From f254484afa4ff3e9cda1d4f30fb17c88a910b9c6 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 22 Apr 2010 08:51:09 +0000
Subject: [PATCH] sequences are now generic property containers

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2101 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
 modules/base/src/CMakeLists.txt               |   2 +-
 .../export_helper}/generic_property_def.hh    |  30 ++--
 modules/base/src/generic_property.hh          | 128 ++++++++-------
 modules/mol/base/pymod/export_atom.cc         |   3 +-
 modules/mol/base/pymod/export_bond.cc         |   4 +-
 modules/mol/base/pymod/export_chain.cc        |   4 +-
 modules/mol/base/pymod/export_entity.cc       |   2 +-
 modules/mol/base/pymod/export_residue.cc      |   7 +-
 modules/mol/base/src/atom_base.hh             |   2 +-
 modules/mol/base/src/bond_handle.hh           |   2 +-
 modules/mol/base/src/chain_base.hh            |   2 +-
 modules/mol/base/src/entity_base.hh           |   2 +-
 modules/mol/base/src/residue_base.hh          |   2 +-
 modules/seq/base/pymod/export_sequence.cc     |  74 +++++----
 modules/seq/base/src/impl/sequence_impl.hh    |   4 +-
 modules/seq/base/src/sequence_handle.cc       | 154 +++++++++++++++++-
 modules/seq/base/src/sequence_handle.hh       |  97 ++++++++++-
 17 files changed, 382 insertions(+), 137 deletions(-)
 rename modules/{mol/base/pymod => base/src/export_helper}/generic_property_def.hh (89%)

diff --git a/modules/base/src/CMakeLists.txt b/modules/base/src/CMakeLists.txt
index 5dbc9b808..b30a8312b 100644
--- a/modules/base/src/CMakeLists.txt
+++ b/modules/base/src/CMakeLists.txt
@@ -31,7 +31,7 @@ fixed_string.hh
 )
 
 module(NAME base SOURCES ${OST_BASE_SOURCES} 
-       HEADERS ${OST_BASE_HEADERS}
+       HEADERS generic_property_def.hh IN_DIR export_helper ${OST_BASE_HEADERS}
        DEPENDS_ON geom
        HEADER_OUTPUT_DIR ost)
 
diff --git a/modules/mol/base/pymod/generic_property_def.hh b/modules/base/src/export_helper/generic_property_def.hh
similarity index 89%
rename from modules/mol/base/pymod/generic_property_def.hh
rename to modules/base/src/export_helper/generic_property_def.hh
index fbed012fb..4b8241be7 100644
--- a/modules/mol/base/pymod/generic_property_def.hh
+++ b/modules/base/src/export_helper/generic_property_def.hh
@@ -24,8 +24,8 @@
   Author: Marco Biasini
  */
  
-template <typename C>
-void generic_prop_def(class_<C>& bp_class)
+template <typename C, typename O>
+void const_generic_prop_def(O& bp_class)
 {
   bool (C::*get_bool1)(const String&, bool) const=&C::GetGenericBoolProperty;
   bool (C::*get_bool2)(const String&)  const=&C::GetGenericBoolProperty;
@@ -40,6 +40,24 @@ void generic_prop_def(class_<C>& bp_class)
   String (C::*get_str2)(const String&) const=&C::GetGenericStringProperty;  
   bp_class
     .def("HasGenericProperty", &C::HasGenericProperty)
+    .def("GetGenericPropertyStringRepresentation",
+         &C::GetGenericPropertyStringRepresentation)          
+    .def("GetGenericBoolProperty", get_bool1)
+    .def("GetGenericBoolProperty", get_bool2)        
+    .def("GetGenericFloatProperty", get_float1)
+    .def("GetGenericFloatProperty", get_float2)    
+    .def("GetGenericIntProperty", get_int1)
+    .def("GetGenericIntProperty", get_int2)    
+    .def("GetGenericStringProperty", get_str1)
+    .def("GetGenericStringProperty", get_str2)    
+  ;
+}
+
+template <typename C, typename O>
+void generic_prop_def(O& bp_class)
+{
+  const_generic_prop_def<C, O>(bp_class);
+  bp_class
     .def("SetGenericBoolProperty",
          &C::SetGenericBoolProperty)
     .def("ClearGenericProperties",  
@@ -52,14 +70,6 @@ void generic_prop_def(class_<C>& bp_class)
         &C::SetGenericIntProperty)
     .def("SetGenericStringProperty",
         &C::SetGenericStringProperty)          
-    .def("GetGenericBoolProperty", get_bool1)
-    .def("GetGenericBoolProperty", get_bool2)        
-    .def("GetGenericFloatProperty", get_float1)
-    .def("GetGenericFloatProperty", get_float2)    
-    .def("GetGenericIntProperty", get_int1)
-    .def("GetGenericIntProperty", get_int2)    
-    .def("GetGenericStringProperty", get_str1)
-    .def("GetGenericStringProperty", get_str2)    
   ;
 }
 
