added indexing access to ConstSequenceHandle, SetSequenceName for

AlignmentHandle


git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1913 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/seq/base/pymod/export_sequence.cc

@@ -97,7 +97,8 @@ void export_sequence()
     .def("GetPos", &ConstSequenceHandle::GetPos)
     .def("GetLength", &ConstSequenceHandle::GetLength)
     .def("GetResidue", &ConstSequenceHandle::GetResidue)
-    .def("GetOneLetterCode", &ConstSequenceHandle::GetOneLetterCode)  
+    .def("GetOneLetterCode", &ConstSequenceHandle::GetOneLetterCode)
+    .def("__getitem__", &ConstSequenceHandle::GetOneLetterCode)
     .def("GetSequenceOffset", &ConstSequenceHandle::GetSequenceOffset)    
     .def("Copy", &ConstSequenceHandle::Copy)
     .def("GetFirstNonGap", &ConstSequenceHandle::GetFirstNonGap)
@@ -158,6 +159,7 @@ void export_sequence()
     .def("Copy", &AlignmentHandle::Copy)
     .def("ToString", &AlignmentHandle::ToString)
     .def("GetLength", &AlignmentHandle::GetLength)
+    .def("__len__", &AlignmentHandle::GetLength)
     .def("GetSequences", &AlignmentHandle::GetSequences)
     .def("AttachView", attach_view_a)
     .def("AttachView", attach_view_b)
@@ -167,6 +169,7 @@ void export_sequence()
     .def("__getitem__", &AlignmentHandle::operator[])
     .def("__iter__", iterator<AlignmentHandle>())
     .add_property("sequences", &AlignmentHandle::GetSequences)
+    .def("SetSequenceName",  &AlignmentHandle::SetSequenceName)
   ;
   class_<AlignedColumn>("AlignedColumn", no_init)
     .def("GetIndex", &AlignedColumn::GetIndex)

modules/seq/base/src/aligned_region.hh

@@ -49,8 +49,10 @@ public:
   void SetMaster(int master);
   /// \brief delete interval and update length of AlignedRegion
   void Delete();
-  ///\brief replace region with content of AlignedRegion and set length to length of \p aln_r
+  /// \brief replace region with content of AlignedRegion and set length to 
+  ///       length of \p aln_r
   void Replace(const AlignedRegion& aln_r);
+  
   /// \brief shift the aligned region of the master sequence to the left by
   ///        n characters.
   void ShiftLeft(int n);

modules/seq/base/src/alignment_handle.cc

@@ -231,4 +231,11 @@ AlignedColumn AlignmentHandle::operator[](int index)
   return AlignedColumn(*this, index);
 }
 
+void AlignmentHandle::SetSequenceName(int seq_index, const String& name)
+
+{
+  this->CheckValidity();
+  impl_->GetSequence(seq_index)->SetName(name);
+}
+
 }}

modules/seq/base/src/alignment_handle.hh

@@ -104,7 +104,10 @@ public:
   /// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)  
   void AttachView(int seq_index, const mol::EntityView& view, 
                   const String& chain_name);
-
+                  
+  /// \brief set name of sequence
+  void SetSequenceName(int seq_index, const String& name);
+  
   /// \brief Get list of sequences (read-only)
   ConstSequenceList GetSequences() const;