Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
ParameterUtils | 35 | 64 | 26 |
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 | ||
35 | public class ParameterUtils | |
36 | { | |
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 | */ | |
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 | jalview.bin.Console |
83 | .outPrintln("WARN ignoring unsuppoted parameter: " + oname); | |
84 | 0 | continue; |
85 | } | |
86 | 0 | if (o instanceof Parameter) |
87 | { | |
88 | 0 | o = copyParameter((Parameter) o); |
89 | } | |
90 | else | |
91 | { | |
92 | 0 | o = copyOption(o); |
93 | } | |
94 | { | |
95 | 0 | try |
96 | { | |
97 | 0 | o.setDefaultValue(isParameter(param, pseparator) |
98 | ? getParamValue(param, pseparator) | |
99 | : param); | |
100 | } catch (WrongParameterException e) | |
101 | { | |
102 | 0 | jalview.bin.Console.outPrintln( |
103 | "Problem setting value for the parameter: " + param); | |
104 | 0 | e.printStackTrace(); |
105 | } | |
106 | } | |
107 | 0 | chosenOptions.add(o); |
108 | } | |
109 | 0 | return chosenOptions; |
110 | } | |
111 | ||
112 | 0 | static String getParamName(String fullName, String pseparator) |
113 | { | |
114 | 0 | assert isParameter(fullName, pseparator); |
115 | 0 | return fullName.substring(0, fullName.indexOf(pseparator)); |
116 | } | |
117 | ||
118 | 0 | static String getParamValue(String fullName, String pseparator) |
119 | { | |
120 | 0 | assert isParameter(fullName, pseparator); |
121 | 0 | return fullName.substring(fullName.indexOf(pseparator) + 1); |
122 | } | |
123 | ||
124 | 0 | static boolean isParameter(String param, String pseparator) |
125 | { | |
126 | 0 | return param.contains(pseparator); |
127 | } | |
128 | ||
129 | 0 | public static Option copyOption(Option option) |
130 | { | |
131 | 0 | Option copy = new Option(option.getName(), option.getDescription()); |
132 | 0 | setOptionFrom(copy, option); |
133 | 0 | return copy; |
134 | } | |
135 | ||
136 | 0 | public static void setOptionFrom(Option copy, Option option) |
137 | { | |
138 | 0 | copy.setName(option.getName()); |
139 | 0 | copy.setDescription(option.getDescription()); |
140 | 0 | copy.setBasicURL(option.getBasicURL()); |
141 | 0 | copy.setFurtherDetails(option.getFurtherDetails()); |
142 | 0 | copy.setRequired(option.isRequired()); |
143 | 0 | List<String> names = option.getOptionNames(); |
144 | 0 | if (names != null) |
145 | { | |
146 | 0 | if (names.size() == 1) |
147 | { | |
148 | 0 | HashSet<String> st = new HashSet(); |
149 | 0 | st.add(names.get(0)); |
150 | 0 | copy.setOptionNames(st); |
151 | } | |
152 | else | |
153 | { | |
154 | 0 | copy.addOptionNames(names.toArray(new String[] {})); |
155 | } | |
156 | } | |
157 | 0 | try |
158 | { | |
159 | 0 | if (option.getDefaultValue() != null) |
160 | { | |
161 | 0 | copy.setDefaultValue(option.getDefaultValue()); |
162 | } | |
163 | } catch (Exception ex) | |
164 | { | |
165 | 0 | ex.printStackTrace(); |
166 | } | |
167 | } | |
168 | ||
169 | 0 | public static ValueConstrain copyValueConstrain(ValueConstrain vc) |
170 | { | |
171 | 0 | try |
172 | { | |
173 | 0 | ValueConstrain copy = new ValueConstrain(); |
174 | 0 | if (vc.getMax() != null) |
175 | { | |
176 | 0 | copy.setMax(vc.getMax().toString()); |
177 | } | |
178 | 0 | if (vc.getMin() != null) |
179 | { | |
180 | 0 | copy.setMin(vc.getMin().toString()); |
181 | } | |
182 | 0 | if (vc.getType() != null) |
183 | { | |
184 | 0 | copy.setType(vc.getType()); |
185 | } | |
186 | 0 | return copy; |
187 | } catch (Exception e) | |
188 | { | |
189 | 0 | e.printStackTrace(); |
190 | 0 | throw new Error(MessageManager.getString( |
191 | "error.implementation_error_couldnt_copy_value_constraint")); | |
192 | } | |
193 | } | |
194 | ||
195 | 0 | public static Parameter copyParameter(Parameter parameter) |
196 | { | |
197 | 0 | Parameter copy = new Parameter(parameter.getName(), |
198 | parameter.getDescription()); | |
199 | 0 | if (parameter.getValidValue() != null) |
200 | { | |
201 | 0 | copy.setValidValue(copyValueConstrain(parameter.getValidValue())); |
202 | } | |
203 | 0 | List<String> pv = parameter.getPossibleValues(); |
204 | 0 | if (pv != null) |
205 | { | |
206 | 0 | copy.addPossibleValues(pv.toArray(new String[] {})); |
207 | } | |
208 | 0 | setOptionFrom(copy, parameter); |
209 | 0 | return copy; |
210 | } | |
211 | ||
212 | } |