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.io.AnnotationFile;
30 import jalview.io.DataSourceType;
31 import jalview.io.FileFormat;
32 import jalview.io.FormatAdapter;
33 import jalview.io.StockholmFileTest;
34 import jalview.ws.jws2.JPred301Client;
35 import jalview.ws.jws2.JabaParamStore;
36 import jalview.ws.jws2.Jws2Discoverer;
37 import jalview.ws.jws2.SequenceAnnotationWSClient;
38 import jalview.ws.jws2.jabaws2.Jws2Instance;
39 import jalview.ws.params.AutoCalcSetting;
41 import java.awt.Component;
42 import java.util.ArrayList;
43 import java.util.List;
45 import javax.swing.JMenu;
46 import javax.swing.JMenuItem;
48 import org.testng.Assert;
49 import org.testng.annotations.AfterClass;
50 import org.testng.annotations.BeforeClass;
51 import org.testng.annotations.Test;
53 import compbio.metadata.Argument;
54 import compbio.metadata.WrongParameterException;
56 public class JpredJabaStructExportImport
58 public static String testseqs = "examples/uniref50.fa";
60 public static Jws2Discoverer disc;
62 public static Jws2Instance jpredws;
64 jalview.ws.jws2.JPred301Client jpredClient;
66 public static jalview.gui.AlignFrame af = null;
68 @BeforeClass(alwaysRun = true)
69 public static void setUpBeforeClass() throws Exception
71 Cache.loadProperties("test/jalview/io/testProps.jvprops");
73 disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
75 for (Jws2Instance svc : disc.getServices())
77 if (svc.getServiceTypeURI().toLowerCase().contains("jpred"))
83 System.out.println("State of jpredws: " + jpredws);
84 Assert.assertNotNull(jpredws, "jpredws is null!");
85 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
86 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
87 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
90 @AfterClass(alwaysRun = true)
91 public static void tearDownAfterClass() throws Exception
100 @Test(groups = { "Functional" })
101 public void testJPredStructOneSeqOnly()
103 af.selectAllSequenceMenuItem_actionPerformed(null);
107 af.getViewport().getSelectionGroup().getSequenceAt(0),
109 af.hideSelSequences_actionPerformed(null);
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 Assert.fail("Jpred Client didn't run with hardwired default parameters.");
144 } catch (InterruptedException x)
148 } while (af.getViewport().getCalcManager().isWorking());
152 @Test(groups = { "Functional" })
153 public void testJPredStructExport()
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()
186 .printAnnotationsForAlignment(al);
190 + "\nAlignment annotation file was not regenerated. Null string",
195 + "\nAlignment annotation file was not regenerated. Empty string",
196 anfileout.length() > "JALVIEW_ANNOTATION".length());
198 System.out.println("Output annotation file:\n" + anfileout
201 // again what format would be appropriate?
202 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
203 DataSourceType.PASTE, FileFormat.Fasta);
207 + "\nregenerated annotation file did not annotate alignment.",
208 new AnnotationFile().readAnnotationFile(al_new, anfileout,
209 DataSourceType.PASTE));
211 // test for consistency in io
212 StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
214 } catch (Exception e)
220 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
223 @Test(groups = { "Functional" })
224 public void testJpredwsSettingsRecovery()
226 Assert.fail("not implemnented");
227 List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
228 for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
229 .getRunnerConfig().getArguments())
231 if (rg.getDescription().contains("emperature"))
236 } catch (WrongParameterException q)
238 Assert.fail("Couldn't set the temperature parameter "
239 + q.getStackTrace());
243 if (rg.getDescription().contains("max"))
248 jpredClient = new JPred301Client(jpredws, af, null, opts);
250 af.getViewport().getCalcManager().startWorker(jpredClient);
257 } catch (InterruptedException x)
261 } while (af.getViewport().getCalcManager().isWorking());
262 AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
263 jpredClient.getCalcId());
264 String oldsettings = oldacs.getWsParamFile();
265 // write out parameters
266 jalview.gui.AlignFrame nalf = null;
267 assertTrue("Couldn't write out the Jar file",
268 new Jalview2XML(false).saveAlignment(af,
269 "testJPredWS_param.jar", "trial parameter writeout"));
270 assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
271 false).loadJalviewAlign("testJpredWS_param.jar")) != null);
274 AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
275 jpredClient.getCalcId());
276 assertTrue("Calc ID settings not recovered from viewport stash",
279 "Serialised Calc ID settings not identical to those recovered from viewport stash",
280 acs.getWsParamFile().equals(oldsettings));
281 JMenu nmenu = new JMenu();
282 new SequenceAnnotationWSClient()
283 .attachWSMenuEntry(nmenu, jpredws, af);
284 assertTrue("Couldn't get menu entry for service",
285 nmenu.getItemCount() > 0);
286 for (Component itm : nmenu.getMenuComponents())
288 if (itm instanceof JMenuItem)
290 JMenuItem i = (JMenuItem) itm;
291 if (i.getText().equals(
292 jpredws.getAlignAnalysisUI().getAAconToggle()))
299 while (af.getViewport().isCalcInProgress())
304 } catch (Exception x)
309 AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
310 jpredClient.getCalcId());
312 "Calc ID settings after recalculation has not been recovered.",
313 acs2.getWsParamFile().equals(oldsettings));