Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequencePojo	25	17	16	0.818181881.8%	Show methods

Class SequencePojo

Class SequencePojo	Line # 25	Total Statements 17	Complexity 16	TOTAL Coverage 0.818181881.8%
SequencePojo()   SequencePojo()	6464	0.00	1.01	-1.0 -1.0 -
SequencePojo(int,int,String,String,String)   SequencePojo(int,int,String,String,String)	6868	3.03	1.01	0.0 0.00%
getSeq() : String   getSeq() : String	7676	1.01	1.01	1.0 1.0100%
setSeq(String) : void   setSeq(String) : void	8181	1.01	1.01	1.0 1.0100%
getName() : String   getName() : String	8686	1.01	1.01	1.0 1.0100%
setName(String) : void   setName(String) : void	9292	1.01	1.01	1.0 1.0100%
getId() : String   getId() : String	9797	1.01	1.01	1.0 1.0100%
setId(String) : void   setId(String) : void	102102	1.01	1.01	1.0 1.0100%
getStart() : int   getStart() : int	107107	1.01	1.01	1.0 1.0100%
setStart(int) : void   setStart(int) : void	112112	1.01	1.01	1.0 1.0100%
getEnd() : int   getEnd() : int	117117	1.01	1.01	1.0 1.0100%
setEnd(int) : void   setEnd(int) : void	122122	1.01	1.01	1.0 1.0100%
getOrder() : int   getOrder() : int	127127	1.01	1.01	1.0 1.0100%
setOrder(int) : void   setOrder(int) : void	132132	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	137137	1.01	1.01	1.0 1.0100%
setType(String) : void   setType(String) : void	142142	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.8181818	jalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNonejalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNone	1PASS
	0.8181818	jalview.io.JSONFileTest.testGrpParsed_colourNonejalview.io.JSONFileTest.testGrpParsed_colourNone	1PASS
	0.8181818	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 com.github.reinert.jjschema.Attributes;
24
		81.8% Uncovered Elements: 6 (33) Complexity: 16 Complexity Density: 0.94
25		public class SequencePojo
26		{
27		@Attributes(
28		required = true,
29		minLength = 3,
30		maxLength = 2147483647,
31		description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters &#x201c;.&#x201d;, &#x201c;-&#x201d; or &#x201c;&nbsp;&#x201d;")
32		private String seq;
33
34		@Attributes(required = true, description = "Sequence name")
35		private String name;
36
37		@Attributes(
38		required = false,
39		description = "Sequence type",
40		enums =
41		{ "DNA", "RNA", "Protein" })
42		private String type;
43
44		@Attributes(
45		required = true,
46		description = "Unique identifier for a given Sequence")
47		private String id;
48
49		@Attributes(
50		required = false,
51		description = "The order/position of a sequence in the alignment space")
52		private int order;
53
54		@Attributes(
55		required = true,
56		description = "The index of the sequence’s first residue in its source database, <br>using a one-based numbering index system")
57		private int start;
58
59		@Attributes(
60		required = true,
61		description = "The index of the sequence’s last residue in its source database, <br>using a one-based numbering index system")
62		private int end;
63
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
64	60	public SequencePojo()...
65		{
66		}
67
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
68	0	public SequencePojo(int start, int end, String id, String name,...
69		String seq)
70		{
71	0	this.id = id;
72	0	this.name = name;
73	0	this.seq = seq;
74		}
75
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
76	60	public String getSeq()...
77		{
78	60	return seq;
79		}
80
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
81	60	public void setSeq(String seq)...
82		{
83	60	this.seq = seq;
84		}
85
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
86	60	public String getName()...
87		{
88
89	60	return name;
90		}
91
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
92	60	public void setName(String name)...
93		{
94	60	this.name = name;
95		}
96
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
97	60	public String getId()...
98		{
99	60	return id;
100		}
101
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
102	60	public void setId(String id)...
103		{
104	60	this.id = id;
105		}
106
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
107	60	public int getStart()...
108		{
109	60	return start;
110		}
111
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
112	60	public void setStart(int start)...
113		{
114	60	this.start = start;
115		}
116
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
117	60	public int getEnd()...
118		{
119	60	return end;
120		}
121
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
122	60	public void setEnd(int end)...
123		{
124	60	this.end = end;
125		}
126
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
127	60	public int getOrder()...
128		{
129	60	return order;
130		}
131
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
132	60	public void setOrder(int order)...
133		{
134	60	this.order = order;
135		}
136
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
137	60	public String getType()...
138		{
139	60	return type;
140		}
141
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	public void setType(String type)...
143		{
144	0	this.type = type;
145		}
146
147		}