Changeset 163

Timestamp:

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

Author:

martijn

Message:

Started implementation of transitive stack
Unfinished methods will return UnsupportedOperationException?

Files:

• trunk/corelib/src/org/bridgedb/IDMapperStack.java (modified) (5 diffs)

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

@@ -66 +66 @@
     }
     
+    private boolean isTransitive = false;
+    
+    /**
+     * Set Transitivity mode, where all mappings are combined to infer
+     * second degree mappings.
+     * @param value true or false
+     */
+    public void setTransitive(boolean value)
+    {
+        isTransitive = value;
+    }
+    
+    /**
+     * @return true if the stack is in transitive mode
+     */
+    public boolean getTransitive()
+    {
+        return isTransitive;
+    }
+    
         /**
          * Remove an idMapper from the stack.
@@ -244 +264 @@
                         Set<DataSource> tgtDataSources) throws IDMapperException 
         {
+                if (isTransitive)
+                {
+                        return mapIDtransitive(srcXrefs, tgtDataSources);
+                }
+                else
+                {
+                        return mapIDnormal(srcXrefs, tgtDataSources);
+                }
+        }
+
+        /**
+         * helper method to map Id's in non-transitive mode.
+         * @param srcXrefs mapping source
+         * @param tgtDataSources target data sources
+         * @return mapping result
+         * @throws IDMapperException if one of the children fail
+         */
+        private Map<Xref, Set<Xref>> mapIDnormal(Set<Xref> srcXrefs,
+                        Set<DataSource> tgtDataSources) throws IDMapperException 
+        {
                 Map<Xref, Set<Xref>> result = new HashMap<Xref, Set<Xref>>();
                 
@@ -265 +305 @@
         }
 
+        /**
+         * helper method to map Id's in transitive mode.
+         * @param srcXrefs mapping source
+         * @param tgtDataSources target data sources
+         * @return mapping result
+         * @throws IDMapperException if one of the children fail
+         */
+        private Map<Xref, Set<Xref>> mapIDtransitive(Set<Xref> srcXrefs,
+                        Set<DataSource> tgtDataSources) throws IDMapperException 
+        {
+                throw new UnsupportedOperationException();
+        }
+
         /** {@inheritDoc} */
         public Set<String> getAttributes(Xref ref, String attrname)
@@ -325 +378 @@
         public Set<Xref> mapID(Xref ref, Set<DataSource> resultDs) throws IDMapperException 
         {
+                if (isTransitive)
+                {
+                        return mapIDtransitive (ref, resultDs);
+                }
+                else
+                {
+                        return mapIDnormal (ref, resultDs);
+                }
+        }
+        
+        
+        /**
+         * helper method to map Id's in transitive mode.
+         * @param ref Xref to map
+         * @param resultDs target data sources
+         * @return mapping result
+         * @throws IDMapperException if one of the children fail
+         */
+        private Set<Xref> mapIDtransitive(Xref ref, Set<DataSource> resultDs) throws IDMapperException 
+        {
+                throw new UnsupportedOperationException();
+        }
+        
+        /**
+         * helper method to map Id's in transitive mode.
+         * @param ref Xref to map
+         * @param resultDs target data sources
+         * @return mapping result
+         * @throws IDMapperException if one of the children fail
+         */
+        private Set<Xref> mapIDnormal(Xref ref, Set<DataSource> resultDs) throws IDMapperException 
+        {
                 Set<Xref> result = new HashSet<Xref>();
                 for (IDMapper child : gdbs)
                 {
-                        if (child != null && child instanceof AttributeMapper && child.isConnected())
+                        if (child != null && child.isConnected())
                         {
                                 result.addAll (child.mapID(ref, resultDs));
@@ -336 +421 @@
         }
         
-        
 }