added cmake option to set hidden visibility for gcc compiles; fixed several...

added cmake option to set hidden visibility for gcc compiles; fixed several missing visibility declarations

CMakeLists.txt

@@ -50,6 +50,7 @@ option(DEPLOYMENT "switch on deployment settings" OFF)
 option(COMPILE_TESTS "whether unit tests should be compiled by default" OFF)
 option(ENABLE_STATIC "whether static libraries should be compiled" OFF)
 option(DEBIAN_STYLE_LIBEXEC "whether 'libexec' should be put under 'lib/openstructure" OFF)
+option(HIDDEN_VISIBILITY "on gcc, use -fvisibility=hidden" OFF)
 
 if (CXX)
   set(CMAKE_CXX_COMPILER ${CXX})
@@ -250,9 +251,14 @@ if (CMAKE_COMPILER_IS_GNUCXX)
   # with multiple -fno-strict-aliasing flags, triggering a complete rebuild whenever
   # cmake is run
   set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing")
+  if(HIDDEN_VISIBILITY) 
+    set (CMAKE_CXX_FLAGS "-fvisibility=hidden")
+    set (_HIDDEN_VIS ON)
+  else(HIDDEN_VISIBILITY)
+    set (_HIDDEN_VIS OFF)
+  endif(HIDDEN_VISIBILITY)
 endif()
 
-
 # basic environment
 include_directories(${Boost_INCLUDE_DIRS} 
                     ${FFTW_INCLUDE_PATH} 
@@ -313,5 +319,6 @@ message(STATUS
         "   Compound Lib                   (-DCOMPOUND_LIB) : ${_COMP_LIB}\n"
         "   TMAlign and TMScore         (-DCOMPILE_TMTOOLS) : ${_TM_TOOLS}\n"
         "   Static Libraries              (-DENABLE_STATIC) : ${ENABLE_STATIC}\n"
-        "   Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}" )
+        "   Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}\n"
+        "   Hidden object visibility  (-DHIDDEN_VISIBILITY) : ${_HIDDEN_VIS}")
 

modules/conop/src/compound.hh

@@ -29,7 +29,7 @@
 
 namespace ost { namespace conop {
 
-struct Date {
+struct DLLEXPORT_OST_CONOP Date {
   Date(int y, int m, int d):
     year(y), month(m), day(d)
   { }
@@ -68,7 +68,7 @@ struct Date {
   int day;  
 };
 
-struct AtomSpec {
+struct DLLEXPORT_OST_CONOP AtomSpec {
   AtomSpec()
     : ordinal(0), is_leaving(false) {
   }
@@ -88,7 +88,7 @@ struct AtomSpec {
   }
 };
 
-struct BondSpec {
+struct DLLEXPORT_OST_CONOP BondSpec {
   BondSpec()
     : atom_one(0), atom_two(0), order(1) {
 

modules/geom/src/composite3.hh

@@ -27,6 +27,7 @@
 #include "mat3.hh"
 #include "quat.hh"
 
+#include "module_config.hh"
 
 /*
   composite classes in 3D space
@@ -47,7 +48,7 @@ private:
   Vec3 ori_,dir_;
 };
 
-std::ostream& operator<<(std::ostream& s, const Line3& l);
+DLLEXPORT_OST_GEOM std::ostream& operator<<(std::ostream& s, const Line3& l);
 
 class DLLEXPORT_OST_GEOM Plane {
 public:
@@ -80,7 +81,7 @@ private:
   Real p_;
 };
 
-class DLLEXPORT Sphere {
+class DLLEXPORT_OST_GEOM Sphere {
 public:
   Sphere();
   Sphere(const Vec3& origin, Real r);
@@ -98,7 +99,7 @@ private:
 ///     half extent
 /// 
 /// \relates Cuboid
-class DLLEXPORT CuboidAxis {
+class DLLEXPORT_OST_GEOM CuboidAxis {
 public:
   CuboidAxis(): axis_(), half_extent_(0.0)
   { }
@@ -112,7 +113,7 @@ private:
 };
 
 /// \brief arbitrary oriented bounding cuboid
-class DLLEXPORT Cuboid {
+class DLLEXPORT_OST_GEOM Cuboid {
 public:
   Cuboid();
   Cuboid(const Vec3& center, const CuboidAxis& a, 
@@ -140,7 +141,7 @@ private:
   CuboidAxis      axes_[3];
 };
 
