+/*
+ * 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.ext.so;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
import jalview.io.gff.SequenceOntologyI;
import org.testng.annotations.BeforeClass;
public class SequenceOntologyTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private SequenceOntologyI so;
@BeforeClass(alwaysRun = true)
assertFalse(so.isA("CDS_region", "CDS"));// part_of
assertFalse(so.isA("polypeptide", "CDS")); // derives_from
}
+
+ @Test(groups = "Functional")
+ public void testIsSequenceVariant()
+ {
+ assertFalse(so.isA("CDS", "sequence_variant"));
+ assertTrue(so.isA("sequence_variant", "sequence_variant"));
+
+ /*
+ * these should all be sub-types of sequence_variant
+ */
+ assertTrue(so.isA("structural_variant", "sequence_variant"));
+ assertTrue(so.isA("feature_variant", "sequence_variant"));
+ assertTrue(so.isA("gene_variant", "sequence_variant"));
+ assertTrue(so.isA("transcript_variant", "sequence_variant"));
+ assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
+ assertTrue(so.isA("missense_variant", "sequence_variant"));
+ assertTrue(so.isA("synonymous_variant", "sequence_variant"));
+ assertTrue(so.isA("frameshift_variant", "sequence_variant"));
+ assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
+ assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
+ assertTrue(so.isA("stop_gained", "sequence_variant"));
+ assertTrue(so.isA("stop_lost", "sequence_variant"));
+ assertTrue(so.isA("inframe_deletion", "sequence_variant"));
+ assertTrue(so.isA("inframe_insertion", "sequence_variant"));
+ }
}