/*
- * 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.schemes;
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
-import java.io.IOException;
import java.util.Map;
-import java.util.Vector;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.Test;
public class DnaCodonTests
{
- @Test
+ @Test(groups = { "Functional" })
public void testAmbiguityCodeGeneration()
{
assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
}
- @Test
+ @Test(groups = { "Functional" })
public void testAmbiguityCodon()
{
for (String ac : ResidueProperties.ambiguityCodes.keySet())
}
}
- @Test
+ @Test(groups = { "Functional" })
public void regenerateCodonTable()
{
for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
}
}
- @Test
+ @Test(groups = { "Functional" })
public void checkOldCodonagainstNewCodonTable()
{
// note - this test will be removed once the old codon table (including
// Vectors) is removed
String additional = "", failtrans = "", differentTr = "";
- for (Object aa : ResidueProperties.codonHash.keySet())
+ for (String amacid : ResidueProperties.codonHash.keySet())
{
- String amacid = (String) aa;
- for (Object codons : ((Vector) ResidueProperties.codonHash
- .get(amacid)))
+ for (String codon : ResidueProperties.codonHash.get(amacid))
{
- String codon = (String) codons;
String trans = ResidueProperties.codonTranslate(codon);
String oldtrans = ResidueProperties._codonTranslate(codon);
if (trans == null)