
151	8	return colourScheme;
152		}
153
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
154	0	public void setColourScheme(String colourScheme)...
155		{
156	0	this.colourScheme = colourScheme;
157		}
158
159		}