+/*
+ * 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.gff;
import static org.testng.AssertJUnit.assertEquals;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ExonerateHelperTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetMappingType()
{
// protein-to-dna:
- assertSame(MappingType.PeptideToNucleotide,
+ assertSame(MappingType.PeptideToGenome,
ExonerateHelper
.getMappingType("exonerate:protein2genome:local"));
- assertSame(MappingType.PeptideToNucleotide,
+ assertSame(MappingType.PeptideToGenome,
ExonerateHelper.getMappingType("exonerate:protein2dna:local"));
// dna-to-dna:
- assertSame(MappingType.NucleotideToNucleotide,
+ assertSame(MappingType.GenomeToCdna,
ExonerateHelper.getMappingType("coding2coding"));
- assertSame(MappingType.NucleotideToNucleotide,
+ assertSame(MappingType.GenomeToCdna,
ExonerateHelper.getMappingType("coding2genome"));
- assertSame(MappingType.NucleotideToNucleotide,
+ assertSame(MappingType.GenomeToCdna,
ExonerateHelper.getMappingType("cdna2genome"));
- assertSame(MappingType.NucleotideToNucleotide,
+ assertSame(MappingType.GenomeToCdna,
ExonerateHelper.getMappingType("genome2genome"));
assertNull(ExonerateHelper.getMappingType("affine:local"));
}
FileLoader loader = new FileLoader(false);
AlignFrame af = loader.LoadFileWaitTillLoaded(
"examples/testdata/exonerateseqs.fa",
- FormatAdapter.FILE);
+ DataSourceType.FILE);
af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
- FormatAdapter.FILE, null, null);
+ DataSourceType.FILE, null, null);
/*
* verify one mapping to a dummy sequence, one to a real one