<classpathentry kind="lib" path="lib/jsoup-1.8.1.jar"/>
<classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
<classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
- <classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
+ <classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
+ <classpathentry kind="lib" path="lib/htsjdk-1.133.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
- import org.testng.Assert;
- import org.testng.annotations.Test;
+ import static org.testng.AssertJUnit.assertFalse;
+ import static org.testng.AssertJUnit.assertTrue;
+ import org.testng.annotations.Test;
+@Test
public class SequenceDummyTest
{
/**
af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
- Assert.assertNotEquals(
- assertTrue("Expected at least one DNA protein association", af
- .getViewport().getAlignment().getDataset().getCodonFrames()
- .size() > 0);
++ assertNotEquals("Expected at least one DNA protein association",
+ 0, af.getViewport().getAlignment().getDataset()
+ .getCodonFrames().size(),
- "Expected at least one DNA protein association");
++ );
}
SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
.findName("seq2");
- Assert.assertNotNull(seq1);
- Assert.assertNotNull(seq2);
- Assert.assertFalse(
+ assertNotNull(seq1);
+ assertNotNull(seq2);
+ assertFalse(
+ "Failed to replace dummy seq1 with real sequence",
seq1 instanceof SequenceDummy
- && ((SequenceDummy) seq1).isDummy(),
- "Failed to replace dummy seq1 with real sequence");
- Assert.assertFalse(
+ && ((SequenceDummy) seq1).isDummy());
+ assertFalse(
+ "Failed to replace dummy seq2 with real sequence",
seq2 instanceof SequenceDummy
- && ((SequenceDummy) seq2).isDummy());
+ && ((SequenceDummy) seq2).isDummy(),
+ "Failed to replace dummy seq2 with real sequence");
String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
- Assert.assertFalse(placeholderseq.equals(seq1.getSequenceAsString()),
- "dummy replacement buggy for seq1");
- Assert.assertNotEquals("dummy replacement buggy for seq2",
+ assertFalse("dummy replacement buggy for seq1",
+ placeholderseq.equals(seq1.getSequenceAsString()));
+ assertFalse("dummy replacement buggy for seq2",
placeholderseq.equals(seq2.getSequenceAsString()));
- Assert.assertNotNull(seq1.getSequenceFeatures(),
- "No features added to seq1");
- Assert.assertEquals(seq1.getSequenceFeatures().length, 3,
- "Wrong number of features");
- Assert.assertNull(seq2.getSequenceFeatures());
- Assert.assertEquals(
- seq2
- .getSequenceFeatures() == null ? 0
- : seq2
- .getSequenceFeatures().length, 0,
- "Wrong number of features");
- Assert.assertTrue(
- assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
- // null);
++ assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
+ assertEquals("Wrong number of features", 3,
+ seq1.getSequenceFeatures().length);
+ assertNull(seq2.getSequenceFeatures());
+ assertEquals(
+ "Wrong number of features",
+ 0,
+ seq2.getSequenceFeatures() == null ? 0 : seq2
+ .getSequenceFeatures().length);
+ assertTrue(
+ "Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
- && dataset.getCodonFrame(seq1).size() > 0);
+ && dataset.getCodonFrame(seq1).size() > 0,
+ "Expected at least one CDNA/Protein mapping for seq1");
}
- // @Test
+ // @Test(groups ={ "Functional" })
// public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
// {
// fail("Not yet implemented");
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
-import static org.junit.Assert.fail;
-
import org.testng.annotations.Test;
public class HtmlFileTest
{
- @Test(enabled = false)
+ @Test(groups = { "Functional" }, enabled = false)
public void test()
{
- fail("Not yet implemented");
+ org.testng.AssertJUnit.fail("Not yet implemented");
}
}
/**
* test servers
*/
- private static String[] serviceUrls = new String[]
- { "http://localhost:8080/jabaws",
+ private static String[] serviceUrls = new String[] {
+ "http://localhost:8080/jabaws",
"http://www.compbio.dundee.ac.uk/jabaws" };
- @Test(enabled = false)
+ @Test(groups = { "Functional" }, enabled = false)
public void testAnnotExport()
{
- fail("Not yet implemented");
+ Assert.fail("Not yet implemented");
}
public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer()
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- <object refID="9a1f46efeefab93"/>
<object refID="1936efeefab93"/>
+ <object refID="1000ddddfab93"/>
-
+ <object refID="10936efeefab93"/>
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<property name="belongsToUninstallPhase">
<boolean>false</boolean>
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<object refID="1f46efeefab93"/>
<object refID="1936efeefab93"/>
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</visualChildren>
</object>
<object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="f44fc5d5aba1">
git://source.jalview.org / jalview.git / commitdiff