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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.alignment;
import java.util.ArrayList;
import java.util.List;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.GappedSequence;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.symbol.BasisSymbol;
import org.biojava.bio.symbol.LocationTools;
/* @author Lachlan Coin */
public class FlexibleAlignmentTest extends TestCase {
public FlexibleAlignmentTest(String name){
super(name);
}
//public static void main(String[] args) throws Exception{
// FlexibleAlignmentTest aat = new FlexibleAlignmentTest();
// aat.setUp();
// aat.testDNA();
// aat.testProtein();
//}
final static String[] alignment = new String[] {"A-C",
"AGC",
"A-A"};
final static String[] names = new String[] {"MOUSE", "HUMAN","SCHPO"};
final static FlexibleAlignment alignDNA = parse(names, alignment, true);
final static FlexibleAlignment alignProt = parse(names, alignment, false);
protected void setUp() throws Exception{
}
public void testDNA()
throws Exception
{
List syms = ((BasisSymbol) alignDNA.symbolAt(2)).getSymbols();
assertEquals(syms.get(0), DNATools.getDNA().getGapSymbol());
assertEquals(syms.get(1), DNATools.g());
}
public void testProtein()
throws Exception
{
List syms = ((BasisSymbol) alignProt.symbolAt(2)).getSymbols();
assertEquals(syms.get(0), ProteinTools.getAlphabet().getGapSymbol());
}
private static FlexibleAlignment parse(String[] names, String[] alignment, boolean dna)
{
try
{
List sequences = new ArrayList();
for(int i=0; i<alignment.length; i++)
{
GappedSequence seq;
if(dna)
seq = DNATools.createGappedDNASequence(alignment[i],names[i]);
else
seq = ProteinTools.createGappedProteinSequence(alignment[i],names[i]);
AlignmentElement ae = new SimpleAlignmentElement(names[i], seq, LocationTools.makeLocation(1, alignment[i].length()));
// System.out.println(seq.seqString());
sequences.add(ae);
}
FlexibleAlignment al = new FlexibleAlignment(sequences);
return al;
}
catch (Throwable t)
{
t.printStackTrace();
//System.exit(0);
return null;
}
}
}
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