diff --git a/modules/base/src/generic_property.hh b/modules/base/src/generic_property.hh
index 66c9212ad..3fe6f037a 100644
--- a/modules/base/src/generic_property.hh
+++ b/modules/base/src/generic_property.hh
@@ -127,11 +127,11 @@ public:
 private:
   mutable PropertyMap* map_;
 };  
-  
-/// \brief base class for the handler classes
+
 template <typename H>
-class  TEMPLATE_EXPORT GenericPropertyContainer
-{
+class TEMPLATE_EXPORT ConstGenericPropertyContainer {
+protected:
+  
   template<typename T>
   T gp_get(const String& key) const {
     if(HasGenericProperty(key)) {
@@ -150,19 +150,21 @@ class  TEMPLATE_EXPORT GenericPropertyContainer
     }
     return def;
   }
+  GenericPropertyContainerImpl* GetImpl() 
+  {
+    return static_cast<H*>(this)->GpImpl();
+  }
 
-
+  const GenericPropertyContainerImpl* GetImpl() const
+  {
+    return static_cast<const H*>(this)->GpImpl();
+  }  
 public:
   /// \brief checks existence of property
   bool HasGenericProperty(const String& key) const {
-    return GetImpl()->HasGenericProperty(key);
+    return this->GetImpl()->HasGenericProperty(key);
   }
-
-  void ClearGenericProperties()
-  {
-    GetImpl()->ClearGenericProperties();
-  }
-
+    
   /// \brief returns a String representation of stored value
   /// 
   /// returns the String representation of this property, or the empty String if 
@@ -174,50 +176,25 @@ public:
   {
     if(!HasGenericProperty(key)) return "";
     std::ostringstream rep("");
-    rep << GetImpl()->GenericProperty(key);
+    rep << this->GetImpl()->GenericProperty(key);
     return rep.str();
-  }
-  
-  /// \brief sets String property
-  void SetGenericStringProperty(const String& key, const String& value)
-  {
-    GetImpl()->GenericProperty(key)=value;
-  }
-
-  /// \brief sets floating point property
-  void SetGenericFloatProperty(const String& key, Real value)
-  {
-    GetImpl()->GenericProperty(key)=value;
-  }
-
-  /// \brief sets integer property
-  void SetGenericIntProperty(const String& key, int value)
-  {
-    GetImpl()->GenericProperty(key)=value;
-  }
-
-  /// \ brief sets boolean property
-  void SetGenericBoolProperty(const String& key, bool value)
-  {
-    GetImpl()->GenericProperty(key)=value;
-  }
-
-  /// \brief returns String property, raises an exception if it does not exist
-  String GetGenericStringProperty(const String& key) const
-  {
-    return gp_get<String>(key);
-  }
+  }  
+    /// \brief returns String property, raises an exception if it does not exist
+    String GetGenericStringProperty(const String& key) const
+    {
+      return this->gp_get<String>(key);
+    }
 
   /// \brief returns floating point property, raises an exception if it does 
   ///     not exist
   Real GetGenericFloatProperty(const String& key) const
   {
     if(HasGenericProperty(key)) {
-      GenericPropertyValue value=GetImpl()->GenericProperty(key);
+      GenericPropertyValue value=this->GetImpl()->GenericProperty(key);
       if (value.which()==1) {
-        return boost::get<Real>(GetImpl()->GenericProperty(key));
+        return boost::get<Real>(this->GetImpl()->GenericProperty(key));
       } else if (value.which()==2) {
-        return boost::get<int>(GetImpl()->GenericProperty(key));
+        return boost::get<int>(this->GetImpl()->GenericProperty(key));
       }
       std::ostringstream m("");
       m << "property '" << key << "' is not numeric";
@@ -229,29 +206,30 @@ public:
     }
   }
 
