+/*
+ * 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.ensembl;
import static org.testng.AssertJUnit.assertEquals;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
public class EnsemblCdsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeClass(alwaysRun = true)
public void setUp()
{
null);
assertFalse(testee.retainFeature(sf, accId));
- sf.setType("CDS_predicted");
+ sf = new SequenceFeature("CDS_predicted", "", 20000, 20500, 0f, null);
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf.setType("sequence_variant");
+ sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
+ 20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
assertTrue(testee.identifiesSequence(sf, accId));
// cds sub-type with right parent is valid
- sf.setType("CDS_predicted");
+ sf = new SequenceFeature("CDS_predicted", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertTrue(testee.identifiesSequence(sf, accId));
// transcript not valid:
- sf.setType("transcript");
+ sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertFalse(testee.identifiesSequence(sf, accId));
// exon not valid:
- sf.setType("exon");
+ sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertFalse(testee.identifiesSequence(sf, accId));
}