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215 lines (167 loc) · 6.07 KB
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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/
*
* Created on Mar 1, 2010
* Author: Andreas Prlic
*
*/
package org.biojava.nbio.structure;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.LocalPDBDirectory;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
import org.biojava.nbio.structure.io.MMCIFFileReader;
import org.biojava.nbio.structure.io.PDBFileReader;
import org.junit.Before;
import org.junit.Test;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import static org.junit.Assert.*;
// TODO dmyersturnbull: we should merge TestAtomCache and AtomCacheTest
public class TestAtomCache {
public static final String lineSplit = System.getProperty("file.separator");
private AtomCache cache;
@Before
public void setUp() throws IOException {
cache = new AtomCache();
// Delete files which were cached in previous tests
String[] uncacheIDs = new String[] {
"1cmw", "1hhb","4hhb"
};
List<LocalPDBDirectory> readers = new ArrayList<LocalPDBDirectory>();
readers.add(new MMCIFFileReader(cache.getPath()) );
readers.add(new PDBFileReader(cache.getPath()) );
for(LocalPDBDirectory reader : readers) {
reader.setFetchBehavior(cache.getFetchBehavior());
reader.setObsoleteBehavior(cache.getObsoleteBehavior());
for(String pdbId : uncacheIDs) {
reader.deleteStructure(pdbId);
}
}
}
// TODO dmyersturnbull: Which of these syntaxes do we support? We should re-enable after
@Test
public void testAtomCacheNameParsing() throws IOException, StructureException {
String name1= "4hhb";
Structure s = cache.getStructure(name1);
assertNotNull(s);
assertTrue(s.getChains().size() == 4);
String name2 = "4hhb.C";
String chainId2 = "C";
s = cache.getStructure(name2);
assertTrue(s.getChains().size() == 1);
Chain c = s.getChainByPDB(chainId2);
assertEquals(c.getChainID(),chainId2);
// Colon separators removed in BioJava 4.1.0
String name2b = "4hhb:A";
try {
s = cache.getStructure(name2b);
fail("Invalid structure format");
} catch(IOException e) {
} catch(StructureException e) {
}
// Numeric chain IDs are allowed but deprecated.
String name3 = "4hhb.1";
String chainId3 = "B";
s = cache.getStructure(name3);
assertNotNull(s);
assertTrue(s.getChains().size() == 1);
c = s.getChainByPDB(chainId3);
assertEquals(c.getChainID(),chainId3);
String name4 = "4hhb.A:10-20,B:10-20,C:10-20";
s = cache.getStructure(name4);
assertNotNull(s);
assertEquals(s.getChains().size(), 3);
c = s.getChainByPDB("B");
assertEquals(c.getAtomLength(),11);
String name5 = "4hhb.(A:10-20,A:30-40)";
s =cache.getStructure(name5);
assertNotNull(s);
assertEquals(s.getChains().size(),1 );
c = s.getChainByPDB("A");
assertEquals(c.getAtomLength(),22);
try {
// This syntax used to work, since the first paren is treated as a separator
String name6 = "4hhb(A:10-20,A:30-40)";
s =cache.getStructure(name6);
fail("A chain separator is required after the ID since 4.2.0");
} catch(StructureException e) {}
// Works since we detect a separator
String name8 = "4hhb.(C)";
s = cache.getStructure(name8);
assertTrue(s.getChains().size() == 1);
c = s.getChainByPDB(chainId2);
assertEquals(c.getChainID(),chainId2);
}
@Test(expected=IOException.class)
public void testObsoleteId() throws StructureException, IOException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.THROW_EXCEPTION);
// OBSOLETE PDB; should throw an exception
cache.setUseMmCif(false);
cache.getStructure("1HHB");
}
// note: we expect an IOException because 1CMW is obsolete and hasn't got a replacement
@Test
public void testFetchCurrent1CMW() throws IOException, StructureException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_CURRENT);
// OBSOLETE PDB; should throw an exception
cache.setUseMmCif(false);
try {
cache.getStructure("1CMW");
fail("Obsolete structure should throw exception");
} catch(IOException e) {}
cache.setUseMmCif(true);
try {
cache.getStructure("1CMW");
fail("Obsolete structure should throw exception");
} catch(IOException e) {}
}
// 1HHB is obsolete with a replacement
@Test
public void testFetchCurrent1HHB() throws IOException, StructureException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_CURRENT);
cache.setUseMmCif(false);
Structure s = cache.getStructure("1HHB");
assertEquals("Failed to get the current ID for 1HHB.","4HHB",s.getPDBCode());
cache.setUseMmCif(true);
s = cache.getStructure("1HHB");
assertEquals("Failed to get the current ID for 1HHB.","4HHB",s.getPDBCode());
}
// Fetching obsolete directly
@Test
public void testFetchObsolete() throws IOException, StructureException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
Structure s;
cache.setUseMmCif(false);
s = cache.getStructure("1CMW");
assertEquals("Failed to get OBSOLETE file 1CMW.","1CMW", s.getPDBCode());
s = cache.getStructure("1HHB");
assertEquals("Failed to get OBSOLETE file 1HHB.","1HHB", s.getPDBCode());
cache.setUseMmCif(true);
s = cache.getStructure("1CMW");
assertEquals("Failed to get OBSOLETE file 1CMW.","1CMW", s.getPDBCode());
s = cache.getStructure("1HHB");
assertEquals("Failed to get OBSOLETE file 1HHB.","1HHB", s.getPDBCode());
}
}