X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FRNAMLfileTest.java;h=d2b6f657224759ef1f8f8b314767be9ee49cd336;hb=320583fd2ac3ea714e6afdac050961978bd34c81;hp=c084792051dfce7a8b9c911a0e0e4ded2ecdbdd2;hpb=cbc07eab0291f023f89b2554c488ae9e4587ae2a;p=jalview.git

diff --git a/test/jalview/io/RNAMLfileTest.java b/test/jalview/io/RNAMLfileTest.java
index c084792..d2b6f65 100644
--- a/test/jalview/io/RNAMLfileTest.java
+++ b/test/jalview/io/RNAMLfileTest.java
@@ -20,16 +20,33 @@
  */
 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
 {
 
   @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
   }
@@ -42,9 +59,20 @@ public class RNAMLfileTest
   @Test(groups = { "Functional" })
   public void testRnamlToStockholmIO()
   {
-    StockholmFileTest.testFileIOwithFormat(new File(
-            "examples/testdata/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);
+  }
+
 }