-class DLLEXPORT Rotation3
+class DLLEXPORT_OST_GEOM Rotation3
 {
 public:
   Rotation3();
@@ -184,8 +185,8 @@ private:
 
 typedef std::vector<Rotation3> Rotation3List;
 
-DLLEXPORT Rotation3List ImportEulerAngles (const boost::filesystem::path& loc);
-DLLEXPORT void ExportEulerAngles (const Rotation3List& rot_list,
+DLLEXPORT_OST_GEOM Rotation3List ImportEulerAngles (const boost::filesystem::path& loc);
+DLLEXPORT_OST_GEOM void ExportEulerAngles (const Rotation3List& rot_list,
                                   const boost::filesystem::path& loc);
 
 } // ns

modules/geom/src/vecmat3_op.hh

@@ -211,15 +211,15 @@ inline Real DistanceWithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_ve
   return sqrt(Distance2WithPBC(v1, v2, basis_vec));
 }
 //! returns the minimal distance between the points in two Vec3List
-Real MinDistance(const Vec3List& l1, const Vec3List& l2);
+DLLEXPORT_OST_GEOM Real MinDistance(const Vec3List& l1, const Vec3List& l2);
 //! returns the minimal distance between the points in two Vec3List 
 //  with periodic boundaries in x,y,z given in basis_vec
-Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec);
+DLLEXPORT_OST_GEOM Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec);
 
 //!wraps a vector in a box with periodic boundaries
-Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec);
-//!wraps all the verctors in a Vec3List in a box with periodic boundaries
-Vec3List WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& basis_vec);
+DLLEXPORT_OST_GEOM Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec);
+//!wraps all the vectors in a Vec3List in a box with periodic boundaries
+DLLEXPORT_OST_GEOM Vec3List WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& basis_vec);
 
   
 } // ns

modules/mol/alg/src/filter_clashes.hh

@@ -25,7 +25,7 @@
 namespace ost { namespace mol { namespace alg {
 
 /// \brief List of reference atom-atom distances to detect clashes between non-bonded atoms 
-class ClashingDistances
+class DLLEXPORT_OST_MOL_ALG ClashingDistances
 {
 
 public:
@@ -61,7 +61,7 @@ private:
 /// \brief List of stereo chemical parameters (Bonds and angles)
 ///
 /// For each item (bond or angle in a specific residue), stores the mean and standard deviation 
-class StereoChemicalParams
+class DLLEXPORT_OST_MOL_ALG StereoChemicalParams
 {
 
 public:

modules/mol/alg/src/local_dist_diff_test.hh

@@ -28,7 +28,7 @@ namespace ost { namespace mol { namespace alg {
 /// \brief Contains the infomation needed to uniquely identify an atom in a structure
 ///
 /// Used by the the Local Distance Difference Test classes and functions
-class UniqueAtomIdentifier
+class DLLEXPORT_OST_MOL_ALG UniqueAtomIdentifier
 {
   
 public:
@@ -169,7 +169,7 @@ Real DLLEXPORT_OST_MOL_ALG LDDTHA(EntityView& v, const GlobalRDMap& global_dist_
 /// \brief Creates a list of distances to check during a Local Difference Distance Test
 ///
 /// Requires a reference structure and an inclusion radius (max_dist)
-GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist);
+GlobalRDMap DLLEXPORT_OST_MOL_ALG CreateDistanceList(const EntityView& ref,Real max_dist);
 
 /// \brief Creates a list of distances to check during a Local Difference Distance Test starting from multiple reference structures
 ///
@@ -193,17 +193,17 @@ GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist);
 /// must be passed to the function. These parameters do not influence the output distance list, which always includes all distances
 /// within the provided max_dist (to make it consistent with the single-reference corresponding function). However, the parameters are used when
 /// dealing with the naming convention of residues with ambiguous nomenclature. 
-GlobalRDMap CreateDistanceListFromMultipleReferences(const std::vector<EntityView>& ref_list,std::vector<Real>& cutoff_list, int sequence_separation, Real max_dist);
+GlobalRDMap DLLEXPORT_OST_MOL_ALG CreateDistanceListFromMultipleReferences(const std::vector<EntityView>& ref_list,std::vector<Real>& cutoff_list, int sequence_separation, Real max_dist);
 
 /// \brief Prints all distances in a global distance list to standard output
-void PrintGlobalRDMap(const GlobalRDMap& glob_dist_list);
+void DLLEXPORT_OST_MOL_ALG PrintGlobalRDMap(const GlobalRDMap& glob_dist_list);
 
