added "role" attribute to sequence

modules/seq/alg/src/merge_pairwise_alignments.cc

@@ -87,7 +87,8 @@ SequenceHandle shift_reference(const ConstSequenceHandle& ref_seq,
   }
   new_sequence << ref_str.substr(last);
   SequenceHandle s=CreateSequence(ref_seq.GetName(), 
-                                  new_sequence.str());
+                                  new_sequence.str(),
+                                  ref_seq.GetRole());
   if (ref_seq.HasAttachedView())
     s.AttachView(ref_seq.GetAttachedView());
   s.SetOffset(ref_seq.GetOffset());
@@ -122,7 +123,8 @@ SequenceHandle realign_sequence(const AlignmentHandle& aln,
     }
     new_sequence << s2.GetOneLetterCode(i);
   }
-  SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str());
+  SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str(), 
+                                  s2.GetRole());
   if (s2.HasAttachedView())
     s.AttachView(s2.GetAttachedView());
   s.SetOffset(s2.GetOffset());

modules/seq/alg/tests/test_merge_pairwise_alignments.cc

@@ -34,15 +34,15 @@ BOOST_AUTO_TEST_SUITE(ost_seq_alg)
 
 BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_one) 
 {
-  SequenceHandle ref=CreateSequence("REF", "abcdefghijklmn");
+  SequenceHandle ref=CreateSequence("REF", "abcdefghijklmn", "R");
   SequenceHandle s1=CreateSequence("S1", "abcd---efghijklmn");
-  SequenceHandle s2=CreateSequence("S2", "abcdxyzefghijklmn");
+  SequenceHandle s2=CreateSequence("S2", "abcdxyzefghijklmn", "X");
   AlignmentHandle aln1=CreateAlignment();
   aln1.AddSequence(s1);
   aln1.AddSequence(s2);
 
   SequenceHandle s3=CreateSequence("S1", "abcdefghij---klmn");
-  SequenceHandle s4=CreateSequence("S2", "abcdefghijxyzklmn");
+  SequenceHandle s4=CreateSequence("S2", "abcdefghijxyzklmn", "Y");
 
   AlignmentHandle aln2=CreateAlignment();
   aln2.AddSequence(s3);
@@ -55,6 +55,9 @@ BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_one)
   BOOST_CHECK_EQUAL(seqs[0].GetString(), "abcd---efghij---klmn");
   BOOST_CHECK_EQUAL(seqs[1].GetString(), "abcdxyzefghij---klmn");
   BOOST_CHECK_EQUAL(seqs[2].GetString(), "abcd---efghijxyzklmn");
+  BOOST_CHECK_EQUAL(seqs[0].GetRole(), "R");
+  BOOST_CHECK_EQUAL(seqs[1].GetRole(), "X");
+  BOOST_CHECK_EQUAL(seqs[2].GetRole(), "Y");
 }
   
 BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_two) 

modules/seq/base/pymod/export_sequence.cc

@@ -257,6 +257,8 @@ void const_seq_handle_def(O& bp_class)
     .add_property("last_non_gap", &C::GetLastNonGap)
     .def("GetAttachedView", &C::GetAttachedView)
     .def("GetGaplessString", &C::GetGaplessString)
+    .add_property("role", make_function(&C::GetRole, 
+                                        return_value_policy<copy_const_reference>()))
     .def("GetString", &C::GetString,
          return_value_policy<copy_const_reference>())
          .def("GetName", &C::GetName,
@@ -299,6 +301,9 @@ void export_sequence()
                   make_function(&SequenceHandle::GetString,
                                 return_value_policy<copy_const_reference>()),
                   &SequenceHandle::SetString)
+    .add_property("role", make_function(&SequenceHandle::GetRole, 
+                                        return_value_policy<copy_const_reference>()),
+                  &SequenceHandle::SetRole)
     .def("SetName", &SequenceHandle::SetName)
     .add_property("name",
                   make_function(&SequenceHandle::GetName,
@@ -312,7 +317,8 @@ void export_sequence()
 
   implicitly_convertible<SequenceHandle, ConstSequenceHandle>();
   