+
   /// \brief returns integer property, raises an exception if it does not exist
   int GetGenericIntProperty(const String& key) const
   {
-    return gp_get<int>(key);
+    return this->gp_get<int>(key);
   }
 
   /// \brief returns boolean property, raises an exception if it does not exist
   bool GetGenericBoolProperty(const String& key) const
   {
-    return gp_get<bool>(key);
+    return this->gp_get<bool>(key);
   }
 
   /// \brief returns String property, or the given default if it does not exist
   String GetGenericStringProperty(const String& key, const String& def) const
   {
-    return gp_get<String>(key,def);
+    return this->gp_get<String>(key,def);
   }
 
   /// \brief returns floating point property, or the given default if it does
   ///     not exist
   Real GetGenericFloatProperty(const String& key, Real def) const
   {
-    if(HasGenericProperty(key)) {
+    if(this->HasGenericProperty(key)) {
       GenericPropertyValue value=GetImpl()->GenericProperty(key);
       if (value.which()==1) {
         return boost::get<Real>(GetImpl()->GenericProperty(key));
@@ -269,29 +247,55 @@ public:
   /// \brief returns integer property, or the given default if it does not exist
   int GetGenericIntProperty(const String& key, int def) const
   {
-    return gp_get<int>(key, def);
+    return this->gp_get<int>(key, def);
   }
 
   /// \brief returns boolean property, or the given default if it does not exist
   bool GetGenericBoolProperty(const String& key, bool def) const
   {
-    return gp_get<bool>(key, def);
+    return this->gp_get<bool>(key, def);
   }
-  
+
   std::map<String,GenericPropertyValue> GetGenericPropertyMap() const
   {
-    return GetImpl()->GetGenericPropertyMap();
-  }
-protected:
-  GenericPropertyContainerImpl* GetImpl() 
+    return this->GetImpl()->GetGenericPropertyMap();
+  }  
+};
+
+/// \brief base class for the handler classes
+template <typename H>
+class  TEMPLATE_EXPORT GenericPropertyContainer : 
+   public ConstGenericPropertyContainer<H>
+{
+public:
+  void ClearGenericProperties()
   {
-    return static_cast<H*>(this)->GpImpl();
+    this->GetImpl()->ClearGenericProperties();
   }
   
-  const GenericPropertyContainerImpl* GetImpl() const
+  /// \brief sets String property
+  void SetGenericStringProperty(const String& key, const String& value)
   {
-    return static_cast<const H*>(this)->GpImpl();
-  }  
+    this->GetImpl()->GenericProperty(key)=value;
+  }
+
+  /// \brief sets floating point property
+  void SetGenericFloatProperty(const String& key, Real value)
+  {
+    this->GetImpl()->GenericProperty(key)=value;
+  }
+
+  /// \brief sets integer property
+  void SetGenericIntProperty(const String& key, int value)
+  {
+    this->GetImpl()->GenericProperty(key)=value;
+  }
+
+  /// \ brief sets boolean property
+  void SetGenericBoolProperty(const String& key, bool value)
+  {
+    this->GetImpl()->GenericProperty(key)=value;
+  }
 };
 
 
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index ccebbfb0a..bb8c9fe31 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -26,7 +26,8 @@ using namespace boost::python;
 using namespace ost;
 using namespace ost::mol;
 
-#include "generic_property_def.hh"
+#include <ost/export_helper/generic_property_def.hh>
+
 void export_Atom()
 {
   class_<AtomBase> atom_base("AtomBase", no_init);
diff --git a/modules/mol/base/pymod/export_bond.cc b/modules/mol/base/pymod/export_bond.cc
index e22adf98e..ddfde4721 100644
--- a/modules/mol/base/pymod/export_bond.cc
+++ b/modules/mol/base/pymod/export_bond.cc
@@ -26,8 +26,8 @@ using namespace boost::python;
 
