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.io.AnnotationFile;
30 import jalview.io.FormatAdapter;
31 import jalview.io.StockholmFileTest;
32 import jalview.ws.jws2.AADisorderClient;
33 import jalview.ws.jws2.Jws2Discoverer;
34 import jalview.ws.jws2.jabaws2.Jws2Instance;
36 import java.util.ArrayList;
37 import java.util.List;
39 import org.testng.Assert;
40 import org.testng.annotations.AfterClass;
41 import org.testng.annotations.BeforeClass;
42 import org.testng.annotations.Test;
44 @Test(groups = { "External" })
45 public class DisorderAnnotExportImport
47 public static String testseqs = "examples/uniref50.fa";
49 public static Jws2Discoverer disc;
51 public static List<Jws2Instance> iupreds;
53 jalview.ws.jws2.AADisorderClient disorderClient;
55 public static jalview.gui.AlignFrame af = null;
57 @BeforeClass(inheritGroups = true)
58 public static void setUpBeforeClass() throws Exception
60 Cache.loadProperties("test/jalview/io/testProps.jvprops");
62 disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
63 iupreds = new ArrayList<Jws2Instance>();
64 for (Jws2Instance svc : disc.getServices())
66 if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
71 assertTrue("Couldn't discover any IUPred services to use to test.",
73 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
74 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
75 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
78 @AfterClass(alwaysRun = true)
79 public static void tearDownAfterClass() throws Exception
90 * test for patches to JAL-1294
93 public void testDisorderAnnotExport()
95 disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
96 af.getViewport().getCalcManager().startWorker(disorderClient);
102 } catch (InterruptedException x)
106 } while (af.getViewport().getCalcManager().isWorking());
107 AlignmentI orig_alig = af.getViewport().getAlignment();
108 // NOTE: Consensus annotation row cannot be exported and reimported
109 // faithfully - so we remove them
110 List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
111 for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
113 if (aa.autoCalculated)
118 for (AlignmentAnnotation aa : toremove)
120 orig_alig.deleteAnnotation(aa);
122 testAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
126 public static void testAnnotationFileIO(String testname, AlignmentI al)
130 String aligfileout = new FormatAdapter().formatSequences("PFAM",
131 al.getSequencesArray());
132 String anfileout = new AnnotationFile()
133 .printAnnotationsForAlignment(al);
137 + "\nAlignment annotation file was not regenerated. Null string",
142 + "\nAlignment annotation file was not regenerated. Empty string",
143 anfileout.length() > "JALVIEW_ANNOTATION".length());
145 System.out.println("Output annotation file:\n" + anfileout
148 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
149 FormatAdapter.PASTE, "PFAM");
153 + "\nregenerated annotation file did not annotate alignment.",
154 new AnnotationFile().readAnnotationFile(al_new, anfileout,
155 FormatAdapter.PASTE));
157 // test for consistency in io
158 StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
160 } catch (Exception e)
166 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");