-  def("CreateSequence", &CreateSequence);
+  def("CreateSequence", &CreateSequence, 
+      (arg("name"), arg("seq"), arg("role")="UNKNOWN"));
   /*class_<SequenceHandleList>("SequenceHandleList", init<>())
     .def(vector_indexing_suite<SequenceHandleList>())
   ;*/
@@ -348,6 +354,9 @@ void export_sequence()
     .def("GetSequences", &AlignmentHandle::GetSequences)
     .def("GetCoverage", &AlignmentHandle::GetCoverage)
     .def("AttachView", attach_view_a)
+    .def("SetSequenceRole", &AlignmentHandle::SetSequenceRole)
+    .def("GetSequenceRole", &AlignmentHandle::GetSequenceRole, 
+         return_value_policy<copy_const_reference>())
     .def("AttachView", attach_view_b)
     .def("Cut", &AlignmentHandle::Cut)
     .def("MakeRegion", &AlignmentHandle::MakeRegion)

modules/seq/base/src/alignment_handle.cc

@@ -313,4 +313,20 @@ mol::EntityViewPair AlignmentHandle::GetMatchingBackboneViews(int idx0, int idx1
   return mol::EntityViewPair(v1, v2);
 }
 
+
+const String& AlignmentHandle::GetSequenceRole(int seq_index)
+{
+  this->CheckValidity();
+  return impl_->GetSequence(seq_index)->GetRole();
+  
+}
+  
+void AlignmentHandle::SetSequenceRole(int seq_index, const String& role)
+{
+  this->CheckValidity();
+  impl_->GetSequence(seq_index)->SetRole(role);
+  
+}
+
+
 }}

modules/seq/base/src/alignment_handle.hh

@@ -170,6 +170,10 @@ public:
   /// between 0 (no coverage) and 1 (full coverage)
   Real GetCoverage(int seq_index) const;
   
+  
+  const String& GetSequenceRole(int seq_index);
+  
+  void SetSequenceRole(int seq_index, const String& role);
 private:
   void CheckValidity() const;
   impl::SequenceListImplPtr impl_;

modules/seq/base/src/impl/sequence_impl.cc

@@ -55,11 +55,12 @@ bool SequenceImpl::IsSequenceStringSane(const String& seq_string)
 }
 
 SequenceImplPtr SequenceImpl::FromString(const String& seq_name,
-                                 const String& seq_string)
+                                         const String& seq_string, 
+                                         const String& role)
 {
 
   if (SequenceImpl::IsSequenceStringSane(seq_string)) {
-    return SequenceImplPtr(new SequenceImpl(seq_name, seq_string));
+    return SequenceImplPtr(new SequenceImpl(seq_name, seq_string, role));
   }
   throw InvalidSequence();
 }
@@ -102,15 +103,15 @@ void SequenceImpl::SetString(const String& seq)
 }
 
 SequenceImpl::SequenceImpl(const String& seq_name,
-                   const String& seq_string)
-  : seq_name_(seq_name), seq_string_(seq_string), offset_(0)
+                   const String& seq_string, const String& role)
+  : seq_name_(seq_name), seq_string_(seq_string), seq_role_(role), offset_(0)
 {
   this->ShiftsFromSequence();
 }
 
 SequenceImplPtr SequenceImpl::Copy() const
 {
-  SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_));
+  SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_, seq_role_));
   new_seq->offset_=offset_;
   new_seq->shifts_=shifts_;
   new_seq->attached_view_=attached_view_;

modules/seq/base/src/impl/sequence_impl.hh

@@ -50,7 +50,8 @@ class DLLEXPORT_OST_SEQ SequenceImpl : public GenericPropContainerImpl {
 public:
   /// \brief       Construct new sequence object from sequence_string.
   static SequenceImplPtr FromString(const String& seq_name,
-                                const String& sequence_string);
+                                    const String& sequence_string,
+                                    const String& role="UNKNOWN");
 