 using namespace ost;
 using namespace ost::mol;
-#include "generic_property_def.hh"
-#include "generic_property_def.hh"
+#include <ost/export_helper/generic_property_def.hh>
+
 void export_Bond()
 {
   void (BondHandle::* apply1)(EntityVisitor&) = &BondHandle::Apply;
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 71896935b..57e717eba 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -24,9 +24,7 @@ using namespace boost::python;
 
 using namespace ost;
 using namespace ost::mol;
-#include "generic_property_def.hh"
-
-#include "generic_property_def.hh"
+#include <ost/export_helper/generic_property_def.hh>
 
 namespace {
   typedef void (ChainHandle::*RnumMethod)(const ResNum&);
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index a3624877a..733c867d6 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -28,7 +28,7 @@ using namespace boost::python;
 using namespace ost;
 using namespace ost::mol;
 
-#include "generic_property_def.hh"
+#include <ost/export_helper/generic_property_def.hh>
 
 namespace {
 EntityHandle create1() {  return CreateEntity(); }
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 1ff735cf6..66214c7d4 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -25,9 +25,8 @@ using namespace boost::python;
 
 using namespace ost;
 using namespace ost::mol;
-#include "generic_property_def.hh"
 
-#include "generic_property_def.hh"
+#include <ost/export_helper/generic_property_def.hh>
 
 namespace {
   typedef EntityView (ResidueHandle::*QueryMethod)(const Query&, uint) const;
@@ -118,9 +117,7 @@ void export_Residue()
                                  return_value_policy<copy_const_reference>()))
     .add_property("qualified_name", &ResidueBase::GetQualifiedName)
   ;
-  generic_prop_def(residue_base);
-
-  generic_prop_def(residue_base);
+  generic_prop_def<ResidueBase>(residue_base);
 
   class_<ResidueHandle, bases<ResidueBase> >("ResidueHandle", init<>())
     .def("GetChain",&ResidueHandle::GetChain)
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 3b10fb8ca..71ec8dbe8 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -49,7 +49,7 @@ public:
   AtomBase();
   AtomBase(const impl::AtomImplPtr& impl);
 public:  
-  friend class GenericPropertyContainer<AtomBase>;  
+  friend class ConstGenericPropertyContainer<AtomBase>;  
   ///\brief Get atom name. 
   ///
   /// In Python the atom name may also be accesssed over the property \c Name
diff --git a/modules/mol/base/src/bond_handle.hh b/modules/mol/base/src/bond_handle.hh
index b23ca0679..114e033a6 100644
--- a/modules/mol/base/src/bond_handle.hh
+++ b/modules/mol/base/src/bond_handle.hh
@@ -34,7 +34,7 @@ namespace ost { namespace mol {
 class DLLEXPORT_OST_MOL BondHandle: 
     public GenericPropertyContainer<BondHandle> {
 public:
-  friend class GenericPropertyContainer<BondHandle>;  
+  friend class ConstGenericPropertyContainer<BondHandle>;  
   /// necessary dummy ctor, creates invalid handle
   BondHandle();
   /// ctor for internal use, in public interface for convenience purposes
diff --git a/modules/mol/base/src/chain_base.hh b/modules/mol/base/src/chain_base.hh
index 4e27e79ed..c8de6551b 100644
--- a/modules/mol/base/src/chain_base.hh
+++ b/modules/mol/base/src/chain_base.hh
@@ -42,7 +42,7 @@ public: // constructors
   ChainBase();
   ChainBase(const impl::ChainImplPtr& impl);
 public:
-  friend class GenericPropertyContainer<ChainBase>;  
+  friend class ConstGenericPropertyContainer<ChainBase>;
   String GetName() const;
   /// \name Handle validity
   //@{
diff --git a/modules/mol/base/src/entity_base.hh b/modules/mol/base/src/entity_base.hh
index 9cb68a0c8..05228c56f 100644
--- a/modules/mol/base/src/entity_base.hh
+++ b/modules/mol/base/src/entity_base.hh
@@ -30,7 +30,7 @@ namespace ost { namespace mol {
 class DLLEXPORT_OST_MOL EntityBase: 
   public GenericPropertyContainer<EntityBase> {
 public:
-  friend class GenericPropertyContainer<EntityBase>;
+  friend class ConstGenericPropertyContainer<EntityBase>;
   EntityBase(const impl::EntityImplPtr& impl);
   EntityBase();
   
