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;
23 import java.io.IOException;
24 import java.util.ArrayList;
25 import java.util.Arrays;
26 import java.util.Hashtable;
27 import java.util.List;
28 import java.util.StringTokenizer;
30 import compbio.metadata.Argument;
31 import compbio.metadata.Option;
32 import compbio.metadata.Parameter;
33 import compbio.metadata.Preset;
34 import compbio.metadata.PresetManager;
35 import compbio.metadata.RunnerConfig;
37 import jalview.util.MessageManager;
38 import jalview.ws.jws2.dm.JabaOption;
39 import jalview.ws.jws2.dm.JabaParameter;
40 import jalview.ws.jws2.dm.JabaWsParamSet;
41 import jalview.ws.jws2.jabaws2.Jws2Instance;
42 import jalview.ws.params.ArgumentI;
43 import jalview.ws.params.ParamDatastoreI;
44 import jalview.ws.params.ParamManager;
45 import jalview.ws.params.WsParamSetI;
47 public class JabaParamStore implements ParamDatastoreI
50 Hashtable<String, JabaWsParamSet> editedParams = new Hashtable<String, JabaWsParamSet>();
52 private Jws2Instance service;
54 private RunnerConfig serviceOptions;
56 private Hashtable<String, JabaPreset> servicePresets;
58 public JabaParamStore(Jws2Instance service)
65 public JabaParamStore(Jws2Instance service, ParamManager manager)
67 this.service = service;
68 serviceOptions = service.getRunnerConfig();
69 this.manager = manager;
70 // discover all the user's locally stored presets for this service and
71 // populate the hash table
74 manager.registerParser(service.getUri(), this);
75 WsParamSetI[] prams = manager.getParameterSet(null, service.getUri(),
79 for (WsParamSetI paramset : prams)
81 if (paramset instanceof JabaWsParamSet)
83 editedParams.put(paramset.getName(), (JabaWsParamSet) paramset);
88 .println("Warning: Ignoring parameter set instance of type "
90 + " : Bound but not applicable for service at "
99 public List<WsParamSetI> getPresets()
101 List<WsParamSetI> prefs = new ArrayList();
102 if (servicePresets == null)
104 servicePresets = new Hashtable<String, JabaPreset>();
106 if ((prman = service.getPresets()) != null)
108 List pset = prman.getPresets();
111 for (Object pr : pset)
113 JabaPreset prset = new JabaPreset(service, (Preset) pr);
114 servicePresets.put(prset.getName(), prset);
119 for (JabaPreset pr : servicePresets.values())
123 for (WsParamSetI wspset : editedParams.values())
131 public WsParamSetI getPreset(String name)
133 for (WsParamSetI pr : getPresets())
135 if (pr.getName().equals(name))
143 public static List<ArgumentI> getJwsArgsfromJaba(List jabargs)
145 return getJwsArgsfromJaba(jabargs, true);
148 public static List<ArgumentI> getJwsArgsfromJaba(List jabargs,
151 List<ArgumentI> rgs = new ArrayList<ArgumentI>();
152 List<String> rgnames = new ArrayList<String>();
153 for (Object rg : jabargs)
155 ArgumentI narg = null;
156 String nargstring = null;
157 if (rg instanceof Parameter)
159 narg = new JabaParameter((Parameter) rg);
160 nargstring = narg.getName(); // just sort by name for this
162 else if (rg instanceof Option)
164 narg = new JabaOption((Option) rg);
165 nargstring = (String) ((Option) rg).getOptionNames().get(0);
169 throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
174 rgnames.add(nargstring);
181 ArgumentI[] rgssort = rgs.toArray(new ArgumentI[rgs.size()]);
182 String[] rgssorton = rgnames.toArray(new String[rgs.size()]);
183 jalview.util.QuickSort.sort(rgssorton, rgssort);
186 while (rgssort.length - i > i)
188 tmp1 = rgssort[rgssort.length - i - 1];
189 rgssort[rgssort.length - i - 1] = rgssort[i];
192 return Arrays.asList(rgssort);
195 public static List getJabafromJwsArgs(List<ArgumentI> jwsargs)
197 List rgs = new ArrayList();
198 for (ArgumentI rg : jwsargs)
200 Argument narg = (rg instanceof JabaOption) ? ((JabaOption) rg)
204 throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
215 public List<ArgumentI> getServiceParameters()
217 return getJwsArgsfromJaba(serviceOptions.getArguments());
221 public boolean presetExists(String name)
223 return (editedParams.containsKey(name) || servicePresets
228 public void deletePreset(String name)
230 if (editedParams.containsKey(name))
232 WsParamSetI parameterSet = editedParams.get(name);
233 editedParams.remove(name);
236 manager.deleteParameterSet(parameterSet);
240 if (servicePresets.containsKey(name))
242 throw new Error(MessageManager.getString("error.implementation_error_attempt_to_delete_service_preset"));
247 public void storePreset(String presetName, String text,
248 List<ArgumentI> jobParams)
250 JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
251 jps.setApplicableUrls(new String[]
252 { service.getUri() });
253 editedParams.put(jps.getName(), jps);
256 manager.storeParameterSet(jps);
261 public void updatePreset(String oldName, String presetName, String text,
262 List<ArgumentI> jobParams)
264 JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) ? getPreset(oldName)
265 : getPreset(presetName));
268 throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_locate_oldname_presetname", new String[]{oldName,presetName}));
270 jps.setName(presetName);
271 jps.setDescription(text);
272 jps.setArguments(jobParams);
273 jps.setApplicableUrls(new String[]
274 { service.getUri() });
275 if (oldName != null && !oldName.equals(jps.getName()))
277 editedParams.remove(oldName);
279 editedParams.put(jps.getName(), jps);
283 manager.storeParameterSet(jps);
288 * create a new, empty parameter set for this service
292 WsParamSetI newWsParamSet()
294 return new JabaWsParamSet();
297 private boolean involves(String[] urls)
299 boolean found = false;
300 for (String url : urls)
302 if (service.getServiceTypeURI().equals(url)
303 || service.getUri().equalsIgnoreCase(url))
313 public WsParamSetI parseServiceParameterFile(String name, String descr,
314 String[] urls, String parameterfile) throws IOException
318 throw new IOException(MessageManager.getString("error.implementation_error_cannot_find_service_url_in_given_set"));
321 JabaWsParamSet wsp = new JabaWsParamSet();
323 wsp.setDescription(descr);
324 wsp.setApplicableUrls(urls.clone());
326 List<String> lines = new ArrayList<String>();
327 StringTokenizer st = new StringTokenizer(parameterfile, "\n");
328 while (st.hasMoreTokens())
330 lines.add(st.nextToken());
332 wsp.setjabaArguments(ParameterUtils.processParameters(lines,
333 serviceOptions, " "));
338 public String generateServiceParameterFile(WsParamSetI pset)
341 if (!involves(pset.getApplicableUrls()))
343 throw new IOException(MessageManager.formatMessage("error.implementation_error_cannot_find_service_url_in_given_set_param_store", new String[]{service.getUri()}));
345 if (!(pset instanceof JabaWsParamSet))
347 throw new Error(MessageManager.getString("error.implementation_error_jabaws_param_set_only_handled_by"));
350 StringBuffer rslt = new StringBuffer();
351 for (String ln : ParameterUtils.writeParameterSet(
352 ((JabaWsParamSet) pset).getjabaArguments(), " "))
358 return rslt.toString();