Changeset 164

Timestamp:

08/19/09 13:33:04 (2 years ago)

Author:

martijn

Message:

Javadoc, style issues in corelib and bio

Location:

trunk

Files:

• bio/src/org/bridgedb/bio/BioDataSource.java (modified) (2 diffs)
• bio/src/org/bridgedb/bio/package.html (added)
• corelib/src/org/bridgedb/IDMapperCapabilities.java (modified) (1 diff)
• corelib/src/org/bridgedb/file/IDMapperFile.java (modified) (4 diffs)
• corelib/src/org/bridgedb/file/IDMapperText.java (modified) (4 diffs)
• corelib/src/org/bridgedb/package.html (modified) (1 diff)
• corelib/src/org/bridgedb/rdb/DBConnectorDerbyServer.java (modified) (2 diffs)

trunk/bio/src/org/bridgedb/bio/BioDataSource.java

@@ -28 +28 @@
 import org.bridgedb.DataSourcePatterns;
 
+/**
+ * Definition of many common biological DataSources.
+ * Meta data about these Data Sources, such as URL templates,
+ * are read from a bundled text file. Call the init() method
+ * at the start of your program to initialize all meta data.  
+ */
 public class BioDataSource 
 {
@@ -454 +460 @@
         
         /**
-         * @returns the species-specific Ensembl DataSource corresponding to a given organism, or null if there isn't one known.
+         * @return the species-specific Ensembl DataSource corresponding to a given organism, or null if there isn't one known.
          * @param org an organism
          */

trunk/corelib/src/org/bridgedb/IDMapperCapabilities.java

@@ -50 +50 @@
      *
      * @param src source data source
-     * @param dest target data source
+     * @param tgt target data source
      * @return true if mapping is supported from src to des
+     * @throws IDMapperException if service is unavailable
      */
-    public boolean isMappingSupported(DataSource src, DataSource tgt) throws IDMapperException ;
+    public boolean isMappingSupported(DataSource src, DataSource tgt) throws IDMapperException;
     
     /**

trunk/corelib/src/org/bridgedb/file/IDMapperFile.java

@@ -41 +41 @@
      * by default.
      * @param reader ID mapping reader
-     * @throws java.io.IDMapperException when failed to read
+     * @throws IDMapperException when failed to read
      */
     public IDMapperFile(final IDMappingReader reader) throws IDMapperException
@@ -82 +82 @@
         Set<DataSource> tgtDss;
         if (tgtDataSources==null) {
-            tgtDss = new HashSet(cap.getSupportedTgtDataSources());
+            tgtDss = new HashSet<DataSource>(cap.getSupportedTgtDataSources());
         } else {
-            tgtDss = new HashSet(tgtDataSources);
+            tgtDss = new HashSet<DataSource>(tgtDataSources);
             tgtDss.retainAll(supportedTgtDatasources);
         }
@@ -108 +108 @@
             Set<Xref> tgtRefs = result.get(srcXref);
             if (tgtRefs==null) {
-                tgtRefs = new HashSet();
+                tgtRefs = new HashSet<Xref>();
                 result.put(srcXref, tgtRefs);
             }
@@ -160 +160 @@
     private boolean isConnected = true;
     // In the case of IDMapperFile, there is no need to discard associated resources.
+    
+    /** {@inheritDoc} */
     public void close() throws IDMapperException { isConnected = false; }
+    /** {@inheritDoc} */
     public boolean isConnected() { return isConnected; }
     

trunk/corelib/src/org/bridgedb/file/IDMapperText.java

@@ -42 +42 @@
         }
         
-        private static class Driver implements org.bridgedb.Driver
+        /** Knows how to instantiate IDMapperText. */
+        private static final class Driver implements org.bridgedb.Driver
         {
-            private Driver() {} // prevent outside instantiation;
+                        /** prevent outside instantiation. */
+            private Driver() {}
                 
+            /** {@inheritDoc} */
             public IDMapper connect(String location) throws IDMapperException
             {
@@ -110 +113 @@
             }
 
+            /** 
+             * parse the separator list part of the connection string.
+             * \@ or \t will be unescaped.
+             * @param config the connection string to parse
+             * @param head the section to look for, either dssep or idsep
+             * @return separators
+             */
             private char[] parseConfig(String config, String head) {
-                Set<Character> delimiters = new HashSet();
+                Set<Character> delimiters = new HashSet<Character>();
                 Pattern p = Pattern.compile(head+"=(.|\\t|\\@),",
                         Pattern.CASE_INSENSITIVE);
@@ -142 +152 @@
         }
 
-    protected final URL url;
-    protected char[] dataSourceDelimiters;
-    protected char[] idDelimiters;
-    protected boolean transitivity;
+    private final URL url;
+    private char[] dataSourceDelimiters;
+    private char[] idDelimiters;
+    private boolean transitivity;
 
     /**
@@ -205 +215 @@
     /**
      * Free search is not supported for delimiter-text file.
+     * This will throw UnsupportedOperationException
+     * @param text ignored
+     * @param limit ignored
+     * @return does not return
+     * @throws IDMapperException will not be thrown
      */
     public Set<Xref> freeSearch (String text, int limit) throws IDMapperException {

trunk/corelib/src/org/bridgedb/package.html

@@ -15 +15 @@
 <p>
 Usually, different DataSources describe the same biological entities. Cross references are
-stored in so called Synonym databases. {@link org.bridgedb.Gdb} has facilities for mapping cross-references
+stored in so called Synonym databases. {@link org.bridgedb.IDMapper} has facilities for mapping cross-references
 and mapping between different DataSources.
 <p>

trunk/corelib/src/org/bridgedb/rdb/DBConnectorDerbyServer.java

@@ -29 +29 @@
 
 /**
- * Database connector that connects to a Derby database server
+ * Database connector that connects to a Derby database server.
  */
 public class DBConnectorDerbyServer extends DBConnector {
@@ -35 +35 @@
         static private String host;
         static private int port;
-        static boolean inited = false;
+        static private boolean inited = false;
         
         /**
-         * Initialize global settings that will be shared by all instances of DBConnectorDerbyServer
-         * @param host  The host on which the database resides
-         * @param port  The port to create the connection on
+         * Initialize global settings that will be shared by all instances of DBConnectorDerbyServer.
+         * @param aHost The host on which the database resides
+         * @param aPort The port to create the connection on
          */
         static public void init (String aHost, int aPort)