biojava-aa-prop/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.11</version>
+		<version>4.2.12</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

biojava-alignment/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.11</version>
+		<version>4.2.12</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.11</version>
+  			<version>4.2.12</version>
   		</dependency>
 	</dependencies>
 </project>

biojava-core/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.11</version>
+		<version>4.2.12</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>

biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java

@@ -88,7 +88,7 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ
 	private static final String TREMBLID_PATTERN = "[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}";
 	public static final Pattern UP_AC_PATTERN = Pattern.compile("(" + SPID_PATTERN + "|" + TREMBLID_PATTERN + ")");
 
-	private static String uniprotbaseURL = "http://www.uniprot.org"; //"http://pir.uniprot.org";
+	private static String uniprotbaseURL = "https://www.uniprot.org"; //"http://pir.uniprot.org";
 	private static String uniprotDirectoryCache = null;
 	private String sequence;
 	private CompoundSet<C> compoundSet;
@@ -415,6 +415,61 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ
 		fw.close();
 	}
 	
+	/**
+	 * Open a URL connection.
+	 * 
+	 * Follows redirects.
+	 * @param url
+	 * @throws IOException 
+	 */
+	private static HttpURLConnection openURLConnection(URL url) throws IOException {
+		// This method should be moved to a utility class in BioJava 5.0
+		
+		final int timeout = 5000;
+		final String useragent = "BioJava";
+		
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty("User-Agent", useragent);
+		conn.setInstanceFollowRedirects(true);
+		conn.setConnectTimeout(timeout);
+		conn.setReadTimeout(timeout);
+
+		int status = conn.getResponseCode();
+		while (status == HttpURLConnection.HTTP_MOVED_TEMP
+				|| status == HttpURLConnection.HTTP_MOVED_PERM
+				|| status == HttpURLConnection.HTTP_SEE_OTHER) {
+			// Redirect!
+			String newUrl = conn.getHeaderField("Location");
+
+			if(newUrl.equals(url.toString())) {
+				throw new IOException("Cyclic redirect detected at "+newUrl);
+			}
+			
+			// Preserve cookies
+			String cookies = conn.getHeaderField("Set-Cookie");
+
+			// open the new connection again
+			url = new URL(newUrl);
+			conn.disconnect();
+			conn = (HttpURLConnection) url.openConnection();
+			if(cookies != null) {
+				conn.setRequestProperty("Cookie", cookies);
+			}
+			conn.addRequestProperty("User-Agent", useragent);
+			conn.setInstanceFollowRedirects(true);
+			conn.setConnectTimeout(timeout);
+			conn.setReadTimeout(timeout);
+			conn.connect();
+			
+			status = conn.getResponseCode();
+			
+			logger.info("Redirecting from {} to {}", url, newUrl);
+		}
+		conn.connect();
+		
+		return conn;
+	}
+
 	private StringBuilder fetchUniprotXML(String uniprotURL)
 			throws IOException, CompoundNotFoundException {
 
@@ -423,11 +478,9 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ
 		int attempt = 5;
 		List<String> errorCodes = new ArrayList<String>();
 		while(attempt > 0) {
-			HttpURLConnection uniprotConnection = (HttpURLConnection) uniprot.openConnection();
-			uniprotConnection.setRequestProperty("User-Agent", "BioJava");
-			uniprotConnection.connect();
+			HttpURLConnection uniprotConnection = openURLConnection(uniprot);
 			int statusCode = uniprotConnection.getResponseCode();
-			if (statusCode == 200) {
+			if (statusCode == HttpURLConnection.HTTP_OK) {
 				BufferedReader in = new BufferedReader(
 						new InputStreamReader(
 						uniprotConnection.getInputStream()));

biojava-genome/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.11</version>
+		<version>4.2.12</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>

biojava-integrationtest/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.11</version>
+    <version>4.2.12</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.11</version>
+    	<version>4.2.12</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>

biojava-modfinder/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.11</version>
+    <version>4.2.12</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.11</version>
+    	<version>4.2.12</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>

biojava-ontology/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.11</version>
+    <version>4.2.12</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>

