1 package jalview.ws.jws2.dm;
3 import java.util.ArrayList;
6 import compbio.metadata.Argument;
7 import compbio.metadata.Option;
8 import compbio.metadata.Preset;
10 import jalview.ws.jws2.JabaParamStore;
11 import jalview.ws.jws2.JabaPreset;
12 import jalview.ws.jws2.ParameterUtils;
13 import jalview.ws.jws2.jabaws2.Jws2Instance;
14 import jalview.ws.params.ArgumentI;
15 import jalview.ws.params.ParamManager;
16 import jalview.ws.params.WsParamSetI;
19 * preferences for running AACons service
21 * @author jprocter TODO: refactor to a generic 'last job and service run'
24 public class AAConsSettings extends jalview.ws.params.AutoCalcSetting
28 public AAConsSettings(boolean autoUpdate, Jws2Instance service,
29 WsParamSetI preset, List<ArgumentI> jobArgset)
31 super(preset, jobArgset, autoUpdate);
32 this.service = service;
35 public Jws2Instance getService()
40 public void setService(Jws2Instance service)
42 this.service = service;
45 // migrate preset to new service
46 for (String url : preset.getApplicableUrls())
48 if (url.equals(service.getUri()))
53 WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
54 if (pr instanceof JabaPreset && preset instanceof JabaPreset)
56 // easy - Presets are identical (we assume)
60 List<ArgumentI> oldargs = new ArrayList<ArgumentI>(), newargs = new ArrayList<ArgumentI>();
61 oldargs.addAll(preset.getArguments());
62 // need to compare parameters
63 for (ArgumentI newparg : pr.getArguments())
65 if (!oldargs.remove(newparg))
70 if (oldargs.size() == 0 && newargs.size() == 0)
76 // Try even harder to migrate arguments.
77 throw new Error("Parameter migration not implemented yet");
81 public List<Argument> getJobArgset()
83 return jobArgset==null ? null : JabaParamStore.getJabafromJwsArgs(jobArgset);
86 public void setJobArgset(List<Argument> jobArgset)
88 // TODO: test if parameters valid for service
89 this.jobArgset = jobArgset==null ? null : JabaParamStore.getJwsArgsfromJaba(jobArgset);
92 public String getWsParamFile()
94 List<Option> opts=null;
97 opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
101 opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
104 if (opts==null || opts.size()==0)
108 StringBuffer pset=new StringBuffer();
109 for (String ps:ParameterUtils.writeParameterSet(opts, " "))
111 pset.append(ps); pset.append("\n");
113 return pset.toString();
117 public String getServiceURI()
119 return service.getServiceTypeURI();