*/
package jalview.io;
+import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+
import java.io.File;
+import java.io.IOException;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import fr.orsay.lri.varna.utils.RNAMLParser;
+import groovy.lang.Sequence;
+
public class RNAMLfileTest
{
@Test(groups = { "Functional" })
public void testRnamlToStockholmIO()
{
- StockholmFileTest.testFileIOwithFormat(new File(
- "examples/testdata/rna-alignment.xml"), FileFormat.Stockholm,
- -1, -1, true);
+ StockholmFileTest.testFileIOwithFormat(
+ new File("examples/testdata/rna-alignment.xml"),
+ FileFormat.Stockholm, -1, -1, true, true, true);
+
+ }
+ @Test(groups = { "Functional" })
+ public void testRnamlSeqImport() throws IOException
+ {
+ RnamlFile parser = new RnamlFile("examples/testdata/7WKP-rna1.xml",
+ DataSourceType.FILE);
+ SequenceI[] seqs = parser.getSeqsAsArray();
+ assertNotNull(seqs);
+ assertEquals(seqs.length, 1);
+ assertEquals(seqs[0].getEnd() - seqs[0].getStart() + 1,
+ seqs[0].getSequence().length);
}
}