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index da5cd0525..0aabe77a3 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -63,7 +63,7 @@ public:
   ResidueBase(const impl::ResidueImplPtr& impl);
   ResidueBase(const ResidueBase& rhs);
 public:
-  friend class GenericPropertyContainer<ResidueBase>;
+  friend class ConstGenericPropertyContainer<ResidueBase>;
   /// \brief return residue number
   const ResNum& GetNumber() const;
 
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index ce05be244..60947f4cb 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -22,6 +22,8 @@
 #include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 using namespace boost::python;
 
+#include <ost/generic_property.hh>
+#include <ost/export_helper/generic_property_def.hh>
 #include <ost/info/info.hh>
 #include <ost/mol/mol.hh>
 #include <ost/seq/sequence_handle.hh>
@@ -145,46 +147,54 @@ RevRegionRangeIter iter_range3(AlignedRegion& aln_region)
   return RevRegionRangeIter(aln_region.begin(), aln_region.end());
 }
 
-}
-
-void export_sequence()
+template <typename C, typename O>
+void const_seq_handle_def(O& bp_class)
 {
-  class_<ConstSequenceHandle>("ConstSequenceHandle", init<>())
-    .def("GetResidueIndex", &ConstSequenceHandle::GetResidueIndex)
-    .def("GetPos", &ConstSequenceHandle::GetPos)
-    .def("GetLength", &ConstSequenceHandle::GetLength)
-    .def("GetResidue", &ConstSequenceHandle::GetResidue)
-    .def("GetOneLetterCode", &ConstSequenceHandle::GetOneLetterCode)
-    .def("__getitem__", &ConstSequenceHandle::GetOneLetterCode)
-    .def("GetSequenceOffset", &ConstSequenceHandle::GetSequenceOffset)
-    .def("Copy", &ConstSequenceHandle::Copy)
-    .def("GetFirstNonGap", &ConstSequenceHandle::GetFirstNonGap)
-    .def("GetLastNonGap", &ConstSequenceHandle::GetLastNonGap)
-    .add_property("first_non_gap", &SequenceHandle::GetFirstNonGap)
-    .add_property("last_non_gap", &SequenceHandle::GetLastNonGap)
-    .def("GetAttachedView", &ConstSequenceHandle::GetAttachedView)
-    .def("GetGaplessString", &ConstSequenceHandle::GetGaplessString)
-    .def("GetString", &ConstSequenceHandle::GetString,
+  bp_class
+    .def("GetResidueIndex", &C::GetResidueIndex)
+    .def("GetPos", &C::GetPos)
+    .def("GetLength", &C::GetLength)
+    .def("GetResidue", &C::GetResidue)
+    .def("GetOneLetterCode", &C::GetOneLetterCode)
+    .def("__getitem__", &C::GetOneLetterCode)
+    .def("GetSequenceOffset", &C::GetSequenceOffset)
+    .def("Copy", &C::Copy)
+    .def("GetFirstNonGap", &C::GetFirstNonGap)
+    .def("GetLastNonGap", &C::GetLastNonGap)
+    .add_property("first_non_gap", &C::GetFirstNonGap)
+    .add_property("last_non_gap", &C::GetLastNonGap)
+    .def("GetAttachedView", &C::GetAttachedView)
+    .def("GetGaplessString", &C::GetGaplessString)
+    .def("GetString", &C::GetString,
          return_value_policy<copy_const_reference>())
-         .def("GetName", &ConstSequenceHandle::GetName,
+         .def("GetName", &C::GetName,
               return_value_policy<copy_const_reference>())
-    .def("HasAttachedView", &ConstSequenceHandle::HasAttachedView)
-    .def("__len__", &SequenceHandle::GetLength)
-    .add_property("length", &SequenceHandle::GetLength)
-    .add_property("attached_view", &ConstSequenceHandle::GetAttachedView)
+    .def("HasAttachedView", &C::HasAttachedView)
+    .def("__len__", &C::GetLength)
+    .add_property("length", &C::GetLength)
+    .add_property("attached_view", &C::GetAttachedView)
     .add_property("name",
-                  make_function(&ConstSequenceHandle::GetName,
+                  make_function(&C::GetName,
                                 return_value_policy<copy_const_reference>()))
-    .add_property("sequence_offset", &ConstSequenceHandle::GetSequenceOffset)
-    .add_property("gapless_string", &ConstSequenceHandle::GetGaplessString)
+    .add_property("sequence_offset", &C::GetSequenceOffset)
+    .add_property("gapless_string", &C::GetGaplessString)
     .add_property("string",
-                  make_function(&ConstSequenceHandle::GetString,
+                  make_function(&C::GetString,
                                 return_value_policy<copy_const_reference>()))
-    .def("__str__", &ConstSequenceHandle::GetString,
+    .def("__str__", &C::GetString,
          return_value_policy<copy_const_reference>())
   ;
+}
 
