2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.jws2.dm;
23 import jalview.util.MessageManager;
24 import jalview.ws.jws2.JabaParamStore;
25 import jalview.ws.jws2.JabaPreset;
26 import jalview.ws.jws2.ParameterUtils;
27 import jalview.ws.jws2.jabaws2.Jws2Instance;
28 import jalview.ws.params.ArgumentI;
29 import jalview.ws.params.WsParamSetI;
31 import java.util.ArrayList;
32 import java.util.List;
34 import compbio.metadata.Argument;
35 import compbio.metadata.Option;
38 * preferences for running AACon service
40 * @author jprocter TODO: refactor to a generic 'last job and service run'
43 public class AAConSettings extends jalview.ws.params.AutoCalcSetting
47 public AAConSettings(boolean autoUpdate, Jws2Instance service,
48 WsParamSetI preset, List<ArgumentI> jobArgset)
50 super(preset, jobArgset, autoUpdate);
51 this.service = service;
54 public Jws2Instance getService()
59 public void setService(Jws2Instance service)
61 this.service = service;
64 // migrate preset to new service
65 for (String url : preset.getApplicableUrls())
67 if (url.equals(service.getUri()))
72 WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
73 if (pr instanceof JabaPreset && preset instanceof JabaPreset)
75 // easy - Presets are identical (we assume)
79 List<ArgumentI> oldargs = new ArrayList<ArgumentI>(),
80 newargs = new ArrayList<ArgumentI>();
81 oldargs.addAll(preset.getArguments());
82 // need to compare parameters
83 for (ArgumentI newparg : pr.getArguments())
85 if (!oldargs.remove(newparg))
90 if (oldargs.size() == 0 && newargs.size() == 0)
96 // Try even harder to migrate arguments.
97 throw new Error(MessageManager
98 .getString("error.parameter_migration_not_implemented_yet"));
102 public List<Argument> getJobArgset()
104 return jobArgset == null ? null
105 : JabaParamStore.getJabafromJwsArgs(jobArgset);
108 public void setJobArgset(List<Argument> jobArgset)
110 // TODO: test if parameters valid for service
111 this.jobArgset = jobArgset == null ? null
112 : JabaParamStore.getJwsArgsfromJaba(jobArgset);
115 public String getWsParamFile()
117 List<Option> opts = null;
118 if (jobArgset != null)
120 opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
126 opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
129 if (opts == null || opts.size() == 0)
133 StringBuffer pset = new StringBuffer();
134 for (String ps : ParameterUtils.writeParameterSet(opts, " "))
139 return pset.toString();
143 public String getServiceURI()
145 return service.getServiceTypeURI();
149 public String[] getServiceURLs()
151 return new String[] { service.getUri() };