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.ws.api.ServiceWithParameters;
24 import jalview.ws.jws2.JabaParamStore;
25 import jalview.ws.jws2.ParameterUtils;
26 import jalview.ws.params.ArgumentI;
27 import jalview.ws.params.WsParamSetI;
29 import java.util.List;
31 import compbio.metadata.Option;
34 * preferences for running AACon service
36 * @author jprocter TODO: refactor to a generic 'last job and service run'
39 public class AAConSettings extends jalview.ws.params.AutoCalcSetting
41 public AAConSettings(boolean autoUpdate, ServiceWithParameters service2,
42 WsParamSetI preset, List<ArgumentI> jobArgset)
44 super(service2, preset, jobArgset, autoUpdate);
48 public String getWsParamFile()
50 List<Option> opts = null;
51 if (jobArgset != null)
53 opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
59 opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
62 if (opts == null || opts.size() == 0)
66 StringBuffer pset = new StringBuffer();
67 for (String ps : ParameterUtils.writeParameterSet(opts, " "))
72 return pset.toString();