Fixed batchmapper.bat. Batchmapper uses transitive mapping by default.

Made transitive mapping observe target datasource

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/trunk@337 e3f1d335-44b1-4163-9530-9b341189ae98

batchmapper.bat

@@ -1 +1 @@
-java -jar dist/bridgedb-batchmapper.jar %*
+java -jar dist/org.bridgedb.tools.batchmapper.jar %*

org.bridgedb.tools.batchmapper/src/org/bridgedb/tools/batchmapper/BatchMapper.java

@@ -92,7 +92,8 @@ public void printUsage()
 				"		[-c <input column, 0-based>]\n" +
 				"		[-r <report file>] \n" +
 				"\n" +
-				"You should specify at least one -g or -t option \n");
+				"You should specify at least one -g or -t option.\n" +
+				"Multiple -g or -t options will be combined transitively.\n");
 	}
 
 	public String parseArgs(Settings settings, String[] args)
@@ -245,6 +246,7 @@ private void connectGdb() throws IDMapperException
 			{
 				gdb.addIDMapper(connectionString);
 			}
+			gdb.setTransitive(true);
 		}
 
 		public void writeMapping() throws IOException, IDMapperException

org.bridgedb/src/org/bridgedb/IDMapperStack.java

@@ -17,6 +17,7 @@
 package org.bridgedb;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -437,13 +438,21 @@ private Set<Xref> mapIDtransitive(Xref ref, DataSource... resultDs) throws IDMap
 	{
 		// first round
 		Set<Xref> result = new HashSet<Xref>();
+		Set<DataSource> dsFilter = new HashSet<DataSource>(Arrays.asList(resultDs));
 		for (IDMapper i : gdbs)
 		{
 			if (i == null || !i.isConnected()) continue;
 
 			// map ref in IDMapper i
 			Set<Xref> round1 = i.mapID(ref);
-			result.addAll (round1);
+
+			for (Xref r1 : round1)
+			{
+				if (resultDs.length == 0 || dsFilter.contains(r1.getDataSource()))
+				{
+					result.add (r1);
+				}
+			}
 
 			// then map the result of that in all IDMappers j (j != i)
 			for (IDMapper j : gdbs)