Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ParameterUtils	35	64	26	101	0.00%	Show methods

Class ParameterUtils

Class ParameterUtils	Line # 35	Total Statements 64	Complexity 26	Uncovered Elements 101	TOTAL Coverage 0.00%
writeParameterSet(List<Option>,String) : List<String>   writeParameterSet(List<Option>,String) : List<String>	3737	4.04	1.01	4.04	0.0 0.00%
processParameters(List<String>,RunnerConfig,String) : List<Option>   processParameters(List<String>,RunnerConfig,String) : List<Option>	6464	19.019	6.06	27.027	0.0 0.00%
getParamName(String,String) : String   getParamName(String,String) : String	111111	1.01	2.02	3.03	0.0 0.00%
getParamValue(String,String) : String   getParamValue(String,String) : String	117117	1.01	2.02	3.03	0.0 0.00%
isParameter(String,String) : boolean   isParameter(String,String) : boolean	123123	1.01	1.01	1.01	0.0 0.00%
copyOption(Option) : Option   copyOption(Option) : Option	128128	3.03	1.01	3.03	0.0 0.00%
setOptionFrom(Option,Option) : void   setOptionFrom(Option,Option) : void	135135	16.016	5.05	22.022	0.0 0.00%
copyValueConstrain(ValueConstrain) : ValueConstrain   copyValueConstrain(ValueConstrain) : ValueConstrain	168168	11.011	5.05	17.017	0.0 0.00%
copyParameter(Parameter) : Parameter   copyParameter(Parameter) : Parameter	194194	8.08	3.03	12.012	0.0 0.00%

 

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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.ws.jws2;
22
23		import jalview.util.MessageManager;
24
25		import java.util.ArrayList;
26		import java.util.HashSet;
27		import java.util.List;
28
29		import compbio.metadata.Option;
30		import compbio.metadata.Parameter;
31		import compbio.metadata.RunnerConfig;
32		import compbio.metadata.ValueConstrain;
33		import compbio.metadata.WrongParameterException;
34
		0% Uncovered Elements: 101 (101) Complexity: 26 Complexity Density: 0.41
35		public class ParameterUtils
36		{
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
37	0	public static List<String> writeParameterSet(List<Option> optSet,...
38		String pseparator)
39		{
40	0	List<String> pset = new ArrayList<String>();
41	0	for (Option o : optSet)
42		{
43	0	pset.add(o.toCommand(pseparator));
44		}
45	0	return pset;
46		}
47
48		/**
49		* Converts options supplied via parameters file into {@code Option} objects
50		* (Refactored from compbio.ws.client.Jws2Client)
51		*
52		* @param <T>
53		* web service type
54		* @param params
55		* @param options
56		* @return List of Options of type T
57		*
58		*/
59		/*
60		* @SuppressWarnings(value = { "true" }) public static <T> List<Option<T>>
61		* processParameters(List<String> params, RunnerConfig<T> options, String
62		* pseparator)
63		*/
		0% Uncovered Elements: 27 (27) Complexity: 6 Complexity Density: 0.32
64	0	public static List<Option> processParameters(List<String> params,...
65		RunnerConfig options, String pseparator)
66		{
67	0	List<Option> chosenOptions = new ArrayList<Option>();
68	0	for (String param : params)
69		{
70	0	String oname = null;
71	0	if (isParameter(param, pseparator))
72		{
73	0	oname = getParamName(param, pseparator);
74		}
75		else
76		{
77	0	oname = param;
78		}
79	0	Option o = options.getArgumentByOptionName(oname);
80	0	if (o == null)
81		{
82	0	System.out.println("WARN ignoring unsuppoted parameter: " + oname);
83	0	continue;
84		}
85	0	if (o instanceof Parameter)
86		{
87	0	o = copyParameter((Parameter) o);
88		}
89		else
90		{
91	0	o = copyOption(o);
92		}
93		{
94	0	try
95		{
96	0	o.setDefaultValue(isParameter(param, pseparator)
97		? getParamValue(param, pseparator)
98		: param);
99		} catch (WrongParameterException e)
100		{
101	0	System.out.println(
102		"Problem setting value for the parameter: " + param);
103	0	e.printStackTrace();
104		}
105		}
106	0	chosenOptions.add(o);
107		}
108	0	return chosenOptions;
109		}
110
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
111	0	static String getParamName(String fullName, String pseparator)...
112		{
113	0	assert isParameter(fullName, pseparator);
114	0	return fullName.substring(0, fullName.indexOf(pseparator));
115		}
116
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
117	0	static String getParamValue(String fullName, String pseparator)...
118		{
119	0	assert isParameter(fullName, pseparator);
120	0	return fullName.substring(fullName.indexOf(pseparator) + 1);
121		}
122
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
123	0	static boolean isParameter(String param, String pseparator)...
124		{
125	0	return param.contains(pseparator);
126		}
127
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
128	0	public static Option copyOption(Option option)...
129		{
130	0	Option copy = new Option(option.getName(), option.getDescription());
131	0	setOptionFrom(copy, option);
132	0	return copy;
133		}
134
		0% Uncovered Elements: 22 (22) Complexity: 5 Complexity Density: 0.31
135	0	public static void setOptionFrom(Option copy, Option option)...
136		{
137	0	copy.setName(option.getName());
138	0	copy.setDescription(option.getDescription());
139	0	copy.setBasicURL(option.getBasicURL());
140	0	copy.setFurtherDetails(option.getFurtherDetails());
141	0	copy.setRequired(option.isRequired());
142	0	List<String> names = option.getOptionNames();
143	0	if (names != null)
144		{
145	0	if (names.size() == 1)
146		{
147	0	HashSet<String> st = new HashSet();
148	0	st.add(names.get(0));
149	0	copy.setOptionNames(st);
150		}
151		else
152		{
153	0	copy.addOptionNames(names.toArray(new String[] {}));
154		}
155		}
156	0	try
157		{
158	0	if (option.getDefaultValue() != null)
159		{
160	0	copy.setDefaultValue(option.getDefaultValue());
161		}
162		} catch (Exception ex)
163		{
164	0	ex.printStackTrace();
165		}
166		}
167
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.45
168	0	public static ValueConstrain copyValueConstrain(ValueConstrain vc)...
169		{
170	0	try
171		{
172	0	ValueConstrain copy = new ValueConstrain();
173	0	if (vc.getMax() != null)
174		{
175	0	copy.setMax(vc.getMax().toString());
176		}
177	0	if (vc.getMin() != null)
178		{
179	0	copy.setMin(vc.getMin().toString());
180		}
181	0	if (vc.getType() != null)
182		{
183	0	copy.setType(vc.getType());
184		}
185	0	return copy;
186		} catch (Exception e)
187		{
188	0	e.printStackTrace();
189	0	throw new Error(MessageManager.getString(
190		"error.implementation_error_couldnt_copy_value_constraint"));
191		}
192		}
193
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
194	0	public static Parameter copyParameter(Parameter parameter)...
195		{
196	0	Parameter copy = new Parameter(parameter.getName(),
197		parameter.getDescription());
198	0	if (parameter.getValidValue() != null)
199		{
200	0	copy.setValidValue(copyValueConstrain(parameter.getValidValue()));
201		}
202	0	List<String> pv = parameter.getPossibleValues();
203	0	if (pv != null)
204		{
205	0	copy.addPossibleValues(pv.toArray(new String[] {}));
206		}
207	0	setOptionFrom(copy, parameter);
208	0	return copy;
209		}
210
211		}