biojava-phylo/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.11</version>
+    <version>4.2.12</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.11</version>
+      <version>4.2.12</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

biojava-protein-disorder/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.11</version>
+		<version>4.2.12</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->

biojava-sequencing/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.11</version>
+		<version>4.2.12</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 			<scope>compile</scope>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

biojava-structure-gui/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-        <version>4.2.11</version>
+        <version>4.2.12</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.11</version>
+            <version>4.2.12</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.11</version>
+            <version>4.2.12</version>
             <scope>compile</scope>
         </dependency>
 

biojava-structure/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.11</version>
+		<version>4.2.12</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.11</version>
+			<version>4.2.12</version>
 			<scope>compile</scope>
 		</dependency>
 

biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java

@@ -120,6 +120,11 @@ public class StructureIO {
 		cache = c;
 	}
 	
+	public static AtomCache getAtomCache() {
+		checkInitAtomCache();
+		return cache;
+	}
+
 	/**
 	 * Returns the first biologicalAssembly that is available for a protein structure. For more documentation on quaternary structures see:
 	 * {@link http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html}

biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java

@@ -636,6 +636,7 @@ public class CathInstallation implements CathDatabase{
 
 	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
 //        System.out.println("downloading " + remoteURL + " to: " + localFile);
+		LOGGER.info("Downloading file {} to local file {}", remoteURL, localFile);
 
 		long timeS = System.currentTimeMillis();
 		File tempFile  = File.createTempFile(FileDownloadUtils.getFilePrefix(localFile), "."+ FileDownloadUtils.getFileExtension(localFile));
@@ -665,7 +666,7 @@ public class CathInstallation implements CathDatabase{
 			disp = disp / 1024.0;
 		}
 		long timeE = System.currentTimeMillis();
-		LOGGER.info("Downloaded file {} ({}) to local file {} in {} sec.", remoteURL, String.format("%.1f",disp) + unit, localFile, (timeE - timeS)/1000);
+		LOGGER.info("Downloaded {} in {} sec. to {}", String.format("%.1f",disp) + unit, (timeE - timeS)/1000, localFile);
 	}
 
 	private boolean domainDescriptionFileAvailable(){

biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java

@@ -35,6 +35,7 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
+import java.nio.file.Files;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.*;
@@ -127,6 +128,9 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 
 	protected static final String lineSplit = System.getProperty("file.separator");
 
+	/** Minimum size for a valid structure file (CIF or PDB), in bytes */
+	public static final long MIN_PDB_FILE_SIZE = 40;  // Empty gzip files are 20bytes. Add a few more for buffer.
+
 	private File path;
 	private List<String> extensions;
 
@@ -402,8 +406,9 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 	 * Attempts to delete all versions of a structure from the local directory.
 	 * @param pdbId
 	 * @return True if one or more files were deleted
+	 * @throws IOException if the file cannot be deleted
 	 */
-	public boolean deleteStructure(String pdbId){
+	public boolean deleteStructure(String pdbId) throws IOException{
 		boolean deleted = false;
 		// Force getLocalFile to check in obsolete locations
 		ObsoleteBehavior obsolete = getObsoleteBehavior();
@@ -421,7 +426,7 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 				// delete file
 				boolean success = existing.delete();
 				if(success) {
-					logger.info("Deleting "+existing.getAbsolutePath());
+					logger.debug("Deleting "+existing.getAbsolutePath());
 				}
 				deleted = deleted || success;
 
@@ -430,7 +435,7 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 				if(parent != null) {
 					success = parent.delete();
 					if(success) {
-						logger.info("Deleting "+parent.getAbsolutePath());
+						logger.debug("Deleting "+parent.getAbsolutePath());
 					}
 				}
 
@@ -660,8 +665,9 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 	 * Searches for previously downloaded files
 	 * @param pdbId
 	 * @return A file pointing to the existing file, or null if not found
+	 * @throws IOException If the file exists but is empty and can't be deleted
 	 */
-	public File getLocalFile(String pdbId) {
+	public File getLocalFile(String pdbId) throws IOException {
 
