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.AlignmentI;
28 import jalview.gui.Jalview2XML;
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.ws.jws2.JPred301Client;
36 import jalview.ws.jws2.JabaParamStore;
37 import jalview.ws.jws2.Jws2Discoverer;
38 import jalview.ws.jws2.SequenceAnnotationWSClient;
39 import jalview.ws.jws2.jabaws2.Jws2Instance;
40 import jalview.ws.params.AutoCalcSetting;
42 import java.awt.Component;
43 import java.util.ArrayList;
44 import java.util.List;
46 import javax.swing.JMenu;
47 import javax.swing.JMenuItem;
49 import org.testng.Assert;
50 import org.testng.annotations.AfterClass;
51 import org.testng.annotations.BeforeClass;
52 import org.testng.annotations.BeforeGroups;
53 import org.testng.annotations.Test;
55 import compbio.metadata.Argument;
56 import compbio.metadata.WrongParameterException;
58 public class JpredJabaStructExportImport
61 @BeforeClass(alwaysRun = true)
62 public void setUpJvOptionPane()
64 JvOptionPane.setInteractiveMode(false);
65 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
68 public static String testseqs = "examples/uniref50.fa";
70 public static Jws2Discoverer disc;
72 public static Jws2Instance jpredws;
74 jalview.ws.jws2.JPred301Client jpredClient;
76 public static jalview.gui.AlignFrame af = null;
78 @BeforeGroups(groups = { "Network" })
79 public static void setUpBeforeClass() throws Exception
81 Cache.loadProperties("test/jalview/io/testProps.jvprops");
83 disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
85 for (Jws2Instance svc : disc.getServices())
87 if (svc.getServiceTypeURI().toLowerCase().contains("jpred"))
93 System.out.println("State of jpredws: " + jpredws);
94 Assert.assertNotNull(jpredws, "jpredws is null!");
95 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
96 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
97 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
100 @AfterClass(alwaysRun = true)
101 public static void tearDownAfterClass() throws Exception
105 af.setVisible(false);
110 @Test(groups = { "Network" }, enabled = false)
111 public void testJPredStructOneSeqOnly()
113 af.selectAllSequenceMenuItem_actionPerformed(null);
117 af.getViewport().getSelectionGroup().getSequenceAt(0),
119 af.hideSelSequences_actionPerformed(null);
120 jpredClient = new JPred301Client(jpredws, af, null, null);
123 "Didn't find any default args to check for. Buggy implementation of hardwired arguments in client.",
124 jpredClient.selectDefaultArgs().size() > 0);
126 boolean success = false;
127 af.getViewport().getCalcManager().startWorker(jpredClient);
133 List<Argument> args = JabaParamStore.getJabafromJwsArgs(af
135 .getCalcIdSettingsFor(jpredClient.getCalcId())
136 .getArgumentSet()), defargs = jpredClient
137 .selectDefaultArgs();
138 for (Argument rg : args)
140 for (Argument defg : defargs)
150 jpredClient.cancelCurrentJob();
151 Assert.fail("Jpred Client didn't run with hardwired default parameters.");
154 } catch (InterruptedException x)
158 } while (af.getViewport().getCalcManager().isWorking());
162 @Test(groups = { "Network" }, enabled = false)
163 public void testJPredStructExport()
166 jpredClient = new JPred301Client(jpredws, af, null, null);
168 af.getViewport().getCalcManager().startWorker(jpredClient);
175 } catch (InterruptedException x)
179 } while (af.getViewport().getCalcManager().isWorking());
181 AlignmentI orig_alig = af.getViewport().getAlignment();
183 testAnnotationFileIO("Testing JPredWS Annotation IO", orig_alig);
187 public static void testAnnotationFileIO(String testname, AlignmentI al)
191 // what format would be appropriate for RNAalifold annotations?
192 String aligfileout = FileFormat.Pfam.getWriter(null).print(
193 al.getSequencesArray(), true);
195 String anfileout = new AnnotationFile()
196 .printAnnotationsForAlignment(al);
200 + "\nAlignment annotation file was not regenerated. Null string",
205 + "\nAlignment annotation file was not regenerated. Empty string",
206 anfileout.length() > "JALVIEW_ANNOTATION".length());
208 System.out.println("Output annotation file:\n" + anfileout
211 // again what format would be appropriate?
212 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
213 DataSourceType.PASTE, FileFormat.Fasta);
217 + "\nregenerated annotation file did not annotate alignment.",
218 new AnnotationFile().readAnnotationFile(al_new, anfileout,
219 DataSourceType.PASTE));
221 // test for consistency in io
222 StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
225 } catch (Exception e)
231 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
234 @Test(groups = { "Network" }, enabled = false)
235 public void testJpredwsSettingsRecovery()
237 Assert.fail("not implemnented");
238 List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
239 for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
240 .getRunnerConfig().getArguments())
242 if (rg.getDescription().contains("emperature"))
247 } catch (WrongParameterException q)
249 Assert.fail("Couldn't set the temperature parameter "
250 + q.getStackTrace());
254 if (rg.getDescription().contains("max"))
259 jpredClient = new JPred301Client(jpredws, af, null, opts);
261 af.getViewport().getCalcManager().startWorker(jpredClient);
268 } catch (InterruptedException x)
272 } while (af.getViewport().getCalcManager().isWorking());
273 AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
274 jpredClient.getCalcId());
275 String oldsettings = oldacs.getWsParamFile();
276 // write out parameters
277 jalview.gui.AlignFrame nalf = null;
278 assertTrue("Couldn't write out the Jar file",
279 new Jalview2XML(false).saveAlignment(af,
280 "testJPredWS_param.jar", "trial parameter writeout"));
281 assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
282 false).loadJalviewAlign("testJpredWS_param.jar")) != null);
285 AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
286 jpredClient.getCalcId());
287 assertTrue("Calc ID settings not recovered from viewport stash",
290 "Serialised Calc ID settings not identical to those recovered from viewport stash",
291 acs.getWsParamFile().equals(oldsettings));
292 JMenu nmenu = new JMenu();
293 new SequenceAnnotationWSClient()
294 .attachWSMenuEntry(nmenu, jpredws, af);
295 assertTrue("Couldn't get menu entry for service",
296 nmenu.getItemCount() > 0);
297 for (Component itm : nmenu.getMenuComponents())
299 if (itm instanceof JMenuItem)
301 JMenuItem i = (JMenuItem) itm;
302 if (i.getText().equals(
303 jpredws.getAlignAnalysisUI().getAAconToggle()))
310 while (af.getViewport().isCalcInProgress())
315 } catch (Exception x)
320 AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
321 jpredClient.getCalcId());
323 "Calc ID settings after recalculation has not been recovered.",
324 acs2.getWsParamFile().equals(oldsettings));