-  class_<SequenceHandle, bases<ConstSequenceHandle> >("SequenceHandle", init<>())
+}
+
+void export_sequence()
+{
+  class_<ConstSequenceHandle> const_seq("ConstSequenceHandle", init<>());
+  const_seq_handle_def<ConstSequenceHandle>(const_seq);
+  const_generic_prop_def<ConstSequenceHandle>(const_seq);
+  class_<SequenceHandle> seq_handle("SequenceHandle", init<>());
+  seq_handle
     .def("SetSequenceOffset", &SequenceHandle::SetSequenceOffset)
     .def("AttachView", attach_one)
     .def("AttachView", attach_two)
@@ -201,6 +211,10 @@ void export_sequence()
     .add_property("sequence_offset", &SequenceHandle::GetSequenceOffset,
                   &SequenceHandle::SetSequenceOffset)
   ;
+  const_seq_handle_def<SequenceHandle>(seq_handle);
+  generic_prop_def<SequenceHandle>(seq_handle);
+  implicitly_convertible<SequenceHandle, ConstSequenceHandle>();
+  
   def("CreateSequence", &CreateSequence);
   /*class_<SequenceHandleList>("SequenceHandleList", init<>())
     .def(vector_indexing_suite<SequenceHandleList>())
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index 033bf50bf..6ac241970 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/modules/seq/base/src/impl/sequence_impl.hh
@@ -26,7 +26,7 @@
 #include <list>
 
 #include <boost/shared_ptr.hpp>
-
+#include <ost/generic_property.hh>
 #include <ost/info/info_fw.hh>
 #include <ost/mol/residue_prop.hh>
 #include <ost/mol/entity_view.hh>
@@ -43,7 +43,7 @@ class SequenceImpl;
 typedef boost::shared_ptr<SequenceImpl> SequenceImplPtr;
 
 /// \internal
-class DLLEXPORT_OST_SEQ SequenceImpl {
+class DLLEXPORT_OST_SEQ SequenceImpl : public GenericPropertyContainerImpl {
 public:
   /// \brief       Construct new sequence object from sequence_string.
   static SequenceImplPtr FromString(const String& seq_name,
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index d24fff1ae..60216f9ae 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -32,7 +32,7 @@ ConstSequenceHandle::ConstSequenceHandle()
 { }
 
 SequenceHandle::SequenceHandle(const impl::SequenceImplPtr& impl):
-  ConstSequenceHandle(impl)
+  impl_(impl)
 { }
 
 ConstSequenceHandle::ConstSequenceHandle(const impl::SequenceImplPtr& impl):
@@ -75,10 +75,6 @@ SequenceHandle CreateSequence(const String& name, const String& seq)
   return SequenceHandle(impl::SequenceImpl::FromString(name, seq));
 }
 
-SequenceHandle::SequenceHandle():
-  ConstSequenceHandle()
-{ }
-
 
 String ConstSequenceHandle::GetGaplessString() const
 {
@@ -175,8 +171,6 @@ void SequenceHandle::SetName(const String& name)
   return Impl()->SetName(name);   
 }
 
-
-
 void SequenceHandle::SetString(const String& seq)
 {
   this->CheckValidity();
@@ -228,4 +222,150 @@ std::ostream& operator<<(std::ostream& os, const ConstSequenceHandle& sequence)
   return os;
 }
 
