2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.jws2.dm;
21 import java.util.ArrayList;
22 import java.util.List;
24 import compbio.metadata.Argument;
25 import compbio.metadata.Option;
27 import jalview.ws.jws2.JabaParamStore;
28 import jalview.ws.jws2.JabaPreset;
29 import jalview.ws.jws2.ParameterUtils;
30 import jalview.ws.jws2.jabaws2.Jws2Instance;
31 import jalview.ws.params.ArgumentI;
32 import jalview.ws.params.WsParamSetI;
35 * preferences for running AACon service
37 * @author jprocter TODO: refactor to a generic 'last job and service run'
40 public class AAConSettings extends jalview.ws.params.AutoCalcSetting
44 public AAConSettings(boolean autoUpdate, Jws2Instance service,
45 WsParamSetI preset, List<ArgumentI> jobArgset)
47 super(preset, jobArgset, autoUpdate);
48 this.service = service;
51 public Jws2Instance getService()
56 public void setService(Jws2Instance service)
58 this.service = service;
61 // migrate preset to new service
62 for (String url : preset.getApplicableUrls())
64 if (url.equals(service.getUri()))
69 WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
70 if (pr instanceof JabaPreset && preset instanceof JabaPreset)
72 // easy - Presets are identical (we assume)
76 List<ArgumentI> oldargs = new ArrayList<ArgumentI>(), newargs = new ArrayList<ArgumentI>();
77 oldargs.addAll(preset.getArguments());
78 // need to compare parameters
79 for (ArgumentI newparg : pr.getArguments())
81 if (!oldargs.remove(newparg))
86 if (oldargs.size() == 0 && newargs.size() == 0)
92 // Try even harder to migrate arguments.
93 throw new Error("Parameter migration not implemented yet");
97 public List<Argument> getJobArgset()
99 return jobArgset == null ? null : JabaParamStore
100 .getJabafromJwsArgs(jobArgset);
103 public void setJobArgset(List<Argument> jobArgset)
105 // TODO: test if parameters valid for service
106 this.jobArgset = jobArgset == null ? null : JabaParamStore
107 .getJwsArgsfromJaba(jobArgset);
110 public String getWsParamFile()
112 List<Option> opts = null;
113 if (jobArgset != null)
115 opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
121 opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
124 if (opts == null || opts.size() == 0)
128 StringBuffer pset = new StringBuffer();
129 for (String ps : ParameterUtils.writeParameterSet(opts, " "))
134 return pset.toString();
138 public String getServiceURI()
140 return service.getServiceTypeURI();
144 public String[] getServiceURLs()
147 { service.getUri() };