Removed obsolete optimize call and documented better

.cproject

@@ -474,6 +474,14 @@
 <useDefaultCommand>true</useDefaultCommand>
 <runAllBuilders>true</runAllBuilders>
 </target>
+<target name="testChordalBayesNet.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+<buildCommand>make</buildCommand>
+<buildArguments/>
+<buildTarget>testChordalBayesNet.run</buildTarget>
+<stopOnError>true</stopOnError>
+<useDefaultCommand>true</useDefaultCommand>
+<runAllBuilders>true</runAllBuilders>
+</target>
 <target name="install" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
 <buildTarget>install</buildTarget>

cpp/ChordalBayesNet.cpp

@@ -7,7 +7,9 @@
 #include <stdarg.h>
 #include <boost/foreach.hpp>
 #include <boost/tuple/tuple.hpp>
+
 #include "ChordalBayesNet.h"
+#include "VectorConfig.h"
 
 using namespace std;
 using namespace gtsam;
@@ -58,28 +60,17 @@ void ChordalBayesNet::erase(const string& key)
 	nodes.erase(key);
 }
 
-/* ************************************************************************* */
-// optimize, i.e. return x = inv(R)*d
 /* ************************************************************************* */
 boost::shared_ptr<VectorConfig> ChordalBayesNet::optimize() const
 {
   boost::shared_ptr<VectorConfig> result(new VectorConfig);
-	result = optimize(result);
-  return result;
-}
-
-/* ************************************************************************* */
-boost::shared_ptr<VectorConfig> ChordalBayesNet::optimize(const boost::shared_ptr<VectorConfig> &c) const
-{
-  boost::shared_ptr<VectorConfig> result(new VectorConfig);
-	result = c;
 	
   /** solve each node in turn in topological sort order (parents first)*/
   BOOST_FOREACH(string key, keys) {
-    const_iterator cg = nodes.find(key); // get node
-    assert( cg != nodes.end() );
-    Vector x = cg->second->solve(*result);                   // Solve it
-    result->insert(key,x);   // store result in partial solution
+    const_iterator cg = nodes.find(key);		// get node
+    assert( cg != nodes.end() );						// make sure it exists
+    Vector x = cg->second->solve(*result);  // Solve for that variable
+    result->insert(key,x);                  // store result in partial solution
   }
   return result;
 }

cpp/ChordalBayesNet.h

@@ -14,7 +14,6 @@
 #include <boost/serialization/list.hpp>
 
 #include "ConditionalGaussian.h"
-#include "VectorConfig.h"
 #include "Testable.h"
 
 namespace gtsam {
@@ -77,9 +76,10 @@ public:
 	const_iterator const begin() const {return nodes.begin();}
 	const_iterator const end()   const {return nodes.end();}
 
-	/** optimize */
+	/**
+	 * optimize, i.e. return x = inv(R)*d
+	 */
 	boost::shared_ptr<VectorConfig> optimize() const;
-	boost::shared_ptr<VectorConfig> optimize(const boost::shared_ptr<VectorConfig> &c) const;
 
 	/** size is the number of nodes */
 	size_t size() const {return nodes.size();}