/*
* 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.db;
import java.io.File;
import java.net.URL;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import junit.framework.TestCase;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.io.FastaDescriptionLineParser;
import org.biojava.bio.seq.io.FastaFormat;
import org.biojava.bio.seq.io.SequenceBuilderFactory;
import org.biojava.bio.seq.io.SequenceFormat;
import org.biojava.bio.seq.io.SimpleSequenceBuilder;
import org.biojava.bio.seq.io.SymbolTokenization;
import org.biojava.bio.symbol.Alphabet;
/**
* EmblCDROMIndexStoreTest
contains unit tests for EMBL
* CD-ROM format binary index IndexStore
.
*
* @author Keith James
* @since 1.2
*/
public class EmblCDROMIndexStoreTest extends TestCase
{
protected SequenceFormat format;
protected Alphabet alpha;
protected SymbolTokenization parser;
protected SequenceBuilderFactory factory;
protected SequenceDB sequenceDB;
protected IndexStore emblCDIndexStore;
public EmblCDROMIndexStoreTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
URL divURL = EmblCDROMIndexStoreTest.class.getResource("emblcd/division.lkp");
URL entURL = EmblCDROMIndexStoreTest.class.getResource("emblcd/entrynam.idx");
File divisionLkp = new File(divURL.getFile());
File entryNamIdx = new File(entURL.getFile());
format = new FastaFormat();
alpha = ProteinTools.getAlphabet();
parser = alpha.getTokenization("token");
factory =
new FastaDescriptionLineParser.Factory(SimpleSequenceBuilder.FACTORY);
emblCDIndexStore = new EmblCDROMIndexStore(divisionLkp,
entryNamIdx,
format,
factory,
parser);
((EmblCDROMIndexStore) emblCDIndexStore).setPathPrefix(entryNamIdx.getParentFile().getAbsoluteFile());
sequenceDB = new IndexedSequenceDB(emblCDIndexStore);
}
protected void tearDown() throws Exception
{
((EmblCDROMIndexStore) emblCDIndexStore).close();
}
public void testCommit()
{
try
{
emblCDIndexStore.commit();
}
catch (BioException be)
{
return;
}
fail("Expected BioException");
}
public void testFetch() throws Exception
{
// Fetch from file 1
Index i1 = emblCDIndexStore.fetch("NMA0007");
// Fetch from file 2
Index i2 = emblCDIndexStore.fetch("NMA0020");
// Fetch from file 3
Index i3 = emblCDIndexStore.fetch("NMA0030");
// Test index fetches
assertEquals(1811, i1.getStart());
assertEquals("protDB1.aa", i1.getFile().getName());
assertEquals(2379, i2.getStart());
assertEquals("protDB2.aa", i2.getFile().getName());
assertEquals(2510, i3.getStart());
assertEquals("protDB3.aa", i3.getFile().getName());
// Test actual sequence fetches
Sequence seq = sequenceDB.getSequence("NMA0007");
assertEquals("NMA0007", seq.getName());
assertEquals(235, seq.length());
seq = sequenceDB.getSequence("NMA0020");
assertEquals("NMA0020", seq.getName());
assertEquals(494, seq.length());
seq = sequenceDB.getSequence("NMA0030");
assertEquals("NMA0030", seq.getName());
assertEquals(245, seq.length());
}
public void testIllegalIDFetch() throws BioException
{
try
{
Index i = emblCDIndexStore.fetch("xxxxx");
i = i==null?null:i; //trick
}
catch (IllegalIDException iie)
{
return;
}
fail("Expected IllegalIDException");
}
public void testGetFiles()
{
Set files = emblCDIndexStore.getFiles();
Set names = new HashSet();
names.add("protDB1.aa");
names.add("protDB2.aa");
names.add("protDB3.aa");
for (Iterator i = files.iterator(); i.hasNext();)
{
String name = (String) i.next();
assertTrue(names.contains(name));
}
}
public void testGetFormat()
{
assertEquals(format, emblCDIndexStore.getFormat());
}
public void testGetIDs()
{
Set ids = emblCDIndexStore.getIDs();
assertTrue(30 == ids.size());
}
public void testGetName()
{
assertEquals("protDB", emblCDIndexStore.getName());
}
public void testGetSBFactory()
{
assertEquals(factory, emblCDIndexStore.getSBFactory());
}
public void testGetSymbolParser()
{
assertEquals(parser, emblCDIndexStore.getSymbolParser());
}
public void testRollback()
{
emblCDIndexStore.rollback();
}
public void testStore()
{
try
{
emblCDIndexStore.store(new SimpleIndex(new File("dummy"),
0,
-1,
"dummyID"));
}
catch (BioException be)
{
return;
}
fail("Expected BioException");
}
}