   /// \brief       Get residue index corresponding to given sequence position
   /// \param pos   zero-based index
@@ -105,7 +106,8 @@ public:
   ///
   /// If you want to check whether the sequence String does only contain
   /// valid characters use \c CreateSequence instead.
-  SequenceImpl(const String& seq_name, const String& sequence_string);
+  SequenceImpl(const String& seq_name, const String& sequence_string, 
+               const String& role);
 
   /// \brief get one letter code of residue at position
   char GetOneLetterCode(int position) const;
@@ -148,7 +150,15 @@ public:
   {
     return seq_string_[index];
   }
+  const String& GetRole() const
+  {
+    return seq_role_;
+  }
   
+  void SetRole(const String& role)
+  {
+    seq_role_=role;
+  }
 private:
 
   /// \brief       Recalculates gap shifts from sequence.
@@ -169,6 +179,7 @@ private:
   } Shift;
   String              seq_name_;
   String              seq_string_;
+  String              seq_role_;
   std::list<Shift>    shifts_;
   bool                editing_;
   int                 offset_;

modules/seq/base/src/sequence_handle.cc

@@ -59,6 +59,25 @@ char ConstSequenceHandle::operator[](int index) const
 
 
 
+const String& ConstSequenceHandle::GetRole() const
+{
+  this->CheckValidity();
+  return Impl()->GetRole();
+}
+
+
+const String& SequenceHandle::GetRole() const
+{
+  this->CheckValidity();
+  return Impl()->GetRole();
+}
+  
+void SequenceHandle::SetRole(const String& role) const
+{
+  this->CheckValidity();
+  Impl()->SetRole(role);
+}
+
 
 void ConstSequenceHandle::CheckValidity() const
 {
@@ -78,9 +97,10 @@ impl::SequenceImplPtr& ConstSequenceHandle::Impl() const
 }
 
 
-SequenceHandle CreateSequence(const String& name, const String& seq)
+SequenceHandle CreateSequence(const String& name, const String& seq, 
+                              const String& role)
 {
-  return SequenceHandle(impl::SequenceImpl::FromString(name, seq));
+  return SequenceHandle(impl::SequenceImpl::FromString(name, seq, role));
 }
 
 
@@ -222,6 +242,7 @@ SequenceHandle SequenceFromInfo(info::InfoGroup& group)
 }
 #endif
 
+
 std::ostream& operator<<(std::ostream& os, const ConstSequenceHandle& sequence)
 {
   if (sequence.IsValid()) {

modules/seq/base/src/sequence_handle.hh

@@ -122,6 +122,8 @@ public:
   /// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)
   bool HasAttachedView() const;
   
+  const String& GetRole() const;
+  
   bool operator==(const ConstSequenceHandle& rhs) const;
   bool operator!=(const ConstSequenceHandle& rhs) const;  
   
@@ -286,6 +288,10 @@ public:
   /// \internal
   SequenceHandle(const impl::SequenceImplPtr& impl);  
   
+  const String& GetRole() const;
+  
+  void SetRole(const String& role) const;
+  
   impl::SequenceImplPtr& Impl() const;  
 
   GenericPropContainerImpl* GpImpl();
@@ -297,9 +303,9 @@ private:
 };
 
 SequenceHandle DLLEXPORT_OST_SEQ CreateSequence(const String& name, 
-                                                const String& seq);
-
-#if(OST_INFO_ENABLED)
+                                                const String& seq, 
+                                                const String& role="UNKNOWN");
+                                                
 /// \brief export sequence to info
 void DLLEXPORT_OST_SEQ SequenceToInfo(const ConstSequenceHandle& sequence,
                                       info::InfoGroup& group);