/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
* Copyright (C) 2014 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import static org.junit.Assert.*;
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;
public class DnaCodonTests
{
@Test
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"));
}
}
@Test
public void regenerateCodonTable() {
for (Map.Entry codon:ResidueProperties.codonHash2.entrySet())
{
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())
{
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);
}
}
}
assertTrue(""+additional+"\n"+failtrans+"\n"+differentTr,additional.length()==0 && failtrans.length()==0 && differentTr.length()==0);
}
}