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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/
*
*/
/*
* AAindexTest.java
*/
package org.biojava.bio.proteomics.aaindex;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.symbol.IllegalSymbolException;
/**
* Test class for {@link org.biojava.bio.proteomics.aaindex.AAindex}.
* @author <a href="mailto:Martin.Szugat@GMX.net">Martin Szugat</a>
* @version $Revision: 4023 $
*/
public class AAindexTest extends TestCase {
/**
* Main entry point.
* @param args command line arguments
*/
public static void main(String[] args) {
junit.textui.TestRunner.run(AAindexTest.class);
}
/**
* AAindex object.
*/
private AAindex aaindex = null;
/**
* {@inheritDoc}
*/
protected void setUp() throws Exception {
super.setUp();
aaindex = new AAindex("test");
}
/**
* Test for {@link AAindex#accessionNumber()}.
*/
public void testAccessionNumber() {
assertEquals("test", aaindex.accessionNumber());
}
/**
* Test for {@link AAindex#getArticleAuthors()}.
*/
public void testGetArticleAuthors() {
assertNull(aaindex.getArticleAuthors());
}
/**
* Test for {@link AAindex#setArticleAuthors(String)}.
*/
public void testSetArticleAuthors() {
aaindex.setArticleAuthors("authors");
assertEquals("authors", aaindex.getArticleAuthors());
}
/**
* Test for {@link AAindex#getComment()}.
*/
public void testGetComment() {
assertNull(aaindex.getComment());
}
/**
* Test for {@link AAindex#setComment(String)}.
*/
public void testSetComment() {
aaindex.setComment("comment");
assertEquals("comment", aaindex.getComment());
}
/**
* Test for {@link AAindex#getArticleTitle()}.
*/
public void testGetArticleTitle() {
assertNull(aaindex.getArticleTitle());
}
/**
* Test for {@link AAindex#setArticleTitle(String)}.
*/
public void testSetArticleTitle() {
aaindex.setArticleTitle("title");
assertEquals("title", aaindex.getArticleTitle());
}
/**
* Test for {@link AAindex#getDescription()}.
*/
public void testGetDescription() {
assertNull(aaindex.getDescription());
}
/**
* Test for {@link AAindex#setDescription(String)}.
*/
public void testSetDescription() {
aaindex.setDescription("description");
assertEquals("description", aaindex.getDescription());
}
/**
* Test for {@link AAindex#getJournalReference()}
*/
public void testGetJournalReference() {
assertNull(aaindex.getJournalReference());
}
/**
* Test for {@link AAindex#setJournalReference(String)}.
*/
public void testSetJournalReference() {
aaindex.setJournalReference("journal");
assertEquals("journal", aaindex.getJournalReference());
}
/**
* Test for {@link AAindex#getLITDBEntryNumbers()}.
*/
public void testGetLITDBEntryNumbers() {
assertNull(aaindex.getLITDBEntryNumbers());
}
/**
* Test for {@link AAindex#setLITDBEntryNumbers(String[])}.
*/
public void testSetLITDBEntryNumbers() {
aaindex.setLITDBEntryNumbers(new String[] {"lit"});
assertEquals("lit", aaindex.getLITDBEntryNumbers()[0]);
}
/**
* Test for {@link AAindex#similarEntries()}.
*/
public void testSimilarEntries() {
assertEquals(0, aaindex.similarEntries().size());
aaindex.similarEntries().put("test", new Double(0.0));
assertEquals(new Double(0.0), aaindex.similarEntries().get("test"));
}
/**
* Test for {@link org.biojava.bio.symbol.SymbolPropertyTable#getName()}.
*/
public void testGetName() {
assertEquals("test", aaindex.getName());
}
/**
* Test for {@link org.biojava.bio.symbol.SymbolPropertyTable#getAlphabet()}.
*/
public void testGetAlphabet() {
assertEquals(ProteinTools.getAlphabet(), aaindex.getAlphabet());
}
/**
* Test for {@link org.biojava.bio.symbol.SymbolPropertyTable#getDoubleValue(org.biojava.bio.symbol.Symbol)}.
* @throws IllegalSymbolException if a symbol is illegal.
*/
public void testDoubleValue() throws IllegalSymbolException {
aaindex.setDoubleProperty(ProteinTools.gln(), "1.0");
assertEquals(1.0, aaindex.getDoubleValue(ProteinTools.gln()), 0.0);
try {
aaindex.getDoubleValue(DNATools.a());
fail("IllegalSymbolException not thrown.");
} catch (IllegalSymbolException e) {
e.printStackTrace();
}
}
}
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