 		// Search for existing files
 
@@ -687,6 +693,11 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 				for(String ex : getExtensions() ){
 					File f = new File(searchdir,prefix + pdbId.toLowerCase() + ex) ;
 					if ( f.exists()) {
+						// delete files that are too short to have contents
+						if( f.length() < MIN_PDB_FILE_SIZE ) {
+							Files.delete(f.toPath());
+							return null;
+						}
 						return f;
 					}
 				}
@@ -697,9 +708,11 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 	}
 
 	protected boolean checkFileExists(String pdbId){
+		try {
 			File path =  getLocalFile(pdbId);
 			if ( path != null)
 				return true;
+		} catch(IOException e) {}
 		return false;
 	}
 

biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java

@@ -68,9 +68,8 @@ public class ChemCompGroupFactory {
 	 * again. Note that this change can have unexpected behavior of
 	 * code executed afterwards.
 	 * <p>
-	 * Changing the provider does not reset the cache, so Chemical
-	 * Component definitions already downloaded from previous providers
-	 * will be used. To reset the cache see {@link #getCache()).
+	 * Changing the provider also resets the cache, so any groups
+	 * previously accessed will be reread or re-downloaded.
 	 *
 	 * @param provider
 	 */
@@ -85,6 +84,15 @@ public class ChemCompGroupFactory {
 		return chemCompProvider;
 	}
 	
+	/**
+	 * Force the in-memory cache to be reset.
+	 * 
+	 * Note that the ChemCompProvider may have additional memory or disk caches that need to be cleared too.
+	 */
+	public static void clearCache() {
+		cache.clear();
+	}
+
 	public static Group getGroupFromChemCompDictionary(String recordName) {
 
 		// make sure we work with upper case records

biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java

@@ -42,6 +42,7 @@ import java.util.zip.GZIPOutputStream;
 import org.biojava.nbio.core.util.InputStreamProvider;
 import org.biojava.nbio.structure.align.util.HTTPConnectionTools;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
+import org.biojava.nbio.structure.io.LocalPDBDirectory;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -86,31 +87,36 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 		protectedIDs.add("NUL");
 	}
 	
+	private static ChemCompProvider fallback = null; // Fallback provider if the download fails
+
 	/** by default we will download only some of the files. User has to request that all files should be downloaded...
 	 *
 	 */
 	boolean downloadAll = false;
 
 	public DownloadChemCompProvider(){
-		logger.debug("Initialising DownloadChemCompProvider");
-
-		// note that path is static, so this is just to make sure that all non-static methods will have path initialised
-		initPath();
+		this(null);
 	}
 
 	public DownloadChemCompProvider(String cacheFilePath){
 		logger.debug("Initialising DownloadChemCompProvider");
 
 		// note that path is static, so this is just to make sure that all non-static methods will have path initialised
+		if(cacheFilePath != null) {
 			path = new File(cacheFilePath);
 		}
+	}
 
-	private static void initPath(){
-
+	/**
+	 * Get this provider's cache path
+	 * @return
+	 */
+	public static File getPath(){
 		if (path==null) {
 			UserConfiguration config = new UserConfiguration();
 			path = new File(config.getCacheFilePath());
 		}
+		return path;
 	}
 
 	/**
@@ -127,7 +133,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 		// this makes sure there is a file separator between every component,
 		// if path has a trailing file separator or not, it will work for both cases
-		File dir = new File(path, CHEM_COMP_CACHE_DIRECTORY);
+		File dir = new File(getPath(), CHEM_COMP_CACHE_DIRECTORY);
 		File f = new File(dir, "components.cif.gz");
 
 		if ( ! f.exists()) {
@@ -161,7 +167,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 		logger.info("Installing individual chem comp files ...");
 
-		File dir = new File(path, CHEM_COMP_CACHE_DIRECTORY);
+		File dir = new File(getPath(), CHEM_COMP_CACHE_DIRECTORY);
 		File f = new File(dir, "components.cif.gz");
 
 
@@ -212,7 +218,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 	 */
 	private void writeID(String contents, String currentID) throws IOException{
 
