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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.db.emblcd;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import junit.framework.TestCase;
/**
* <code>EntryNamRandomAccessTest</code> is a unit test of random
* access reading the binary entrynam.idx file type.
*
* @author Keith James
* @since 1.2
*/
public class EntryNamRandomAccessTest extends TestCase
{
protected EntryNamRandomAccess rand;
protected String [] seqID;
protected long [] rPos;
protected long [] sPos;
protected int [] fileNum;
public EntryNamRandomAccessTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
URL url = EntryNamRandomAccessTest.class.getResource("entrynam.idx");
File f = new File(url.getFile());
rand = new EntryNamRandomAccess(f, 300, 30, 30);
// First 10 sequence IDs.
seqID = new String [] {"NMA0001", "NMA0003", "NMA0004", "NMA0007", "NMA0011",
"NMA0012", "NMA0013", "NMA0020", "NMA0021", "NMA0022" };
// First 10 sequence byte offsets. There is more than one 0
// byte offset because the database consists of more than one
// sequence file.
rPos = new long [] { 0, 917, 1097, 1811, 0, 156, 270, 2379, 0, 283};
// First 10 sequence file numbers.
fileNum = new int [] { 1, 1, 1, 1, 2, 2, 2, 2, 3, 3 };
}
protected void tearDown() throws Exception
{
rand.close();
}
public void testFindRecord() throws IOException
{
for (int i = 0; i < 10; i++)
{
Object [] rec = rand.findRecord(seqID[i]);
assertEquals(seqID[i], (String) rec[0]);
assertEquals(rPos[i], ((Long) rec[1]).longValue());
assertEquals(0, ((Long) rec[2]).longValue());
assertEquals(fileNum[i], ((Integer) rec[3]).intValue());
}
}
public void testGetFile()
{
assertEquals("entrynam.idx", rand.getFile().getName());
}
}
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