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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.symbol;
import java.util.Iterator;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
/**
* Tests for SimpleSymbolList
*
* @author Thomas Down
* @since 1.2
*/
public class SimpleSymbolListTest extends TestCase {
protected SymbolList sl1;
protected SymbolList sl2;
public SimpleSymbolListTest(String name) {
super(name);
}
protected void setUp()
throws Exception
{
sl1 = DNATools.createDNA("gataca");
sl2 = DNATools.createDNA("atgga");
}
public void testCopyConstructor()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
assertTrue(compareSymbolList(tsl, sl1));
}
public void testEquals() throws Exception{
SymbolList sl = DNATools.createDNA("gataca");
assertTrue(sl.equals(sl1));
assertTrue(sl1.equals(sl));
assertTrue(! sl.equals(sl2));
}
public void testAddSymbol()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
tsl.addSymbol(DNATools.a());
assertTrue(compareSymbolList(tsl, DNATools.createDNA("gatacaa")));
}
public void testInsertAtStart()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
tsl.edit(new Edit(1, 0, sl2));
assertTrue(compareSymbolList(tsl, DNATools.createDNA("atggagataca")));
}
public void testInsertInMiddle()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
tsl.edit(new Edit(4, 0, sl2));
assertTrue(compareSymbolList(tsl, DNATools.createDNA("gatatggaaca")));
}
public void testInsertAtEnd() throws Exception {
SimpleSymbolList ts1 = new SimpleSymbolList(sl1);
ts1.edit(new Edit(7,0,sl2));
assertTrue(compareSymbolList(ts1, DNATools.createDNA("gatacaatgga")));
ts1.edit(new Edit(ts1.length()+1, 0, sl2));
assertTrue(compareSymbolList(ts1, DNATools.createDNA("gatacaatggaatgga")));
}
public void testDeletion()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
tsl.edit(new Edit(4, 2, SymbolList.EMPTY_LIST));
assertTrue(compareSymbolList(tsl, DNATools.createDNA("gata")));
}
public void testReplacement()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
tsl.edit(new Edit(4, 2, sl2));
assertTrue(compareSymbolList(tsl, DNATools.createDNA("gatatggaa")));
}
public void testEditSuperlist()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
SymbolList sub_tsl = tsl.subList(2, 6);
tsl.edit(new Edit(4, 2, sl2));
assertTrue(compareSymbolList(tsl, DNATools.createDNA("gatatggaa")));
assertTrue(compareSymbolList(sub_tsl, DNATools.createDNA("ataca")));
}
public void testEditSublist()
throws Exception
{
SimpleSymbolList tsl = new SimpleSymbolList(sl1);
SymbolList sub_tsl = tsl.subList(2, 6);
sub_tsl.edit(new Edit(3, 2, sl2));
assertTrue(compareSymbolList(sub_tsl, DNATools.createDNA("atatggaa")));
assertTrue(compareSymbolList(tsl, DNATools.createDNA("gataca")));
}
private boolean compareSymbolList(SymbolList sl1, SymbolList sl2) {
if (sl1.length() != sl2.length()) {
return false;
}
Iterator si1 = sl1.iterator();
Iterator si2 = sl2.iterator();
while (si1.hasNext()) {
if (! (si1.next() == si2.next())) {
return false;
}
}
return true;
}
}
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