propagaingt server config to the remote domain lookup services

andreasprlic · andreasprlic · commit 78b722128011 · 2013-03-22T17:53:35.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@10102 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/FarmJobRunnable.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/FarmJobRunnable.java
@@ -30,7 +30,10 @@
 import org.biojava.bio.structure.align.util.ResourceManager;
 import org.biojava.bio.structure.align.xml.AFPChainXMLConverter;
 import org.biojava.bio.structure.align.xml.PdbPairsMessage;
+import org.biojava.bio.structure.domain.RemotePDPProvider;
 import org.biojava.bio.structure.io.FileParsingParameters;
+import org.biojava.bio.structure.scop.RemoteScopInstallation;
+import org.biojava.bio.structure.scop.ScopFactory;
 import org.biojava3.core.util.FlatFileCache;
 import org.biojava3.core.util.PrettyXMLWriter;
 
@@ -89,6 +92,22 @@ public FarmJobRunnable(FarmJobParameters params){
 		// multiple farm jobs share the same SoftHashMap for caching coordinates
 		cache = new AtomCache( params.getPdbFilePath(), params.isPdbDirSplit());
 		
+		
+		if ( params.getServer()!= null && (!params.getServer().equals("") ) ) {
+			RemotePDPProvider pdpprovider = new RemotePDPProvider();
+		
+			pdpprovider.setServer(params.getServer()+"/domains/");
+			
+			cache.setPdpprovider(pdpprovider);
+			
+			RemoteScopInstallation scop = new RemoteScopInstallation();
+			
+			scop.setServer(params.getServer()+"/domains/");
+			ScopFactory.setScopDatabase(scop);
+			
+		}
+		
+		
 		// enforce to replace remediated files with new versions...
 		FileParsingParameters fparams = cache.getFileParsingParams();
 		fparams.setUpdateRemediatedFiles(params.isUpdateRemediatedFiles());
