Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceGrpPojo	27	20	20	0.9595%	Show methods

Class SequenceGrpPojo

Class SequenceGrpPojo	Line # 27	Total Statements 20	Complexity 20	TOTAL Coverage 0.9595%
getColourScheme() : String   getColourScheme() : String	8181	1.01	1.01	1.0 1.0100%
setColourScheme(String) : void   setColourScheme(String) : void	8686	1.01	1.01	1.0 1.0100%
getGroupName() : String   getGroupName() : String	9191	1.01	1.01	1.0 1.0100%
setGroupName(String) : void   setGroupName(String) : void	9696	1.01	1.01	1.0 1.0100%
getDescription() : String   getDescription() : String	101101	1.01	1.01	1.0 1.0100%
setDescription(String) : void   setDescription(String) : void	106106	1.01	1.01	1.0 1.0100%
isDisplayBoxes() : boolean   isDisplayBoxes() : boolean	111111	1.01	1.01	1.0 1.0100%
setDisplayBoxes(boolean) : void   setDisplayBoxes(boolean) : void	116116	1.01	1.01	1.0 1.0100%
isDisplayText() : boolean   isDisplayText() : boolean	121121	1.01	1.01	1.0 1.0100%
setDisplayText(boolean) : void   setDisplayText(boolean) : void	126126	1.01	1.01	1.0 1.0100%
isColourText() : boolean   isColourText() : boolean	131131	1.01	1.01	1.0 1.0100%
setColourText(boolean) : void   setColourText(boolean) : void	136136	1.01	1.01	1.0 1.0100%
isShowNonconserved() : boolean   isShowNonconserved() : boolean	141141	1.01	1.01	1.0 1.0100%
setShowNonconserved(boolean) : void   setShowNonconserved(boolean) : void	146146	1.01	1.01	1.0 1.0100%
getStartRes() : int   getStartRes() : int	151151	1.01	1.01	1.0 1.0100%
setStartRes(int) : void   setStartRes(int) : void	156156	1.01	1.01	1.0 1.0100%
getEndRes() : int   getEndRes() : int	161161	1.01	1.01	1.0 1.0100%
setEndRes(int) : void   setEndRes(int) : void	166166	1.01	1.01	1.0 1.0100%
getSequenceRefs() : ArrayList<String>   getSequenceRefs() : ArrayList<String>	171171	1.01	1.01	1.0 1.0100%
setSequenceRefs(ArrayList<String>) : void   setSequenceRefs(ArrayList<String>) : void	176176	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.95	jalview.io.JSONFileTest.testGrpParsed_colourNonejalview.io.JSONFileTest.testGrpParsed_colourNone	1PASS
	0.95	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
25		import com.github.reinert.jjschema.Attributes;
26
		95% Uncovered Elements: 2 (40) Complexity: 20 Complexity Density: 1
27		public class SequenceGrpPojo
28		{
29		@Attributes(
30		required = false,
31		description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the Sequence Group")
32		private String colourScheme;
33
34		@Attributes(
35		required = true,
36		description = "The name assigned to the seqGroup")
37		private String groupName;
38
39		@Attributes(
40		required = false,
41		description = "Serial version identifier for the <b>seqGroup</b> object model")
42		private String description;
43
44		@Attributes(
45		required = false,
46		description = "Determines if the seqGroup border should be visible or not")
47		private boolean displayBoxes;
48
49		@Attributes(
50		required = false,
51		description = "Determines if the texts of the group is displayed or not")
52		private boolean displayText;
53
54		@Attributes(
55		required = false,
56		description = "Determines if the residues text for the group is coloured")
57		private boolean colourText;
58
59		@Attributes(
60		required = false,
61		description = "Boolean value indicating whether residues should only be shown <br/>that are different from current reference or consensus sequence")
62		private boolean showNonconserved;
63
64		@Attributes(
65		required = true,
66		description = "The index of the group’s first residue in the alignment space")
67		private int startRes;
68
69		@Attributes(
70		required = true,
71		description = "The index of the group’s last residue in the alignment space")
72		private int endRes;
73
74		@Attributes(
75		required = true,
76		minItems = 1,
77		uniqueItems = true,
78		description = "An array of the unique id's for the sequences belonging to the group")
79		private ArrayList<String> sequenceRefs = new ArrayList<String>();
80
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
81	3	public String getColourScheme()...
82		{
83	3	return colourScheme;
84		}
85
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
86	3	public void setColourScheme(String colourScheme)...
87		{
88	3	this.colourScheme = colourScheme;
89		}
90
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
91	3	public String getGroupName()...
92		{
93	3	return groupName;
94		}
95
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
96	3	public void setGroupName(String groupName)...
97		{
98	3	this.groupName = groupName;
99		}
100
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
101	3	public String getDescription()...
102		{
103	3	return description;
104		}
105
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
106	3	public void setDescription(String description)...
107		{
108	3	this.description = description;
109		}
110
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
111	3	public boolean isDisplayBoxes()...
112		{
113	3	return displayBoxes;
114		}
115
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
116	3	public void setDisplayBoxes(boolean displayBoxes)...
117		{
118	3	this.displayBoxes = displayBoxes;
119		}
120
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
121	3	public boolean isDisplayText()...
122		{
123	3	return displayText;
124		}
125
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
126	3	public void setDisplayText(boolean displayText)...
127		{
128	3	this.displayText = displayText;
129		}
130
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
131	3	public boolean isColourText()...
132		{
133	3	return colourText;
134		}
135
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
136	3	public void setColourText(boolean colourText)...
137		{
138	3	this.colourText = colourText;
139		}
140
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
141	3	public boolean isShowNonconserved()...
142		{
143	3	return showNonconserved;
144		}
145
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
146	3	public void setShowNonconserved(boolean showNonconserved)...
147		{
148	3	this.showNonconserved = showNonconserved;
149		}
150
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
151	3	public int getStartRes()...
152		{
153	3	return startRes;
154		}
155
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
156	3	public void setStartRes(int startRes)...
157		{
158	3	this.startRes = startRes;
159		}
160
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
161	3	public int getEndRes()...
162		{
163	3	return endRes;
164		}
165
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
166	3	public void setEndRes(int endRes)...
167		{
168	3	this.endRes = endRes;
169		}
170
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
171	15	public ArrayList<String> getSequenceRefs()...
172		{
173	15	return sequenceRefs;
174		}
175
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
176	0	public void setSequenceRefs(ArrayList<String> sequenceRefs)...
177		{
178	0	this.sequenceRefs = sequenceRefs;
179		}
180
181		}