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.jabaws;
23 import static org.junit.Assert.assertNotNull;
24 import static org.junit.Assert.assertTrue;
25 import static org.junit.Assert.fail;
26 import jalview.datamodel.AlignmentI;
27 import jalview.gui.Jalview2XML;
28 import jalview.io.AnnotationFile;
29 import jalview.io.FormatAdapter;
30 import jalview.io.StockholmFileTest;
31 import jalview.ws.jws2.JPred301Client;
32 import jalview.ws.jws2.JabaParamStore;
33 import jalview.ws.jws2.Jws2Discoverer;
34 import jalview.ws.jws2.SequenceAnnotationWSClient;
35 import jalview.ws.jws2.jabaws2.Jws2Instance;
36 import jalview.ws.params.ArgumentI;
37 import jalview.ws.params.AutoCalcSetting;
39 import java.awt.Component;
40 import java.util.ArrayList;
41 import java.util.List;
43 import javax.swing.JMenu;
44 import javax.swing.JMenuItem;
46 import org.junit.AfterClass;
47 import org.junit.BeforeClass;
48 import org.junit.Test;
50 import compbio.metadata.Argument;
51 import compbio.metadata.WrongParameterException;
53 public class JpredJabaStructExportImport
55 public static String testseqs = "examples/uniref50.fa";
57 public static Jws2Discoverer disc;
59 public static Jws2Instance jpredws;
61 jalview.ws.jws2.JPred301Client jpredClient;
63 public static jalview.gui.AlignFrame af = null;
66 public static void setUpBeforeClass() throws Exception
69 jalview.bin.Cache.initLogger();
70 disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
72 for (Jws2Instance svc : disc.getServices())
75 if (svc.getServiceTypeURI().toLowerCase().contains("jpred"))
81 System.out.println("State of jpredws: " + jpredws);
86 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
88 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
90 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
95 public static void tearDownAfterClass() throws Exception
105 public void testJPredStructOneSeqOnly()
107 af.selectAllSequenceMenuItem_actionPerformed(null);
111 af.getViewport().getSelectionGroup().getSequenceAt(0),
113 af.hideSelSequences_actionPerformed(null);
114 jpredClient = new JPred301Client(jpredws, af, null, null);
117 "Didn't find any default args to check for. Buggy implementation of hardwired arguments in client.",
118 jpredClient.selectDefaultArgs().size() > 0);
120 boolean success = false;
121 af.getViewport().getCalcManager().startWorker(jpredClient);
127 List<Argument> args = JabaParamStore.getJabafromJwsArgs(af
129 .getCalcIdSettingsFor(jpredClient.getCalcId())
130 .getArgumentSet()), defargs = jpredClient
131 .selectDefaultArgs();
132 for (Argument rg : args)
134 for (Argument defg : defargs)
144 jpredClient.cancelCurrentJob();
145 fail("Jpred Client didn't run with hardwired default parameters.");
148 } catch (InterruptedException x)
152 } while (af.getViewport().getCalcManager().isWorking());
157 public void testJPredStructExport()
160 jpredClient = new JPred301Client(jpredws, af, null, null);
162 af.getViewport().getCalcManager().startWorker(jpredClient);
169 } catch (InterruptedException x)
173 } while (af.getViewport().getCalcManager().isWorking());
175 AlignmentI orig_alig = af.getViewport().getAlignment();
177 testAnnotationFileIO("Testing JPredWS Annotation IO", orig_alig);
181 public static void testAnnotationFileIO(String testname, AlignmentI al)
185 // what format would be appropriate for RNAalifold annotations?
186 String aligfileout = new FormatAdapter().formatSequences("PFAM",
187 al.getSequencesArray());
189 String anfileout = new AnnotationFile().printAnnotations(
190 al.getAlignmentAnnotation(), al.getGroups(),
195 + "\nAlignment annotation file was not regenerated. Null string",
200 + "\nAlignment annotation file was not regenerated. Empty string",
201 anfileout.length() > "JALVIEW_ANNOTATION".length());
203 System.out.println("Output annotation file:\n" + anfileout
206 // again what format would be appropriate?
207 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
208 FormatAdapter.PASTE, "PFAM");
212 + "\nregenerated annotation file did not annotate alignment.",
213 new AnnotationFile().readAnnotationFile(al_new, anfileout,
214 FormatAdapter.PASTE));
216 // test for consistency in io
217 StockholmFileTest.testAlignmentEquivalence(al, al_new);
219 } catch (Exception e)
225 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
229 public void testJpredwsSettingsRecovery()
231 fail("not implemnented");
232 List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
233 for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
234 .getRunnerConfig().getArguments())
236 if (rg.getDescription().contains("emperature"))
241 } catch (WrongParameterException q)
243 fail("Couldn't set the temperature parameter "
244 + q.getStackTrace());
248 if (rg.getDescription().contains("max"))
253 jpredClient = new JPred301Client(jpredws, af, null, opts);
255 af.getViewport().getCalcManager().startWorker(jpredClient);
262 } catch (InterruptedException x)
266 } while (af.getViewport().getCalcManager().isWorking());
267 AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
268 jpredClient.getCalcId());
269 String oldsettings = oldacs.getWsParamFile();
270 // write out parameters
271 jalview.gui.AlignFrame nalf = null;
272 assertTrue("Couldn't write out the Jar file",
273 new Jalview2XML(false).SaveAlignment(af,
274 "testJPredWS_param.jar", "trial parameter writeout"));
275 assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
276 false).LoadJalviewAlign("testJpredWS_param.jar")) != null);
279 AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
280 jpredClient.getCalcId());
281 assertTrue("Calc ID settings not recovered from viewport stash",
284 "Serialised Calc ID settings not identical to those recovered from viewport stash",
285 acs.getWsParamFile().equals(oldsettings));
286 JMenu nmenu = new JMenu();
287 new SequenceAnnotationWSClient()
288 .attachWSMenuEntry(nmenu, jpredws, af);
289 assertTrue("Couldn't get menu entry for service",
290 nmenu.getItemCount() > 0);
291 for (Component itm : nmenu.getMenuComponents())
293 if (itm instanceof JMenuItem)
295 JMenuItem i = (JMenuItem) itm;
296 if (i.getText().equals(
297 jpredws.getAlignAnalysisUI().getAAconToggle()))
304 while (af.getViewport().isCalcInProgress())
309 } catch (Exception x)
314 AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
315 jpredClient.getCalcId());
317 "Calc ID settings after recalculation has not been recovered.",
318 acs2.getWsParamFile().equals(oldsettings));