/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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
- 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(ResidueProperties.ambiguityCodes.size() > 0);
}
- @Test
- public void regenerateCodonTable() {
- for (Map.Entry<String, String> codon:ResidueProperties.codonHash2.entrySet())
+
+ @Test(groups = { "Functional" })
+ public void testAmbiguityCodon()
+ {
+ for (String ac : ResidueProperties.ambiguityCodes.keySet())
{
- System.out.println("ResidueProperties.codonHash2.set(\""+codon.getKey()+"\", \""+codon.getValue()+"\");");
+ assertTrue("Couldn't resolve GGN as glycine codon",
+ ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
}
}
- @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 regenerateCodonTable()
+ {
+ for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
+ .entrySet())
{
- String amacid=(String) aa;
- for (Object codons:((Vector)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 (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);
- }
- }
+ System.out.println("ResidueProperties.codonHash2.set(\""
+ + codon.getKey() + "\", \"" + codon.getValue() + "\");");
}
- assertTrue(""+additional+"\n"+failtrans+"\n"+differentTr,additional.length()==0 && failtrans.length()==0 && differentTr.length()==0);
}
}