More fixes for PDB_DIR reading, plus some biojava#111 and biojava#155

biojava3-structure/src/main/java/org/biojava/bio/structure/io/LocalCacheStructureProvider.java

@@ -13,7 +13,9 @@
 
 import org.biojava.bio.structure.Structure;
 import org.biojava.bio.structure.StructureException;
-import org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor;
+import org.biojava.bio.structure.align.util.UserConfiguration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 
 
@@ -25,6 +27,8 @@
  */
 public class LocalCacheStructureProvider implements StructureProvider{
 
+	private static final Logger logger = LoggerFactory.getLogger(LocalCacheStructureProvider.class);
+
 	FileParsingParameters params ;
 
 	String path;
@@ -38,14 +42,9 @@ public LocalCacheStructureProvider(){
 
 		// set the path to cache files
 
+		UserConfiguration config = new UserConfiguration();
 
-		String defaultPath = System.getProperty(AbstractUserArgumentProcessor.PDB_DIR);
-		if ( defaultPath == null) {
-			String property = "java.io.tmpdir";
-			defaultPath = System.getProperty(property);
-		}
-
-		setPath(defaultPath);
+		setPath(config.getPdbFilePath());
 
 	}
 
@@ -75,8 +74,7 @@ public Structure getStructureById(String pdbId) throws IOException {
 	}
 
 	private PDBFileReader getPdbFilereader(){
-		PDBFileReader reader = new PDBFileReader();
-		reader.setPath(path);
+		PDBFileReader reader = new PDBFileReader(path);
 		reader.setAutoFetch(true);
 		reader.setFileParsingParameters(params);
 		reader.setPdbDirectorySplit(isSplit);
@@ -134,42 +132,36 @@ private void downloadBiolUnit(String pdbId, File localFile) throws IOException{
 
 		String ur = String.format(u,pdbId);
 
-		System.out.println("Fetching " + ur);
+		logger.info("Fetching " + ur);
 
 		// prepare destination
-		System.out.println("writing to " + localFile);
-
-		try {
-			URL url = new URL(ur);
-
-			InputStream uStream = url.openStream();
-			InputStream conn = new GZIPInputStream(uStream);
-
-
-			FileOutputStream outPut = new FileOutputStream(localFile);
-			GZIPOutputStream gzOutPut = new GZIPOutputStream(outPut);
-			PrintWriter pw = new PrintWriter(gzOutPut);
-
-			BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(conn));
-			String line;
-			while ((line = fileBuffer.readLine()) != null) {
-				pw.println(line);
-			}
-			pw.flush();
-			pw.close();
-
-			outPut.flush();
-			outPut.close();
-			conn.close();
-			uStream.close();
-
-		} catch (Exception e){
-			System.err.println("Problem while downloading PDB ID " + pdbId + " from " + ur );
-
-			//e.printStackTrace();
-			throw new IOException("Could not download biol. unit for PDB ID " + pdbId);
-
+		logger.info("writing to " + localFile);
+
+
+		URL url = new URL(ur);
+
+		InputStream uStream = url.openStream();
+		InputStream conn = new GZIPInputStream(uStream);
+
+
+		FileOutputStream outPut = new FileOutputStream(localFile);
+		GZIPOutputStream gzOutPut = new GZIPOutputStream(outPut);
+		PrintWriter pw = new PrintWriter(gzOutPut);
+
+		BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(conn));
+		String line;
+		while ((line = fileBuffer.readLine()) != null) {
+			pw.println(line);
 		}
+		pw.flush();
+		pw.close();
+
+		outPut.flush();
+		outPut.close();
+		conn.close();
+		uStream.close();
+
+
 	}
 
 	public void setFileParsingParameters(FileParsingParameters params) {

biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopInstallation.java

@@ -43,9 +43,10 @@
 
 import org.biojava.bio.structure.Structure;
 import org.biojava.bio.structure.StructureTools;
-import org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor;
 import org.biojava.bio.structure.align.util.UserConfiguration;
 import org.biojava3.core.util.InputStreamProvider;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 
 /** This class provides access to the SCOP protein structure classification.
@@ -68,6 +69,8 @@
 public class ScopInstallation implements LocalScopDatabase {
 
 	public static final String DEFAULT_VERSION = "1.75";
+
+	private static final Logger logger = LoggerFactory.getLogger(ScopInstallation.class);
 
 	protected String scopVersion;
 
@@ -790,7 +793,7 @@ protected void downloadComFile() throws FileNotFoundException, IOException{
 	}
 
 	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException{
-		System.out.println("downloading " + remoteURL + " to: " + localFile);
+		logger.info("Downloading " + remoteURL + " to: " + localFile);
 		FileOutputStream out = new FileOutputStream(localFile);
 
 		InputStream in = remoteURL.openStream();