 /// \brief Prints all distances in a residue distance list to standard output
-void PrintResidueRDMap(const ResidueRDMap& res_dist_list);
+void DLLEXPORT_OST_MOL_ALG PrintResidueRDMap(const ResidueRDMap& res_dist_list);
 
 // required by some helper function. Cannot reuse similar functions in other modules without creating
 // circular dependencies
-bool IsStandardResidue(String rn);
+bool DLLEXPORT_OST_MOL_ALG IsStandardResidue(String rn);
 
 }}}
 

modules/mol/base/src/chain_type.hh

@@ -22,6 +22,8 @@
 #include <ost/base.hh>
 #include <ost/string_ref.hh>
 
+#include "module_config.hh"
+
 namespace ost { namespace mol {
 
 /// \enum different kinds of chains
@@ -46,7 +48,7 @@ typedef enum {
 ///
 /// \return The ChainType corresponding to the input, throws a
 ///         std::runtime_error on unknown type
-ChainType ChainTypeFromString(const StringRef identifier);
+ChainType DLLEXPORT_OST_MOL ChainTypeFromString(const StringRef identifier);
 
 /// \brief Create a ChainType item for a given string
 ///
@@ -54,7 +56,7 @@ ChainType ChainTypeFromString(const StringRef identifier);
 ///
 /// \return The ChainType corresponding to the input, throws a
 ///         std::runtime_error on unknown type
-ChainType ChainTypeFromString(const String& identifier);
+ChainType DLLEXPORT_OST_MOL ChainTypeFromString(const String& identifier);
 
 /// \brief Return the String identifier for a given type
 ///
@@ -62,7 +64,7 @@ ChainType ChainTypeFromString(const String& identifier);
 ///
 /// \return String corresponding to the input, throws a std::runtime_error on
 ///         unknown type
-String StringFromChainType(ChainType type);
+String DLLEXPORT_OST_MOL StringFromChainType(ChainType type);
 
 }} //ns
 

modules/mol/base/src/coord_frame.hh

@@ -216,31 +216,31 @@ public:
     This function returns a vector containing the atom indices of the atoms in an EntityView;
     it is used to accelerate the extraction of information from a trajectory
   */
-  void GetIndices(const EntityView& sele, std::vector<unsigned long>& indices);
+  DLLEXPORT_OST_MOL void GetIndices(const EntityView& sele, std::vector<unsigned long>& indices);
 
   /*!
     This function returns a vector containing the atom masses of the atoms in an EntityView;
     it is used together with GetIndices to accelerate the extraction of RMSD from a trajectory
   */
-  void GetMasses(const EntityView& sele, std::vector<Real>& masses);
+  DLLEXPORT_OST_MOL void GetMasses(const EntityView& sele, std::vector<Real>& masses);
 
   //! conveniece for GetIndices and GetMasses in one call
-  void GetIndicesAndMasses(const EntityView& sele,
-                           std::vector<unsigned long>& indices,
-                           std::vector<Real>& masses);
+  DLLEXPORT_OST_MOL void GetIndicesAndMasses(const EntityView& sele,
+                                             std::vector<unsigned long>& indices,
+                                             std::vector<Real>& masses);
 
   //! Writes the positions of all atoms in the EntityView into the provided vec3 list
-  void GetPositions(const EntityView& sele, std::vector<geom::Vec3>& ref_pos);
-
+  DLLEXPORT_OST_MOL void GetPositions(const EntityView& sele, std::vector<geom::Vec3>& ref_pos);
+  
   //! Writes the indices of all atoms in the EntityView into the provided list
-  void GetCaIndices(const EntityView& segment, std::vector<unsigned long>& indices_ca);
-
+  DLLEXPORT_OST_MOL void GetCaIndices(const EntityView& segment, std::vector<unsigned long>& indices_ca);
+  
   //! Writes the backbone indices of all residues in the EntityView into the provided list
-  void GetCaCONIndices(const EntityView& segment, 
-                       std::vector<unsigned long>& indices_ca, 
-                       std::vector<unsigned long>& indices_c,
-                       std::vector<unsigned long>& indices_o, 
-                       std::vector<unsigned long>& indices_n);
+  DLLEXPORT_OST_MOL void GetCaCONIndices(const EntityView& segment, 
+                                         std::vector<unsigned long>& indices_ca, 
+                                         std::vector<unsigned long>& indices_c,
+                                         std::vector<unsigned long>& indices_o, 
+                                         std::vector<unsigned long>& indices_n);
 
 
 }}