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.AlignFrame;
30 import jalview.gui.JvOptionPane;
31 import jalview.io.AnnotationFile;
32 import jalview.io.DataSourceType;
33 import jalview.io.FileFormat;
34 import jalview.io.FormatAdapter;
35 import jalview.io.StockholmFileTest;
36 import jalview.ws.api.ServiceWithParameters;
37 import jalview.ws.jws2.Jws2Discoverer;
38 import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
40 import java.util.ArrayList;
41 import java.util.List;
43 import org.testng.Assert;
44 import org.testng.annotations.AfterClass;
45 import org.testng.annotations.BeforeClass;
46 import org.testng.annotations.Test;
49 * All methods in this class are set to the Network group because setUpBeforeClass will fail
50 * if there is no network.
52 @Test(singleThreaded = true)
53 public class DisorderAnnotExportImport
56 @BeforeClass(alwaysRun = true)
57 public void setUpJvOptionPane()
59 JvOptionPane.setInteractiveMode(false);
60 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
63 public static String testseqs = "examples/uniref50.fa";
65 public static Jws2Discoverer disc;
67 public static List<ServiceWithParameters> aacon;
69 jalview.ws.jws2.SeqAnnotationServiceCalcWorker aaconClient;
71 public static jalview.gui.AlignFrame af = null;
73 @BeforeClass(alwaysRun = true)
74 public static void setUpBeforeClass() throws Exception
76 Cache.loadProperties("test/jalview/io/testProps.jvprops");
78 disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
80 while (disc.isRunning())
82 // don't get services until discoverer has finished
86 aacon = new ArrayList<>();
87 for (ServiceWithParameters svc : disc.getServices())
89 if (svc.getNameURI().toLowerCase().contains("aacon"))
94 assertTrue("Couldn't discover any AACon services to use to test.",
96 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
97 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
98 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
101 @AfterClass(alwaysRun = true)
102 public static void tearDownAfterClass() throws Exception
106 af.setVisible(false);
113 * Run AACon on an alignment with defaults and verify Just Shenkin annotation
116 @Test(groups = { "External", "Network" })
117 public void testAAConAnnotAndRecovery()
119 testAAConClient(af, aacon.get(0));
122 static void testAAConClient(AlignFrame af, ServiceWithParameters aacon)
124 SeqAnnotationServiceCalcWorker aaconClient = new SeqAnnotationServiceCalcWorker(
127 af.getViewport().getCalcManager().startWorker(aaconClient);
133 } catch (InterruptedException x)
137 } while (af.getViewport().getCalcManager().isWorking());
138 AlignmentI orig_alig = af.getViewport().getAlignment();
139 boolean foundShenkin = false;
140 for (AlignmentAnnotation aa : orig_alig
141 .findAnnotation(aacon.getAlignAnalysisUI().getCalcId()))
143 assertTrue("AACon annotation not marked as autocalculated!",
145 if ("shenkin".equals(aa.label.toLowerCase()))
151 assertTrue("Failed to locate 'SHENKIN' annotation row.", foundShenkin);
154 static void checkAnnotationFileIO(String testname, AlignmentI al)
158 String aligfileout = FileFormat.Pfam.getWriter(al).print(
159 al.getSequencesArray(), true);
160 String anfileout = new AnnotationFile()
161 .printAnnotationsForAlignment(al);
165 + "\nAlignment annotation file was not regenerated. Null string",
170 + "\nAlignment annotation file was not regenerated. Empty string",
171 anfileout.length() > "JALVIEW_ANNOTATION".length());
173 System.out.println("Output annotation file:\n" + anfileout
176 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
177 DataSourceType.PASTE, FileFormat.Pfam);
181 + "\nregenerated annotation file did not annotate alignment.",
182 new AnnotationFile().readAnnotationFile(al_new, anfileout,
183 DataSourceType.PASTE));
185 // test for consistency in io
186 StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
189 } catch (Exception e)
195 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");