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Fix 969 Update SCOP version to 2.08 #972

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Merged
josemduarte merged 1 commit into from
Sep 27, 2021
Merged

Fix 969 Update SCOP version to 2.08 #972

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3 changes: 2 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@ public class ScopFactory {
private static final Logger logger = LoggerFactory.getLogger(ScopFactory.class);

// berkeley 2
public static final String VERSION_2_0_8 = "2.08";
public static final String VERSION_2_0_7 = "2.07";
public static final String VERSION_2_0_6 = "2.06";
public static final String VERSION_2_0_5 = "2.05";
Expand Down Expand Up @@ -78,7 +79,7 @@ public class ScopFactory {
public static final String VERSION_1_55 = "1.55";

// The most recent version as of compilation time
public static final String LATEST_VERSION = VERSION_2_0_7;
public static final String LATEST_VERSION = VERSION_2_0_8;

// Hold one instance for each version
private static Map<String,ScopDatabase> versionedScopDBs = new HashMap<>();
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4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
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Expand Up @@ -58,7 +58,7 @@
*/
public class ScopInstallation implements LocalScopDatabase {

public static final String DEFAULT_VERSION = "1.75";
public static final String DEFAULT_VERSION = ScopFactory.LATEST_VERSION;

private static final Logger logger = LoggerFactory.getLogger(ScopInstallation.class);

Expand Down Expand Up @@ -354,7 +354,7 @@ public ScopDomain getDomainByScopID(String scopId) {
if ( scopId.length() < 6) {
throw new ScopIOException("Does not look like a scop ID! " + scopId);
}
String pdbId = scopId.substring(1,5);
String pdbId = scopId.substring(1,5); //TODO handle this when you handle extended PDBId (PDB ID)
List<ScopDomain> doms = getDomainsForPDB(pdbId);
if ( doms == null)
return null;
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4 changes: 3 additions & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
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Expand Up @@ -64,6 +64,7 @@
import org.biojava.nbio.structure.test.util.GlobalsHelper;
import org.junit.After;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand All @@ -88,7 +89,7 @@ public void setUp() {
StructureIO.setAtomCache(cache);

// Use a fixed SCOP version for stability
ScopFactory.setScopDatabase(ScopFactory.VERSION_1_75B);
ScopFactory.setScopDatabase(ScopFactory.LATEST_VERSION);
}

@After
Expand Down Expand Up @@ -166,6 +167,7 @@ public void testGetStructureForDomain3() throws IOException, StructureException
* @throws IOException
* @throws StructureException
*/
@Ignore("SCOP files < 2.08 are no longer available")
@Test
public void testGetStructureForChainlessDomains() throws IOException, StructureException {
ScopDatabase scop = ScopFactory.getSCOP(ScopFactory.VERSION_1_71); // Uses the range '1-135' without a chain
Expand Down