1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.io

File JalviewExportPropertiesTests.java

 

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Classes

Class
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Actions
JalviewExportPropertiesTests 41 18 5
0.958333395.8%
 

Contributing tests

This file is covered by 1 test. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.io;
22   
23    import static org.testng.AssertJUnit.assertTrue;
24   
25    import org.testng.annotations.AfterClass;
26    import org.testng.annotations.BeforeClass;
27    import org.testng.annotations.Test;
28   
29    import jalview.datamodel.SequenceGroup;
30    import jalview.gui.AlignFrame;
31    import jalview.gui.Desktop;
32    import jalview.gui.JvOptionPane;
33   
34    /**
35    * tests which verify that properties and preferences are correctly interpreted
36    * when exporting/importing data
37    *
38    * @author jprocter
39    *
40    */
 
41    public class JalviewExportPropertiesTests
42    {
43   
 
44  1 toggle @BeforeClass(alwaysRun = true)
45    public void setUpJvOptionPane()
46    {
47  1 JvOptionPane.setInteractiveMode(false);
48  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49    }
50   
51    /**
52    * @throws java.lang.Exception
53    */
 
54  1 toggle @BeforeClass(alwaysRun = true)
55    public static void setUpBeforeClass() throws Exception
56    {
57  1 jalview.bin.Jalview
58    .main(new String[]
59    { "--props", "test/jalview/io/testProps.jvprops" });
60    }
61   
62    /**
63    * @throws java.lang.Exception
64    */
 
65  1 toggle @AfterClass(alwaysRun = true)
66    public static void tearDownAfterClass() throws Exception
67    {
68  1 if (Desktop.instance != null)
69  1 Desktop.instance.closeAll_actionPerformed(null);
70   
71    }
72   
 
73  1 toggle @Test(groups = { "Functional" })
74    public void testImportExportPeriodGaps() throws Exception
75    {
76  1 jalview.bin.Cache.setProperty("GAP_SYMBOL", ".");
77  1 assertTrue("Couldn't set gap character to '.'",
78    ".".equals("" + jalview.bin.Cache.getProperty("GAP_SYMBOL")));
79  1 AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
80    "examples/uniref50.fa", DataSourceType.FILE);
81  1 assertTrue("Didn't read in the example file correctly.", af != null);
82  1 assertTrue("Didn't set the gap character correctly", af.getViewport()
83    .getAlignment().getSequenceAt(0).getCharAt(5) == '.');
84   
85  1 SequenceGroup sg = new SequenceGroup();
86  1 sg.addSequence(af.getViewport().getAlignment().getSequenceAt(0), false);
87  1 sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
88  1 sg.setStartRes(1);
89  1 sg.setEndRes(7);
90  1 af.getViewport().setSelectionGroup(sg);
91  1 String fseqs = new FormatAdapter(af.alignPanel)
92    .formatSequences(FileFormat.Fasta, af.alignPanel, true);
93  1 assertTrue("Couldn't find '.' in the exported region\n" + fseqs,
94    fseqs.indexOf(".") > -1);
95    }
96    }