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JAL-1926 JAL-2106 fix name for flag controlling addition of secondary structure annot...
[jalview.git]
/
test
/
jalview
/
schemes
/
DnaCodonTests.java
diff --git
a/test/jalview/schemes/DnaCodonTests.java
b/test/jalview/schemes/DnaCodonTests.java
index
d8529f8
..
ff2f2aa
100644
(file)
--- a/
test/jalview/schemes/DnaCodonTests.java
+++ b/
test/jalview/schemes/DnaCodonTests.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,31
+20,22
@@
*/
package jalview.schemes;
*/
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.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
{
public class DnaCodonTests
{
- @Test
+ @Test(groups = { "Functional" })
public void testAmbiguityCodeGeneration()
{
assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
}
public void testAmbiguityCodeGeneration()
{
assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
}
- @Test
+ @Test(groups = { "Functional" })
public void testAmbiguityCodon()
{
for (String ac : ResidueProperties.ambiguityCodes.keySet())
public void testAmbiguityCodon()
{
for (String ac : ResidueProperties.ambiguityCodes.keySet())
@@
-54,7
+45,7
@@
public class DnaCodonTests
}
}
}
}
- @Test
+ @Test(groups = { "Functional" })
public void regenerateCodonTable()
{
for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
public void regenerateCodonTable()
{
for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
@@
-65,19
+56,16
@@
public class DnaCodonTests
}
}
}
}
- @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 = "";
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)
String trans = ResidueProperties.codonTranslate(codon);
String oldtrans = ResidueProperties._codonTranslate(codon);
if (trans == null)