X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FRNAMLfileTest.java;h=d2b6f657224759ef1f8f8b314767be9ee49cd336;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=a838cf73660fee42f58fc7be7d433539571881fb;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/io/RNAMLfileTest.java b/test/jalview/io/RNAMLfileTest.java
index a838cf7..d2b6f65 100644
--- a/test/jalview/io/RNAMLfileTest.java
+++ b/test/jalview/io/RNAMLfileTest.java
@@ -20,30 +20,59 @@
  */
 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.Test;
 import org.testng.annotations.BeforeClass;
-import java.io.File;
+import org.testng.annotations.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", -1, -1);
+    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);
+  }
+
 }