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.jabaws;
23 import static org.testng.AssertJUnit.assertNotNull;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.gui.JvOptionPane;
30 import jalview.io.AnnotationFile;
31 import jalview.io.DataSourceType;
32 import jalview.io.FileFormat;
33 import jalview.io.FormatAdapter;
34 import jalview.io.StockholmFileTest;
35 import jalview.project.Jalview2XML;
36 import jalview.ws.jws2.AbstractJabaCalcWorker;
37 import jalview.ws.jws2.JabaParamStore;
38 import jalview.ws.jws2.Jws2Discoverer;
39 import jalview.ws.jws2.SequenceAnnotationWSClient;
40 import jalview.ws.jws2.jabaws2.Jws2Instance;
41 import jalview.ws.params.AutoCalcSetting;
43 import java.awt.Component;
45 import java.util.ArrayList;
46 import java.util.List;
48 import javax.swing.JMenu;
49 import javax.swing.JMenuItem;
51 import org.testng.Assert;
52 import org.testng.annotations.AfterClass;
53 import org.testng.annotations.BeforeClass;
54 import org.testng.annotations.Test;
56 import compbio.metadata.Argument;
57 import compbio.metadata.WrongParameterException;
60 * All methods in this class are set to the Network group because setUpBeforeClass will fail
61 * if there is no network.
63 @Test(singleThreaded = true)
64 public class RNAStructExportImport
67 @BeforeClass(alwaysRun = true)
68 public void setUpJvOptionPane()
70 JvOptionPane.setInteractiveMode(false);
71 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
74 private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
76 public static String testseqs = "examples/RF00031_folded.stk";
78 public static Jws2Discoverer disc;
80 public static Jws2Instance rnaalifoldws;
82 AbstractJabaCalcWorker alifoldClient;
84 public static jalview.gui.AlignFrame af = null;
86 @BeforeClass(alwaysRun = true)
87 public static void setUpBeforeClass() throws Exception
89 Cache.loadProperties("test/jalview/io/testProps.jvprops");
91 disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
93 while (disc.isRunning())
95 // don't get services until discoverer has finished
99 for (Jws2Instance svc : disc.getServices())
102 if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
108 System.out.println("State of rnaalifoldws: " + rnaalifoldws);
110 if (rnaalifoldws == null)
112 Assert.fail("no web service");
115 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
117 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
119 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
121 // remove any existing annotation
122 List<AlignmentAnnotation> aal = new ArrayList<>();
123 for (AlignmentAnnotation rna : af.getViewport().getAlignment()
124 .getAlignmentAnnotation())
131 for (AlignmentAnnotation rna : aal)
133 af.getViewport().getAlignment().deleteAnnotation(rna);
135 af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel
139 @AfterClass(alwaysRun = true)
140 public static void tearDownAfterClass() throws Exception
144 af.setVisible(false);
146 File f = new File(JAR_FILE_NAME);
154 @Test(groups = { "Network" })
155 public void testRNAAliFoldValidStructure()
158 alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
161 af.getViewport().getCalcManager().startWorker(alifoldClient);
168 } catch (InterruptedException x)
171 } while (af.getViewport().getCalcManager().isWorking());
173 AlignmentI orig_alig = af.getViewport().getAlignment();
174 for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
176 if (alifoldClient.involves(aa))
181 "Did not create valid structure from RNAALiFold prediction",
188 @Test(groups = { "Network" })
189 public void testRNAStructExport()
192 alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
195 af.getViewport().getCalcManager().startWorker(alifoldClient);
202 } catch (InterruptedException x)
205 } while (af.getViewport().getCalcManager().isWorking());
207 AlignmentI orig_alig = af.getViewport().getAlignment();
208 // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
209 // annotation is mistakenly recognised as an RNA annotation row when read in
210 // as an annotation file. bug is JAL-3122
211 verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
215 static void verifyAnnotationFileIO(String testname, AlignmentI al)
219 // what format would be appropriate for RNAalifold annotations?
220 String aligfileout = FileFormat.Pfam.getWriter(null).print(
221 al.getSequencesArray(), true);
223 String anfileout = new AnnotationFile()
224 .printAnnotationsForAlignment(al);
228 + "\nAlignment annotation file was not regenerated. Null string",
233 + "\nAlignment annotation file was not regenerated. Empty string",
234 anfileout.length() > "JALVIEW_ANNOTATION".length());
236 System.out.println("Output annotation file:\n" + anfileout
239 // again what format would be appropriate?
240 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
241 DataSourceType.PASTE, FileFormat.Pfam);
245 + "\nregenerated annotation file did not annotate alignment.",
246 new AnnotationFile().readAnnotationFile(al_new, anfileout,
247 DataSourceType.PASTE));
249 // test for consistency in io
250 StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
253 } catch (Exception e)
259 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
262 @Test(groups = { "Network" })
263 public void testRnaalifoldSettingsRecovery()
265 List<Argument> opts = new ArrayList<>();
266 for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
269 if (rg.getDescription().contains("emperature"))
274 } catch (WrongParameterException q)
276 Assert.fail("Couldn't set the temperature parameter "
277 + q.getStackTrace());
281 if (rg.getDescription().contains("max"))
286 alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
287 JabaParamStore.getJwsArgsfromJaba(opts));
289 af.getViewport().getCalcManager().startWorker(alifoldClient);
296 } catch (InterruptedException x)
300 } while (af.getViewport().getCalcManager().isWorking());
301 AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
302 alifoldClient.getCalcId());
303 String oldsettings = oldacs.getWsParamFile();
304 // write out parameters
305 jalview.gui.AlignFrame nalf = null;
306 assertTrue("Couldn't write out the Jar file",
307 new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME,
308 "trial parameter writeout"));
309 assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
310 false).loadJalviewAlign(JAR_FILE_NAME)) != null);
313 AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
314 alifoldClient.getCalcId());
315 assertTrue("Calc ID settings not recovered from viewport stash",
318 "Serialised Calc ID settings not identical to those recovered from viewport stash",
319 acs.getWsParamFile().equals(oldsettings));
320 JMenu nmenu = new JMenu();
321 new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
323 assertTrue("Couldn't get menu entry for service",
324 nmenu.getItemCount() > 0);
325 for (Component itm : nmenu.getMenuComponents())
327 if (itm instanceof JMenuItem)
329 JMenuItem i = (JMenuItem) itm;
330 if (i.getText().equals(
331 rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
338 while (af.getViewport().isCalcInProgress())
343 } catch (Exception x)
348 AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
349 alifoldClient.getCalcId());
351 "Calc ID settings after recalculation has not been recovered.",
352 acs2.getWsParamFile().equals(oldsettings));