import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DnaCodonTests
{
- @Test(groups ={ "Functional" })
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
public void testAmbiguityCodeGeneration()
{
assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testAmbiguityCodon()
{
for (String ac : ResidueProperties.ambiguityCodes.keySet())
}
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void regenerateCodonTable()
{
for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
+ codon.getKey() + "\", \"" + codon.getValue() + "\");");
}
}
-
- @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 (String amacid : ResidueProperties.codonHash.keySet())
- {
- for (String codon : ResidueProperties.codonHash.get(amacid))
- {
- String trans = ResidueProperties.codonTranslate(codon);
- String oldtrans = ResidueProperties._codonTranslate(codon);
- if (trans == null)
- {
- additional += "\nOld translation table includes additional codons for "
- + amacid + " : " + codon;
- }
- if (oldtrans == null)
- {
- failtrans += ("\nold translation routine failed for old translation entry (aa was "
- + amacid + " codon was " + codon + ")");
- }
- if (!oldtrans.equals(trans))
- {
- differentTr += ("\nDifferent translation for old and new routines: "
- + amacid
- + " "
- + codon
- + " => expected "
- + oldtrans
- + " and got " + trans);
- }
- }
- }
- assertTrue("" + additional + "\n" + failtrans + "\n" + differentTr,
- additional.length() == 0 && failtrans.length() == 0
- && differentTr.length() == 0);
- }
}