Changeset 337

Timestamp:

04/08/10 11:04:53 (22 months ago)

Author:

martijn

Message:

Fixed batchmapper.bat. Batchmapper uses transitive mapping by default.
Made transitive mapping observe target datasource

Location:

trunk

Files:

• batchmapper.bat (modified) (1 diff)
• org.bridgedb.tools.batchmapper/src/org/bridgedb/tools/batchmapper/BatchMapper.java (modified) (2 diffs)
• org.bridgedb/src/org/bridgedb/IDMapperStack.java (modified) (3 diffs)

trunk/batchmapper.bat

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

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

@@ -93 +93 @@
                                 "               [-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");
         }
         
@@ -246 +247 @@
                                 gdb.addIDMapper(connectionString);
                         }
+                        gdb.setTransitive(true);
                 }
                 

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

@@ -18 +18 @@
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -438 +439 @@
                 // first round
                 Set<Xref> result = new HashSet<Xref>();
+                Set<DataSource> dsFilter = new HashSet<DataSource>(Arrays.asList(resultDs));
                 for (IDMapper i : gdbs)
                 {
@@ -444 +446 @@
                         // 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)