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.DataSourceType;
31 import jalview.io.FileFormat;
32 import jalview.io.FormatAdapter;
33 import jalview.io.StockholmFileTest;
34 import jalview.ws.jws2.AADisorderClient;
35 import jalview.ws.jws2.Jws2Discoverer;
36 import jalview.ws.jws2.jabaws2.Jws2Instance;
38 import java.util.ArrayList;
39 import java.util.List;
41 import org.testng.Assert;
42 import org.testng.annotations.AfterClass;
43 import org.testng.annotations.BeforeClass;
44 import org.testng.annotations.Test;
46 @Test(groups = { "External" })
47 public class DisorderAnnotExportImport
49 public static String testseqs = "examples/uniref50.fa";
51 public static Jws2Discoverer disc;
53 public static List<Jws2Instance> iupreds;
55 jalview.ws.jws2.AADisorderClient disorderClient;
57 public static jalview.gui.AlignFrame af = null;
59 @BeforeClass(inheritGroups = true)
60 public static void setUpBeforeClass() throws Exception
62 Cache.loadProperties("test/jalview/io/testProps.jvprops");
64 disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
65 iupreds = new ArrayList<Jws2Instance>();
66 for (Jws2Instance svc : disc.getServices())
68 if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
73 assertTrue("Couldn't discover any IUPred services to use to test.",
75 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
76 af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
77 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
80 @AfterClass(alwaysRun = true)
81 public static void tearDownAfterClass() throws Exception
92 * test for patches to JAL-1294
95 public void testDisorderAnnotExport()
97 disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
98 af.getViewport().getCalcManager().startWorker(disorderClient);
104 } catch (InterruptedException x)
108 } while (af.getViewport().getCalcManager().isWorking());
109 AlignmentI orig_alig = af.getViewport().getAlignment();
110 // NOTE: Consensus annotation row cannot be exported and reimported
111 // faithfully - so we remove them
112 List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
113 for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
115 if (aa.autoCalculated)
120 for (AlignmentAnnotation aa : toremove)
122 orig_alig.deleteAnnotation(aa);
124 testAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
128 public static void testAnnotationFileIO(String testname, AlignmentI al)
132 String aligfileout = new FormatAdapter().formatSequences("PFAM",
133 al.getSequencesArray());
134 String anfileout = new AnnotationFile()
135 .printAnnotationsForAlignment(al);
139 + "\nAlignment annotation file was not regenerated. Null string",
144 + "\nAlignment annotation file was not regenerated. Empty string",
145 anfileout.length() > "JALVIEW_ANNOTATION".length());
147 System.out.println("Output annotation file:\n" + anfileout
150 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
151 DataSourceType.PASTE, FileFormat.Pfam);
155 + "\nregenerated annotation file did not annotate alignment.",
156 new AnnotationFile().readAnnotationFile(al_new, anfileout,
157 DataSourceType.PASTE));
159 // test for consistency in io
160 StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
162 } catch (Exception e)
168 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");