/*
- * 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 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);
+ assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
}
- @Test
- public void testAmbiguityCodon() {
- for (String ac:ResidueProperties.ambiguityCodes.keySet())
+
+ @Test(groups = { "Functional" })
+ public void testAmbiguityCodon()
+ {
+ for (String ac : ResidueProperties.ambiguityCodes.keySet())
{
- assertTrue("Couldn't resolve GGN as glycine codon",ResidueProperties.codonHash2.get("GG"+ac).equals("G"));
+ assertTrue("Couldn't resolve GGN as glycine codon",
+ ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
}
}
- @Test
- public void regenerateCodonTable() {
- for (Map.Entry<String, String> codon:ResidueProperties.codonHash2.entrySet())
+
+ @Test(groups = { "Functional" })
+ public void regenerateCodonTable()
+ {
+ for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
+ .entrySet())
{
- System.out.println("ResidueProperties.codonHash2.set(\""+codon.getKey()+"\", \""+codon.getValue()+"\");");
+ System.out.println("ResidueProperties.codonHash2.set(\""
+ + codon.getKey() + "\", \"" + codon.getValue() + "\");");
}
}
- @Test
- 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())
+
+ @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())
{
- 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) {
- additional+="\nOld translation table includes additional codons for "+amacid+" : "+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 == 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);
+ 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);
+ assertTrue("" + additional + "\n" + failtrans + "\n" + differentTr,
+ additional.length() == 0 && failtrans.length() == 0
+ && differentTr.length() == 0);
}
}