Changeset 166

Timestamp:

08/19/09 17:47:05 (2 years ago)

Author:

jgao

Message:

checkstyle fix

Location:

trunk/corelib/src/org/bridgedb/webservice/biomart

Files:

• BiomartStub.java (modified) (10 diffs)
• IDMapperBiomart.java (modified) (4 diffs)
• util/BiomartClient.java (modified) (1 diff)

trunk/corelib/src/org/bridgedb/webservice/biomart/BiomartStub.java

@@ -23 +23 @@
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
-import java.util.Vector;
 
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.bridgedb.DataSource;
 import org.bridgedb.IDMapperException;
-import org.bridgedb.Xref;
-import org.bridgedb.file.IDMappingReaderFromDelimitedReader;
 import org.bridgedb.webservice.biomart.util.Attribute;
 import org.bridgedb.webservice.biomart.util.BiomartClient;
@@ -44 +39 @@
 
 /**
- * Cache for SynergizerClient
+ * Wrapp-up for BiomartClient.
  * @author gjj
  */
-public class BiomartStub {
+public final class BiomartStub {
     public static final String defaultBaseURL
             = BiomartClient.defaultBaseURL;
 
-    // cache data
-//    private Map<String,Map<String,Map<String,Set<String>>>>
-//            mapAuthSpeciesDomainRange = null;
-
     // one instance per url
     private static Map<String, BiomartStub> instances = new HashMap();
@@ -60 +51 @@
     /**
      *
-     * @return SynergizerStub with the default server url
+     * @return BiomartStub with the default server url
      * @throws IOException if failed to connect
      */
@@ -70 +61 @@
      *
      * @param baseUrl server url
-     * @return SynergizerStub from the server
+     * @return BiomartStub from the server
      * @throws IOException if failed to connect
      */
@@ -129 +120 @@
      * @param mart mart name
      * @return mart display name or null if not exist
-     * @throws IDMapperException if failed to connect
      */
     public String martDisplayName(String mart) {
@@ -142 +132 @@
     /**
      *
-     * @param authority mart name
+     * @param mart mart name
      * @return available datasets from this mart
-     * @throws IDMapperException if failed
      */
     public Set<String> availableDatasets(String mart)
@@ -170 +159 @@
      * @param dataset dataset name
      * @return dataset display name or null if not exist
-     * @throws IDMapperException if failed to connect
      */
     public String datasetDisplayName(String dataset) {
@@ -211 +199 @@
     /**
      *
-     * @param mart mart name
-     * @param dataset dataset name
+     * @param mart mart name.
+     * @param dataset dataset name.
+     * @param idOnly filter the attributes ending with "ID" or "Accession"
+     *        if true; no filter otherwise.
      * @return attribute names / target id types of the dataset from this
-     *         mart
+     *         mart.
      * @throws IDMapperException if failed.
      */
@@ -239 +229 @@
             result = new HashSet();
             for (String name : attributes.keySet()) {
-                String displayName = client.getAttribute(dataset, name).getDisplayName();
+                String displayName = client.getAttribute(dataset, name)
+                        .getDisplayName();
                 if (displayName.endsWith("ID")
                         || displayName.endsWith("Accession")
@@ -264 +255 @@
      *         key: source id
      *         value: corresponding target ids
-     * @throws IDMapperException
+     * @throws IDMapperException if failed to connect
      */
     public Map<String,Set<String>[]> translate(final String mart,

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

@@ -140 +140 @@
      * @param idOnlyForTgtDataSource id-only option, filter data source ends
      *        with 'ID' or 'Accession'.
-     * @param transitivity transitivity option
      * @throws IDMapperException if failed to link to the dataset
      */
@@ -168 +167 @@
      * @param idOnlyForTgtDataSource id-only option, filter data source ends
      *        with 'ID' or 'Accession'.
-     * @param transitivity transitivity option
      * @throws IDMapperException if failed to link to the dataset
      */
@@ -335 +333 @@
 
     /**
-     * Get supported source data sources
+     * Get supported source data sources.
      * @return supported source data sources
-     * @throws IOException if failed to read the filters
+     * @throws IDMapperException if failed to read the filters
      */
     protected Set<DataSource> getSupportedSrcDataSources()
@@ -353 +351 @@
 
     /**
-     * Get supported target data sources
+     * Get supported target data sources.
      * @return supported target data sources
-     * @throws IOException if failed to read the filters
+     * @throws IDMapperException if failed to read the filters
      */
     protected Set<DataSource> getSupportedTgtDataSources() 

trunk/corelib/src/org/bridgedb/webservice/biomart/util/BiomartClient.java

@@ -127 +127 @@
     /**
      *
-     * @param dataset
-     * @param filter
-     * @return
+     * @param dataset dataset name
+     * @param filter filter name
+     * @return Attribute converted from filter
      */
     public Attribute filterToAttribute(String dataset, String filter) {