2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
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 java.util.ArrayList;
24 import java.util.List;
26 import compbio.metadata.Argument;
27 import compbio.metadata.Option;
29 import jalview.ws.jws2.JabaParamStore;
30 import jalview.ws.jws2.JabaPreset;
31 import jalview.ws.jws2.ParameterUtils;
32 import jalview.ws.jws2.jabaws2.Jws2Instance;
33 import jalview.ws.params.ArgumentI;
34 import jalview.ws.params.WsParamSetI;
37 * preferences for running AACon service
39 * @author jprocter TODO: refactor to a generic 'last job and service run'
42 public class AAConSettings extends jalview.ws.params.AutoCalcSetting
46 public AAConSettings(boolean autoUpdate, Jws2Instance service,
47 WsParamSetI preset, List<ArgumentI> jobArgset)
49 super(preset, jobArgset, autoUpdate);
50 this.service = service;
53 public Jws2Instance getService()
58 public void setService(Jws2Instance service)
60 this.service = service;
63 // migrate preset to new service
64 for (String url : preset.getApplicableUrls())
66 if (url.equals(service.getUri()))
71 WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
72 if (pr instanceof JabaPreset && preset instanceof JabaPreset)
74 // easy - Presets are identical (we assume)
78 List<ArgumentI> oldargs = new ArrayList<ArgumentI>(), newargs = new ArrayList<ArgumentI>();
79 oldargs.addAll(preset.getArguments());
80 // need to compare parameters
81 for (ArgumentI newparg : pr.getArguments())
83 if (!oldargs.remove(newparg))
88 if (oldargs.size() == 0 && newargs.size() == 0)
94 // Try even harder to migrate arguments.
95 throw new Error("Parameter migration not implemented yet");
99 public List<Argument> getJobArgset()
101 return jobArgset == null ? null : JabaParamStore
102 .getJabafromJwsArgs(jobArgset);
105 public void setJobArgset(List<Argument> jobArgset)
107 // TODO: test if parameters valid for service
108 this.jobArgset = jobArgset == null ? null : JabaParamStore
109 .getJwsArgsfromJaba(jobArgset);
112 public String getWsParamFile()
114 List<Option> opts = null;
115 if (jobArgset != null)
117 opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
123 opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
126 if (opts == null || opts.size() == 0)
130 StringBuffer pset = new StringBuffer();
131 for (String ps : ParameterUtils.writeParameterSet(opts, " "))
136 return pset.toString();
140 public String getServiceURI()
142 return service.getServiceTypeURI();
146 public String[] getServiceURLs()
149 { service.getUri() };