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.AutoCalcSetting;
38 import java.awt.Component;
39 import java.util.ArrayList;
40 import java.util.List;
42 import javax.swing.JMenu;
43 import javax.swing.JMenuItem;
45 import org.junit.AfterClass;
46 import org.junit.BeforeClass;
47 import org.junit.Test;
49 import compbio.metadata.Argument;
50 import compbio.metadata.WrongParameterException;
52 public class JpredJabaStructExportImport
54 public static String testseqs = "examples/uniref50.fa";
56 public static Jws2Discoverer disc;
58 public static Jws2Instance jpredws;
60 jalview.ws.jws2.JPred301Client jpredClient;
62 public static jalview.gui.AlignFrame af = null;
65 public static void setUpBeforeClass() throws Exception
68 jalview.bin.Cache.initLogger();
69 disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
71 for (Jws2Instance svc : disc.getServices())
74 if (svc.getServiceTypeURI().toLowerCase().contains("jpred"))
80 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
82 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
84 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
89 public static void tearDownAfterClass() throws Exception
99 public void testJPredStructOneSeqOnly()
101 af.selectAllSequenceMenuItem_actionPerformed(null);
105 af.getViewport().getSelectionGroup().getSequenceAt(0),
107 af.hideSelSequences_actionPerformed(null);
109 assertNotNull(jpredws);
110 jpredClient = new JPred301Client(jpredws, af, null, null);
113 "Didn't find any default args to check for. Buggy implementation of hardwired arguments in client.",
114 jpredClient.selectDefaultArgs().size() > 0);
116 boolean success = false;
117 af.getViewport().getCalcManager().startWorker(jpredClient);
123 List<Argument> args = JabaParamStore.getJabafromJwsArgs(af
125 .getCalcIdSettingsFor(jpredClient.getCalcId())
126 .getArgumentSet()), defargs = jpredClient
127 .selectDefaultArgs();
128 for (Argument rg : args)
130 for (Argument defg : defargs)
140 jpredClient.cancelCurrentJob();
141 fail("Jpred Client didn't run with hardwired default parameters.");
144 } catch (InterruptedException x)
148 } while (af.getViewport().getCalcManager().isWorking());
153 public void testJPredStructExport()
155 assertNotNull(jpredws);
156 jpredClient = new JPred301Client(jpredws, af, null, null);
158 af.getViewport().getCalcManager().startWorker(jpredClient);
165 } catch (InterruptedException x)
169 } while (af.getViewport().getCalcManager().isWorking());
171 AlignmentI orig_alig = af.getViewport().getAlignment();
173 testAnnotationFileIO("Testing JPredWS Annotation IO", orig_alig);
177 public static void testAnnotationFileIO(String testname, AlignmentI al)
181 // what format would be appropriate for RNAalifold annotations?
182 String aligfileout = new FormatAdapter().formatSequences("PFAM",
183 al.getSequencesArray());
185 String anfileout = new AnnotationFile().printAnnotations(
186 al.getAlignmentAnnotation(), al.getGroups(),
191 + "\nAlignment annotation file was not regenerated. Null string",
196 + "\nAlignment annotation file was not regenerated. Empty string",
197 anfileout.length() > "JALVIEW_ANNOTATION".length());
199 System.out.println("Output annotation file:\n" + anfileout
202 // again what format would be appropriate?
203 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
204 FormatAdapter.PASTE, "PFAM");
208 + "\nregenerated annotation file did not annotate alignment.",
209 new AnnotationFile().readAnnotationFile(al_new, anfileout,
210 FormatAdapter.PASTE));
212 // test for consistency in io
213 StockholmFileTest.testAlignmentEquivalence(al, al_new);
215 } catch (Exception e)
221 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
225 public void testJpredwsSettingsRecovery()
227 fail("not implemnented");
228 List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
229 for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
230 .getRunnerConfig().getArguments())
232 if (rg.getDescription().contains("emperature"))
237 } catch (WrongParameterException q)
239 fail("Couldn't set the temperature parameter "
240 + q.getStackTrace());
244 if (rg.getDescription().contains("max"))
250 assertNotNull(jpredws);
251 jpredClient = new JPred301Client(jpredws, af, null, opts);
253 af.getViewport().getCalcManager().startWorker(jpredClient);
260 } catch (InterruptedException x)
264 } while (af.getViewport().getCalcManager().isWorking());
265 AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
266 jpredClient.getCalcId());
267 String oldsettings = oldacs.getWsParamFile();
268 // write out parameters
269 jalview.gui.AlignFrame nalf = null;
270 assertTrue("Couldn't write out the Jar file",
271 new Jalview2XML(false).SaveAlignment(af,
272 "testJPredWS_param.jar", "trial parameter writeout"));
273 assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
274 false).LoadJalviewAlign("testJpredWS_param.jar")) != null);
277 AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
278 jpredClient.getCalcId());
279 assertTrue("Calc ID settings not recovered from viewport stash",
282 "Serialised Calc ID settings not identical to those recovered from viewport stash",
283 acs.getWsParamFile().equals(oldsettings));
284 JMenu nmenu = new JMenu();
285 new SequenceAnnotationWSClient()
286 .attachWSMenuEntry(nmenu, jpredws, af);
287 assertTrue("Couldn't get menu entry for service",
288 nmenu.getItemCount() > 0);
289 for (Component itm : nmenu.getMenuComponents())
291 if (itm instanceof JMenuItem)
293 JMenuItem i = (JMenuItem) itm;
294 if (i.getText().equals(
295 jpredws.getAlignAnalysisUI().getAAconToggle()))
302 while (af.getViewport().isCalcInProgress())
307 } catch (Exception x)
312 AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
313 jpredClient.getCalcId());
315 "Calc ID settings after recalculation has not been recovered.",
316 acs2.getWsParamFile().equals(oldsettings));