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 java.util.Locale;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertTrue;
28 import jalview.bin.Cache;
29 import jalview.bin.Console;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
32 import jalview.gui.JvOptionPane;
33 import jalview.io.AnnotationFile;
34 import jalview.io.DataSourceType;
35 import jalview.io.FileFormat;
36 import jalview.io.FormatAdapter;
37 import jalview.io.StockholmFileTest;
38 import jalview.ws.jws2.AADisorderClient;
39 import jalview.ws.jws2.Jws2Discoverer;
40 import jalview.ws.jws2.jabaws2.Jws2Instance;
42 import java.util.ArrayList;
43 import java.util.List;
45 import org.testng.Assert;
46 import org.testng.annotations.AfterClass;
47 import org.testng.annotations.BeforeClass;
48 import org.testng.annotations.Test;
51 * All methods in this class are set to the Network group because setUpBeforeClass will fail
52 * if there is no network.
54 @Test(singleThreaded = true)
55 public class DisorderAnnotExportImport
58 @BeforeClass(alwaysRun = true)
59 public void setUpJvOptionPane()
61 JvOptionPane.setInteractiveMode(false);
62 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
65 public static String testseqs = "examples/uniref50.fa";
67 public static Jws2Discoverer disc;
69 public static List<Jws2Instance> iupreds;
71 jalview.ws.jws2.AADisorderClient disorderClient;
73 public static jalview.gui.AlignFrame af = null;
75 @BeforeClass(alwaysRun = true)
76 public static void setUpBeforeClass() throws Exception
78 Cache.loadProperties("test/jalview/io/testProps.jvprops");
80 disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
82 while (disc.isRunning())
84 // don't get services until discoverer has finished
88 iupreds = new ArrayList<Jws2Instance>();
89 for (Jws2Instance svc : disc.getServices())
91 if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("iupredws"))
96 assertTrue("Couldn't discover any IUPred services to use to test.",
98 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
99 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
100 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
103 @AfterClass(alwaysRun = true)
104 public static void tearDownAfterClass() throws Exception
108 af.setVisible(false);
115 * test for patches to JAL-1294
117 @Test(groups = { "External", "Network" })
118 public void testDisorderAnnotExport()
120 disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
121 af.getViewport().getCalcManager().startWorker(disorderClient);
127 } catch (InterruptedException x)
131 } while (af.getViewport().getCalcManager().isWorking());
132 AlignmentI orig_alig = af.getViewport().getAlignment();
133 // NOTE: Consensus annotation row cannot be exported and reimported
134 // faithfully - so we remove them
135 List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
136 for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
138 if (aa.autoCalculated)
143 for (AlignmentAnnotation aa : toremove)
145 orig_alig.deleteAnnotation(aa);
147 checkAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
151 static void checkAnnotationFileIO(String testname, AlignmentI al)
155 String aligfileout = FileFormat.Pfam.getWriter(al).print(
156 al.getSequencesArray(), true);
157 String anfileout = new AnnotationFile()
158 .printAnnotationsForAlignment(al);
162 + "\nAlignment annotation file was not regenerated. Null string",
167 + "\nAlignment annotation file was not regenerated. Empty string",
168 anfileout.length() > "JALVIEW_ANNOTATION".length());
170 System.out.println("Output annotation file:\n" + anfileout
173 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
174 DataSourceType.PASTE, FileFormat.Pfam);
178 + "\nregenerated annotation file did not annotate alignment.",
179 new AnnotationFile().readAnnotationFile(al_new, anfileout,
180 DataSourceType.PASTE));
182 // test for consistency in io
183 StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
186 } catch (Exception e)
192 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");