+bool SequenceHandle::operator==(const SequenceHandle& rhs) const
+{
+  return impl_==rhs.impl_;
+}
+
+bool SequenceHandle::operator!=(const SequenceHandle& rhs) const
+{
+  return impl_!=rhs.impl_;
+}
+
+
+void SequenceHandle::CheckValidity() const
+{
+  if (!impl_) {
+    throw InvalidHandle();
+  }
+}
+
+bool SequenceHandle::IsValid() const
+{
+  return impl_.get()!=0;
+}
+
+impl::SequenceImplPtr& SequenceHandle::Impl() const 
+{
+  return impl_;
+}
+
+
+SequenceHandle::SequenceHandle():
+  impl_()
+{ }
+
+
+String SequenceHandle::GetGaplessString() const
+{
+  this->CheckValidity();
+  return Impl()->GetGaplessString();
+}
+
+int SequenceHandle::GetSequenceOffset() const
+{
+  this->CheckValidity();
+  return Impl()->GetSequenceOffset();  
+}
+
+SequenceHandle::operator ConstSequenceHandle() const
+{
+  return ConstSequenceHandle(impl_);
+}
+
+int SequenceHandle::GetLength() const
+{
+  this->CheckValidity();
+  return Impl()->GetLength();
+}
+
+
+char SequenceHandle::GetOneLetterCode(int position) const
+{
+  this->CheckValidity();
+  return Impl()->GetOneLetterCode(position);
+}
+
+mol::ResidueView SequenceHandle::GetResidue(int position) const
+{
+  this->CheckValidity();
+  return Impl()->GetResidue(position);  
+}
+
+mol::EntityView SequenceHandle::GetAttachedView() const
+{
+  this->CheckValidity();
+  return Impl()->GetAttachedView(); 
+}
+
+SequenceHandle SequenceHandle::Copy() const
+{
+  this->CheckValidity();
+  return Impl()->Copy();     
+}
+
+bool SequenceHandle::HasAttachedView() const
+{
+  this->CheckValidity();
+  return Impl()->HasAttachedView();   
+}
+
+
+int SequenceHandle::GetResidueIndex(int pos) const
+{
+  this->CheckValidity();
+  return Impl()->GetResidueIndex(pos);   
+}
+
+int SequenceHandle::GetPos(int residue_index) const
+{
+  this->CheckValidity();
+  return Impl()->GetPos(residue_index);   
+}
+
+
+int SequenceHandle::GetFirstNonGap() const
+{
+  this->CheckValidity();
+  return Impl()->GetFirstNonGap(); 
+}
+
+
+int SequenceHandle::GetLastNonGap() const
+{
+  this->CheckValidity();
+  return Impl()->GetLastNonGap(); 
+}
+
+const String& SequenceHandle::GetName() const
+{
+  this->CheckValidity();
+  return Impl()->GetName();
+}
+
+const String& SequenceHandle::GetString() const
+{
+  this->CheckValidity();
+  return Impl()->GetString(); 
+}
+
+GenericPropertyContainerImpl* ConstSequenceHandle::GpImpl()
+{
+  return Impl().get();
+}
+
+const GenericPropertyContainerImpl* ConstSequenceHandle::GpImpl() const
+{
+  return Impl().get();
+}
+
+GenericPropertyContainerImpl* SequenceHandle::GpImpl()
+{
+  return Impl().get();
+}
+
+const GenericPropertyContainerImpl* SequenceHandle::GpImpl() const
+{
+  return Impl().get();
+}
 }}
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index ba9b2eabe..c76c3298c 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -24,6 +24,7 @@
  */
 
 #include <ost/base.hh>
+#include <ost/generic_property.hh>
 #include <ost/info/info_fw.hh>
 #include <ost/seq/module_config.hh>
 
@@ -41,8 +42,10 @@ class AlignmentHandle;
 /// 
 /// The ConstSequenceHandle provides all read-only methods of the 
 /// \ref SequenceHandle "sequence handle".
-class DLLEXPORT_OST_SEQ ConstSequenceHandle {
+class DLLEXPORT_OST_SEQ ConstSequenceHandle : 
+  public ConstGenericPropertyContainer<ConstSequenceHandle> {
 public:
+  friend class ConstGenericPropertyContainer<ConstSequenceHandle>;
   friend class AlignmentHandle;
   friend class ConstSequenceList;
   friend class SequenceList;
@@ -116,14 +119,15 @@ public:
   /// \brief whether the sequence is valid
   bool IsValid() const;
   /// \internal
+protected:
+  GenericPropertyContainerImpl* GpImpl();
+
+  const GenericPropertyContainerImpl* GpImpl() const;
 public:
   ConstSequenceHandle(const impl::SequenceImplPtr& impl);
   impl::SequenceImplPtr& Impl() const;  
-protected:
-  void CheckValidity() const;
-
-
 private:
+  void CheckValidity() const;
   mutable impl::SequenceImplPtr impl_;  
 };
 
