Changeset 149

Timestamp:

08/09/09 05:23:13 (2 years ago)

Author:

jgao

Message:

Checkstype fix

Location:

trunk/corelib

Files:

• src/org/bridgedb/webservice/IDMapperBiomart.java (modified) (8 diffs)
• test/org/bridgedb/TestBiomart.java (modified) (3 diffs)

trunk/corelib/src/org/bridgedb/webservice/IDMapperBiomart.java

@@ -81 +81 @@
         }
 
-    protected String datasetName;
-    protected BiomartStub stub;
-    protected boolean transitivity;
-    protected boolean idOnlyForTgtDataSource;
-
-    protected String baseURL;
+    private String datasetName;
+    private BiomartStub stub;
+    private boolean transitivity;
+    private boolean idOnlyForTgtDataSource;
+
+    private String baseURL;
 
     private Map<DataSource, Filter> mapSrcDSFilter;
@@ -242 +242 @@
     }
 
+    /**
+     *
+     * @return URL of the dataset
+     */
     public String toString() {
         return getBaseURL()+"?dataset="+getDataset();
@@ -249 +253 @@
      * {@inheritDoc}
      */
-    public Map<Xref, Set<Xref>> mapID(Set<Xref> srcXrefs, Set<DataSource> tgtDataSources) throws IDMapperException {
-        if (srcXrefs==null) {
-            throw new java.lang.IllegalArgumentException("srcXrefs cannot be null");
+    public Map<Xref, Set<Xref>> mapID(Set<Xref> srcXrefs,
+                Set<DataSource> tgtDataSources) throws IDMapperException {
+        if (srcXrefs==null || tgtDataSources==null) {
+            throw new java.lang.IllegalArgumentException(
+                        "srcXrefs or tgtDataSources cannot be null");
         }
 
@@ -257 +263 @@
 
         // remove unsupported source datasources
-        Set<DataSource> supportedSrcDatasources = cap.getSupportedSrcDataSources();
+        Set<DataSource> supportedSrcDatasources
+                    = cap.getSupportedSrcDataSources();
         Map<DataSource, String> queryFilters = getQueryFilters(srcXrefs);
         Iterator<DataSource> it = queryFilters.keySet().iterator();
@@ -345 +352 @@
     /**
      * Create filters from the source xrefs.
-     * @param srcXrefs
+     * @param srcXrefs source xrefs
      * @return map from data source to IDs
      */
@@ -382 +389 @@
     /**
      * This code is bollowed from IDMapperClient from Cytoscape.
-     * @param tgtDataSources
+     * @param tgtDataSources target data sources
+     * @param filterName filter name
      * @return attributes
      */
@@ -435 +443 @@
     }
 
+    /**
+     * Get supported source data sources
+     * @return supported source data sources
+     * @throws IOException if failed to read the filters
+     */
     protected Set<DataSource> getSupportedSrcDataSources() throws IOException {
         Set<DataSource> dss = new HashSet();
@@ -452 +465 @@
     }
 
+    /**
+     * Get supported target data sources
+     * @return supported target data sources
+     * @throws IOException if failed to read the filters
+     */
     protected Set<DataSource> getSupportedTgtDataSources() throws IOException {
         Map<String, Attribute> attributeVals = stub.getAttributes(datasetName);

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

@@ -62 +62 @@
                 System.out.println ("\t" + ds.getName());
                 IDMapperBiomart idMapper = new IDMapperBiomart(ds.getName());
+                //IDMapper idMapper = BridgeDb.connect("idmapper-biomart:dataset="+ds.getName());
                 IDMapperCapabilities cap = idMapper.getCapabilities();
                 if (cap.getSupportedSrcDataSources().isEmpty()
@@ -104 +105 @@
         
          IDMapperBiomart mapper = new IDMapperBiomart("hsapiens_gene_ensembl");
+         System.out.println("\n===Supported source data sources===");
          for (DataSource ds : mapper.getCapabilities().getSupportedSrcDataSources())
          {
                  System.out.println (ds);
          }
+
+         System.out.println("\n===Supported target data sources===");
          for (DataSource ds : mapper.getCapabilities().getSupportedTgtDataSources())
          {
@@ -124 +128 @@
          //IDMapperBiomart mapper = new IDMapperBiomart("hsapiens_gene_ensembl");
         IDMapper mapper = BridgeDb.connect ("idmapper-biomart:dataset=hsapiens_gene_ensembl");
+        System.out.println("\n===Supported source data sources===");
          for (DataSource ds : mapper.getCapabilities().getSupportedSrcDataSources())
          {
                  System.out.println (ds);
          }
+
+         System.out.println("\n===Supported target data sources===");
          for (DataSource ds : mapper.getCapabilities().getSupportedTgtDataSources())
          {