Changeset 156 for trunk/corelib/test/org/bridgedb/TestBiomart.java

Timestamp:

08/14/09 21:50:23 (3 years ago)

Author:

jgao

Message:

IDMapperText & IDMapperBiomart driver update,
IDMapperBiomart constructor with mart

Files:

• trunk/corelib/test/org/bridgedb/TestBiomart.java (modified) (3 diffs)

trunk/corelib/test/org/bridgedb/TestBiomart.java

@@ -61 +61 @@
             for (Dataset ds : datasets) {
                 System.out.println ("\t" + ds.getName());
-                IDMapperBiomart idMapper = new IDMapperBiomart(ds.getName());
+                IDMapperBiomart idMapper = new IDMapperBiomart(db.getName(),ds.getName());
                 //IDMapper idMapper = BridgeDb.connect("idmapper-biomart:dataset="+ds.getName());
                 IDMapperCapabilities cap = idMapper.getCapabilities();
@@ -100 +100 @@
 //                System.out.println (db.getName());
 //         }
-        BiomartStub biomartStub = BiomartStub.getInstance();
+        //BiomartStub biomartStub = BiomartStub.getInstance();
         
-        Set<Dataset> datasets = new HashSet(biomartStub.getAvailableDatasets("ensembl"));
+        //Set<Dataset> datasets = new HashSet(biomartStub.getAvailableDatasets("ensembl"));
         
-         IDMapperBiomart mapper = new IDMapperBiomart("hsapiens_gene_ensembl");
+         IDMapperBiomart mapper = new IDMapperBiomart("ensembl", "hsapiens_gene_ensembl");
          System.out.println("\n===Supported source data sources===");
          for (DataSource ds : mapper.getCapabilities().getSupportedSrcDataSources())
@@ -127 +127 @@
         
          //IDMapperBiomart mapper = new IDMapperBiomart("hsapiens_gene_ensembl");
-        IDMapper mapper = BridgeDb.connect ("idmapper-biomart:dataset=hsapiens_gene_ensembl");
+        IDMapper mapper = BridgeDb.connect ("idmapper-biomart:mart=ensembl&dataset=hsapiens_gene_ensembl");
         System.out.println("\n===Supported source data sources===");
          for (DataSource ds : mapper.getCapabilities().getSupportedSrcDataSources())