Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SlivkaParamSet	17	35	25	0.00%	Show methods

Class SlivkaParamSet

Class SlivkaParamSet	Line # 17	Total Statements 35	Complexity 25	TOTAL Coverage 0.00%
SlivkaParamSet(SlivkaService)   SlivkaParamSet(SlivkaService)	2323	28.028	17.017	0.0 0.00%
getName() : String   getName() : String	104104	1.01	1.01	0.0 0.00%
getDescription() : String   getDescription() : String	110110	1.01	1.01	0.0 0.00%
getApplicableUrls() : String[]   getApplicableUrls() : String[]	116116	1.01	1.01	0.0 0.00%
getSourceFile() : String   getSourceFile() : String	122122	1.01	1.01	0.0 0.00%
setSourceFile(String) : void   setSourceFile(String) : void	128128	0.00	1.01	-1.0 -1.0 -
isModifiable() : boolean   isModifiable() : boolean	133133	1.01	1.01	0.0 0.00%
getArguments() : List<ArgumentI>   getArguments() : List<ArgumentI>	139139	1.01	1.01	0.0 0.00%
setArguments(List<ArgumentI>) : void   setArguments(List<ArgumentI>) : void	145145	1.01	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.ws.slivkaws;
2
3		import java.io.IOException;
4		import java.util.ArrayList;
5		import java.util.Collections;
6		import java.util.List;
7
8		import jalview.ws.params.ArgumentI;
9		import jalview.ws.params.WsParamSetI;
10		import jalview.ws.params.simple.BooleanOption;
11		import jalview.ws.params.simple.DoubleParameter;
12		import jalview.ws.params.simple.IntegerParameter;
13		import jalview.ws.params.simple.StringParameter;
14		import uk.ac.dundee.compbio.slivkaclient.Parameter;
15		import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
16
		0% Uncovered Elements: 76 (76) Complexity: 25 Complexity Density: 0.71
17		public class SlivkaParamSet implements WsParamSetI
18		{
19		private SlivkaService service;
20
21		private List<ArgumentI> args = new ArrayList<>();
22
		0% Uncovered Elements: 60 (60) Complexity: 17 Complexity Density: 0.61
23	0	SlivkaParamSet(SlivkaService service)...
24		{
25	0	this.service = service;
26	0	for (Parameter param : service.getParameters())
27		{
28	0	Object defaultValue = param.getDefault() instanceof List
29		? ((List<?>) param.getDefault()).get(0)
30		: param.getDefault();
31	0	if (param instanceof Parameter.FlagParameter)
32		{
33	0	args.add(new BooleanOption(param.getId(), param.getDescription(),
34		param.getName(), param.isRequired(), (Boolean) defaultValue, null));
35		}
36	0	else if (param instanceof Parameter.TextParameter)
37		{
38	0	args.add(new StringParameter(param.getId(), param.getDescription(),
39		param.isRequired(), (String) defaultValue, (String) defaultValue));
40		}
41	0	else if (param instanceof Parameter.IntegerParameter)
42		{
43	0	Integer min = ((Parameter.IntegerParameter) param).getMin();
44	0	Integer max = ((Parameter.IntegerParameter) param).getMax();
45	0	Integer defVal = defaultValue != null
46		? ((Number) defaultValue).intValue()
47		: null;
48	0	args.add(new IntegerParameter(param.getId(), param.getDescription(),
49	0	param.isRequired(), defVal, (min == null) ? Integer.MIN_VALUE : min,
50	0	(max == null) ? Integer.MAX_VALUE : max));
51		}
52	0	else if (param instanceof Parameter.DecimalParameter)
53		{
54	0	Double min = ((Parameter.DecimalParameter) param).getMin();
55	0	Double max = ((Parameter.DecimalParameter) param).getMax();
56	0	Double defVal = defaultValue != null
57		? ((Number) defaultValue).doubleValue()
58		: null;
59	0	args.add(new DoubleParameter(param.getId(), param.getDescription(),
60	0	param.isRequired(), defVal, (min == null) ? -Double.MAX_VALUE : min,
61	0	(max == null) ? Double.MAX_VALUE : max));
62		}
63	0	else if (param instanceof Parameter.ChoiceParameter)
64		{
65	0	List<String> choices = ((Parameter.ChoiceParameter) param)
66		.getChoices();
67	0	if (param.isArray())
68		{
69	0	int i = 0;
70	0	List<?> selected = param.getDefault() != null
71		? (List<?>) param.getDefault()
72		: Collections.EMPTY_LIST;
73	0	for (String choice : choices)
74		{
75	0	args.add(new BooleanOption(
76		String.format("%s$%d", param.getId(), i++),
77		param.getDescription(), choice, param.isRequired(),
78		selected.contains(choice), choice, null));
79		}
80		}
81		else
82		{
83	0	args.add(new StringParameter(
84		param.getId(), param.getDescription(),
85		param.isRequired(), (String) param.getDefault(),
86		(String) defaultValue, choices, choices));
87		}
88		}
89	0	else if (param instanceof Parameter.FileParameter)
90		{
91		// skip: files are provided from sequences
92		}
93		else
94		{
95	0	String defaultVal = param.getDefault() != null
96		? param.getDefault().toString()
97		: null;
98	0	args.add(new StringParameter(param.getId(), param.getDescription(),
99		param.isRequired(), defaultVal, defaultVal));
100		}
101		}
102		}
103
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
104	0	@Override...
105		public String getName()
106		{
107	0	return "Default";
108		}
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public String getDescription()
112		{
113	0	return service.getDescription();
114		}
115
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
116	0	@Override...
117		public String[] getApplicableUrls()
118		{
119	0	return new String[] { service.getUrl().toString() };
120		}
121
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
122	0	@Override...
123		public String getSourceFile()
124		{
125	0	return null;
126		}
127
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
128	0	@Override...
129		public void setSourceFile(String newfile)
130		{
131		}
132
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	@Override...
134		public boolean isModifiable()
135		{
136	0	return true;
137		}
138
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
139	0	@Override...
140		public List<ArgumentI> getArguments()
141		{
142	0	return args;
143		}
144
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
145	0	@Override...
146		public void setArguments(List<ArgumentI> args)
147		{
148	0	throw new RuntimeException();
149		}
150
151		}