/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.io;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import java.util.HashMap;
import java.util.Map;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class StockholmFileTest
{
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
- @Test
+ @Test(groups = { "Functional" })
public void pfamFileIO() throws Exception
{
testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
}
- @Test
+ @Test(groups = { "Functional" })
public void pfamFileDataExtraction() throws Exception
{
AppletFormatAdapter af = new AppletFormatAdapter();
int numpdb = 0;
for (SequenceI sq : al.getSequences())
{
- if (sq.getPDBId() != null)
+ if (sq.getAllPDBEntries() != null)
{
- numpdb += sq.getPDBId().size();
+ numpdb += sq.getAllPDBEntries().size();
}
}
assertTrue(
numpdb > 0);
}
- @Test
+ @Test(groups = { "Functional" })
public void rfamFileIO() throws Exception
{
testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
* - label for IO class used to write and read back in the data from
* f
*/
+
public static void testFileIOwithFormat(File f, String ioformat,
int naliannot, int nminseqann)
{
if (naliannot > -1)
{
assertEquals("Number of alignment annotations", naliannot,
- numaliannot);
+ numaliannot);
}
assertTrue(
+ (ignoreFeatures ? " ignoring." : ""),
ignoreFeatures
|| (seq_original[i].getSequenceFeatures() == null && seq_new[in]
- .getSequenceFeatures() == null)
+ .getSequenceFeatures() == null)
|| (seq_original[i].getSequenceFeatures() != null && seq_new[in]
.getSequenceFeatures() != null));
// compare sequence features