-		String localName = DownloadChemCompProvider.getLocalFileName(currentID);
+		String localName = getLocalFileName(currentID);
 
 		try ( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(localName))) ) {
 
@@ -272,7 +278,10 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 				ChemComp chemComp = dict.getChemComp(recordName);
 
+				// May be null if the file was corrupt. Fall back on ReducedChemCompProvider in that case
+				if(chemComp != null) {
 					return chemComp;
+				}
 
 			} catch (IOException e) {
 
@@ -296,9 +305,12 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 		// see https://github.com/biojava/biojava/issues/315
 		// probably a network error happened. Try to use the ReducedChemCOmpProvider
-		ReducedChemCompProvider reduced = new ReducedChemCompProvider();
+		if( fallback == null) {
+			fallback = new ReducedChemCompProvider();
+		}
 
-		return reduced.getChemComp(recordName);
+		logger.warn("Falling back to ReducedChemCompProvider for {}. This could indicate a network error.", recordName);
+		return fallback.getChemComp(recordName);
 
 	}
 
@@ -313,16 +325,15 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 			recordName = "_" + recordName;
 		}
 
-		initPath();
-
-		File f = new File(path, CHEM_COMP_CACHE_DIRECTORY);
+		File f = new File(getPath(), CHEM_COMP_CACHE_DIRECTORY);
 		if (! f.exists()){
 			logger.info("Creating directory " + f);
 
 			boolean success = f.mkdir();
 			// we've checked in initPath that path is writable, so there's no need to check if it succeeds
 			// in the unlikely case that in the meantime it isn't writable at least we log an error
-			if (!success) logger.error("Directory {} could not be created",f);
+			if (!success)
+				logger.error("Directory {} could not be created",f);
 
 		}
 
@@ -337,6 +348,14 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 		File f = new File(fileName);
 
+		// delete files that are too short to have contents
+		if( f.length() < LocalPDBDirectory.MIN_PDB_FILE_SIZE ) {
+			// Delete defensively.
+			// Note that if delete is unsuccessful, we re-download the file anyways
+			f.delete();
+			return false;
+		}
+
 		return f.exists();
 
 	}

biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java

@@ -212,6 +212,9 @@ public class SimpleMMcifParser implements MMcifParser {
 
 		// the first line is a data_PDBCODE line, test if this looks like a mmcif file
 		line = buf.readLine();
+		while( line != null && (line.isEmpty() || line.startsWith(COMMENT_CHAR))) {
+			line = buf.readLine();
+		}
 		if (line == null || !line.startsWith(MMCIF_TOP_HEADER)){
 			logger.error("This does not look like a valid mmCIF file! The first line should start with 'data_', but is: '" + line+"'");
 			triggerDocumentEnd();

biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/FileDownloadUtils.java

@@ -21,9 +21,6 @@
  */
 package org.biojava.nbio.structure.io.util;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -36,6 +33,15 @@ import java.net.URLConnection;
 import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
 import java.nio.channels.ReadableByteChannel;
+import java.nio.file.FileVisitResult;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.attribute.BasicFileAttributes;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class FileDownloadUtils {
 
@@ -241,6 +247,41 @@ public class FileDownloadUtils {
 		return connection;
 	}
 	
+	/**
+	 * Recursively delete a folder & contents
+	 *
+	 * @param dir directory to delete
+	 */
+	public static void deleteDirectory(Path dir) throws IOException {
+		if(dir == null || !Files.exists(dir))
+			return;
+		Files.walkFileTree(dir, new SimpleFileVisitor<Path>() {
+	        @Override
+	        public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
+	            Files.delete(file);
+	            return FileVisitResult.CONTINUE;
+	        }
+
+	        @Override
+	        public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOException {
+	            if (e != null) {
+	                throw e;
+	            }
+	            Files.delete(dir);
+	            return FileVisitResult.CONTINUE;
+	        }
+	    });
+	}
+	/**
+	 * Recursively delete a folder & contents
+	 *
+	 * @param dir directory to delete
+	 */
+	public static void deleteDirectory(String dir) throws IOException {
+		deleteDirectory(Paths.get(dir));
+	}
+
+
 	public static void main(String[] args) {
 		String url;
 		url = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/";