Another small fix for PDB_DIR

josemduarte · josemduarte · commit 49f69e70f543 · 2014-10-01T21:41:14.000+02:00
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/io/SandboxStyleStructureProvider.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/io/SandboxStyleStructureProvider.java
@@ -8,7 +8,7 @@
 
 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.biojava3.core.util.InputStreamProvider;
 
 
@@ -98,14 +98,9 @@ public class SandboxStyleStructureProvider implements StructureProvider {
 	public SandboxStyleStructureProvider() {
 		params = new FileParsingParameters();
 		
+		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());
 	}
 	
 	/** directory where to find PDB files */
@@ -147,7 +142,7 @@ public Structure getStructureById(String pdbId) throws IOException,StructureExce
 			return struc ;
 			
 			
-		} catch (Exception e){
+		} catch (IOException e){
 			e.printStackTrace();
 			// something is wrong with the file!
 			// it probably should be downloaded again...