@@ -149,12 +153,80 @@ private:
 ///
 /// Sequences IO is dealt with in the sequence module. For more information, 
 /// consult \ref module_seq "this page".
-class DLLEXPORT_OST_SEQ SequenceHandle : public ConstSequenceHandle {
+class DLLEXPORT_OST_SEQ SequenceHandle : 
+  public GenericPropertyContainer<SequenceHandle> {
 public:
-  friend class ConstSequenceHandle;
+  friend class GenericPropertyContainer<SequenceHandle>;  
   friend class SequenceList;
 
+  friend class AlignmentHandle;
+  friend class ConstSequenceList;
   
+  /// \brief       Get residue index corresponding to given sequence position
+  /// \param pos   zero-based index
+  /// \throws      out_of_range if pos is not in [0, length-1].
+  int GetResidueIndex(int pos) const;
+
+  /// \brief Get zero-based index for given residue number.
+  /// \throws out_of_range, if number is not included in sequence.
+  int GetPos(int residue_index) const;
+
+  /// \brief Get position of first non-gap character in sequence
+  int GetFirstNonGap() const;
+  
+  /// \brief Get position of last non-gap character in sequence
+  int GetLastNonGap() const;  
+  
+  /// \brief Get name of sequence
+  /// 
+  /// \sa SequenceHandle::GetName()
+  const String& GetName() const;  
+  
+  /// \brief get sequence as a string, including all the gaps
+  /// 
+  /// \sa GetGaplessString()
+  const String& GetString() const;
+  
+  /// \brief Get sequence as string ignoring gaps
+  String GetGaplessString() const;
+
+  /// \brief Get sequence offset from N-terminus
+  ///
+  /// \sa SequenceHandle::SetSequenceOffset
+  int GetSequenceOffset() const;  
+  
+  /// \brief Get lenght of sequence, including gaps.
+  int GetLength() const;
+
+  /// \brief get one letter code of residue at position
+  char GetOneLetterCode(int position) const;
+
+  /// \brief get residue at position
+  ///
+  /// will return the residue view at the given sequence position or an invalid
+  /// residue view when no view is attached, the index is out of bounds or the
+  /// position contains a gap.
+  mol::ResidueView GetResidue(int position) const;
+
+  /// \brief get attached view. may be an invalid entity view
+  /// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)
+  mol::EntityView GetAttachedView() const;
+  
+  /// \brief create copy sequence
+  /// The newly created sequence has the same attached view.
+  SequenceHandle Copy() const;
+  
+  /// \brief whether the sequence has an attached view
+  /// 
+  /// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)
+  bool HasAttachedView() const;
+  
+  bool operator==(const SequenceHandle& rhs) const;
+  bool operator!=(const SequenceHandle& rhs) const;  
+  
+  /// \brief whether the sequence is valid
+  bool IsValid() const;
+    
   /// \brief create invalid sequence handle
   /// 
   /// \sa IsValid()
@@ -178,7 +250,7 @@ public:
   /// \throw IntegrityError when the view contains more than one chain
   void AttachView(const mol::EntityView& view);
 
-
+  operator ConstSequenceHandle() const;
   /// \brief attach entity view to sequence
   ///
   /// The sequence is mapped onto the chain with given name
@@ -186,6 +258,15 @@ public:
   
   /// \internal
   SequenceHandle(const impl::SequenceImplPtr& impl);  
+  
+  impl::SequenceImplPtr& Impl() const;  
+
+  GenericPropertyContainerImpl* GpImpl();
+
+  const GenericPropertyContainerImpl* GpImpl() const;
+private:
+  void CheckValidity() const;  
+  mutable impl::SequenceImplPtr impl_;
 };
 
 SequenceHandle DLLEXPORT_OST_SEQ CreateSequence(const String& name, 
-- 
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