Fix some docs and visiblity

gtsam/inference/BayesTree.h

@@ -119,13 +119,14 @@ namespace gtsam {
     /** Assignment operator */
     This& operator=(const This& other);
 
+  public:
+  
     /// @name Testable
     /// @{
 
     /** check equality */
     bool equals(const This& other, double tol = 1e-9) const;
 
-  public:
     /** print */
     void print(const std::string& s = "",
         const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
@@ -185,18 +186,19 @@ namespace gtsam {
      */
     sharedBayesNet jointBayesNet(Key j1, Key j2, const Eliminate& function = EliminationTraitsType::DefaultEliminate) const;
 
-   /// @name Graph Display
-   /// @{
+    /// @}   
+    /// @name Graph Display
+    /// @{
 
-   /// Output to graphviz format, stream version.
-   void dot(std::ostream& os, const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
+    /// Output to graphviz format, stream version.
+    void dot(std::ostream& os, const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
 
-   /// Output to graphviz format string.
-   std::string dot(
-       const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
+    /// Output to graphviz format string.
+    std::string dot(
+        const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
 
-   /// output to file with graphviz format.
-   void saveGraph(const std::string& filename,
+    /// output to file with graphviz format.
+    void saveGraph(const std::string& filename,
                   const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
   
     /// @}

gtsam/inference/BayesTreeCliqueBase-inst.h

@@ -104,14 +104,16 @@ namespace gtsam {
   }
 
   /* ************************************************************************* */
-  // The shortcut density is a conditional P(S|R) of the separator of this
-  // clique on the root. We can compute it recursively from the parent shortcut
-  // P(Sp|R) as \int P(Fp|Sp) P(Sp|R), where Fp are the frontal nodes in p
-  /* ************************************************************************* */
-  template<class DERIVED, class FACTORGRAPH>
+  // The shortcut density is a conditional P(S|B) of the separator of this
+  // clique on the root or common ancestor B. We can compute it recursively from
+  // the parent shortcut P(Sp|B) as \int P(Fp|Sp) P(Sp|B), where Fp are the
+  // frontal nodes in p
+  /* *************************************************************************
+   */
+  template <class DERIVED, class FACTORGRAPH>
   typename BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::BayesNetType
-    BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::shortcut(const derived_ptr& B, Eliminate function) const
-  {
+  BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::shortcut(
+      const derived_ptr& B, Eliminate function) const {
     gttic(BayesTreeCliqueBase_shortcut);
     // We only calculate the shortcut when this clique is not B
     // and when the S\B is not empty

gtsam/inference/BayesTreeCliqueBase.h

@@ -190,11 +190,11 @@ namespace gtsam {
 
     friend class BayesTree<DerivedType>;
 
-  protected:
-
     /// Calculate set \f$ S \setminus B \f$ for shortcut calculations
     KeyVector separator_setminus_B(const derived_ptr& B) const;
 
+  protected:
+
     /** Determine variable indices to keep in recursive separator shortcut calculation The factor
      *  graph p_Cp_B has keys from the parent clique Cp and from B. But we only keep the variables
      *  not in S union B. */