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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.seq;
import junit.framework.TestCase;
import org.biojava.bio.seq.io.SymbolTokenization;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.bio.symbol.FiniteAlphabet;
import org.biojava.bio.symbol.SymbolList;
/**
* <code>ProteinToolsTest</code> tests are to ensure that the class can be
* instantiated and that the results are internally consistent. The
* functionality of the classes to which <code>ProteinTools</code>
* delegates e.g. <code>AlphabetManager</code> and
* <code>SymbolTokenization</code> should be tested in their own unit
* tests.
*
* @author Mark Schreiber
* @author gwaldon (pyrrolysine)
*/
public class ProteinToolsTest extends TestCase
{
protected SymbolTokenization tokens;
protected FiniteAlphabet proteinAlpha;
protected FiniteAlphabet proteinTAlpha;
public ProteinToolsTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
tokens =
AlphabetManager.alphabetForName("PROTEIN-TERM").getTokenization("token");
proteinAlpha = (FiniteAlphabet) AlphabetManager.alphabetForName("PROTEIN");
proteinTAlpha = (FiniteAlphabet) AlphabetManager.alphabetForName(
"PROTEIN-TERM");
}
public void testGetAlpha()
{
assertEquals(proteinAlpha,
ProteinTools.getAlphabet());
assertEquals(proteinTAlpha,
ProteinTools.getTAlphabet());
assertTrue(proteinAlpha == ProteinTools.getAlphabet());
assertTrue(proteinTAlpha == ProteinTools.getTAlphabet());
}
public void testCreateProtein() throws Exception
{
SymbolList aa = ProteinTools.createProtein(
"arndcqeghilkmfpstwyvuo*x");
assertTrue(aa.symbolAt(1) == ProteinTools.a());
assertTrue(aa.symbolAt(1) == ProteinTools.ala());
assertTrue(aa.symbolAt(2) == ProteinTools.r());
assertTrue(aa.symbolAt(2) == ProteinTools.arg());
assertTrue(aa.symbolAt(3) == ProteinTools.n());
assertTrue(aa.symbolAt(3) == ProteinTools.asn());
assertTrue(aa.symbolAt(4) == ProteinTools.d());
assertTrue(aa.symbolAt(4) == ProteinTools.asp());
assertTrue(aa.symbolAt(5) == ProteinTools.c());
assertTrue(aa.symbolAt(5) == ProteinTools.cys());
assertTrue(aa.symbolAt(6) == ProteinTools.q());
assertTrue(aa.symbolAt(6) == ProteinTools.gln());
assertTrue(aa.symbolAt(7) == ProteinTools.e());
assertTrue(aa.symbolAt(7) == ProteinTools.glu());
assertTrue(aa.symbolAt(8) == ProteinTools.g());
assertTrue(aa.symbolAt(8) == ProteinTools.gly());
assertTrue(aa.symbolAt(9) == ProteinTools.h());
assertTrue(aa.symbolAt(9) == ProteinTools.his());
assertTrue(aa.symbolAt(10) == ProteinTools.i());
assertTrue(aa.symbolAt(10) == ProteinTools.ile());
assertTrue(aa.symbolAt(11) == ProteinTools.l());
assertTrue(aa.symbolAt(11) == ProteinTools.leu());
assertTrue(aa.symbolAt(12) == ProteinTools.k());
assertTrue(aa.symbolAt(12) == ProteinTools.lys());
assertTrue(aa.symbolAt(13) == ProteinTools.m());
assertTrue(aa.symbolAt(13) == ProteinTools.met());
assertTrue(aa.symbolAt(14) == ProteinTools.f());
assertTrue(aa.symbolAt(14) == ProteinTools.phe());
assertTrue(aa.symbolAt(15) == ProteinTools.p());
assertTrue(aa.symbolAt(15) == ProteinTools.pro());
assertTrue(aa.symbolAt(16) == ProteinTools.s());
assertTrue(aa.symbolAt(16) == ProteinTools.ser());
assertTrue(aa.symbolAt(17) == ProteinTools.t());
assertTrue(aa.symbolAt(17) == ProteinTools.thr());
assertTrue(aa.symbolAt(18) == ProteinTools.w());
assertTrue(aa.symbolAt(18) == ProteinTools.trp());
assertTrue(aa.symbolAt(19) == ProteinTools.y());
assertTrue(aa.symbolAt(19) == ProteinTools.tyr());
assertTrue(aa.symbolAt(20) == ProteinTools.v());
assertTrue(aa.symbolAt(20) == ProteinTools.val());
assertTrue(aa.symbolAt(21) == ProteinTools.u());
assertTrue(aa.symbolAt(21) == ProteinTools.sec());
assertTrue(aa.symbolAt(22) == ProteinTools.o());
assertTrue(aa.symbolAt(22) == ProteinTools.pyl());
assertTrue(aa.symbolAt(23) == ProteinTools.ter());
}
}
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