/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.io;
-import static org.junit.Assert.*;
+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 org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import fr.orsay.lri.varna.utils.RNAMLParser;
+import groovy.lang.Sequence;
public class RNAMLfileTest
{
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
- @Test
+ @Test(groups = { "Functional" })
public void testRnamlToStockholmIO()
{
- StockholmFileTest.testFileIOwithFormat(new File("examples/rna-alignment.xml"),"STH");
-
+ 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);
}
}