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.
23 import jalview.bin.Cache;
24 import jalview.bin.Jalview;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.SequenceI;
27 import jalview.gui.Desktop;
29 import java.util.Date;
31 import org.testng.annotations.AfterClass;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.BeforeTest;
35 public class Jalview2xmlBase
39 * @throws java.lang.Exception
41 @BeforeClass(alwaysRun = true)
42 public static void setUpBeforeClass() throws Exception
45 * use read-only test properties file
47 Cache.loadProperties("test/jalview/io/testProps.jvprops");
50 * set news feed last read to a future time to ensure no
51 * 'unread' news item is displayed
53 Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000);
54 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
56 Jalview.main(new String[] {});
60 * @throws java.lang.Exception
62 @AfterClass(alwaysRun = true)
63 public static void tearDownAfterClass() throws Exception
65 jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
68 @BeforeTest(alwaysRun = true)
69 public static void clearDesktop()
71 if (Desktop.instance != null && Desktop.getAlignFrames() != null)
73 Desktop.instance.closeAll_actionPerformed(null);
77 public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
80 for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
82 if (sq.getAnnotation() != null)
84 for (AlignmentAnnotation dssa : sq.getAnnotation())
86 if (dssa.isValidStruc())