fix BZDNG-187 and BZDNG-148

modules/seq/base/pymod/export_sequence.cc

@@ -21,6 +21,8 @@
 #include <boost/python/register_ptr_to_python.hpp>
 #include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 
+
+#include <ost/export_helper/pair_to_tuple_conv.hh>
 #include <ost/generic_property.hh>
 #include <ost/export_helper/generic_property_def.hh>
 #include <ost/info/info.hh>
@@ -206,6 +208,7 @@ void const_seq_handle_def(O& bp_class)
     .def("GetLength", &C::GetLength)
     .def("GetResidue", &C::GetResidue)
     .def("GetOneLetterCode", &C::GetOneLetterCode)
+    .def("__iter__", iterator<C>())
     .def("__getitem__", &C::GetOneLetterCode)
     .def("GetOffset", &C::GetOffset)
     .def("Copy", &C::Copy)
@@ -297,8 +300,6 @@ void export_sequence()
     .def("Copy", &AlignmentHandle::Copy)
     .def("ToString", &AlignmentHandle::ToString)
     .def("GetLength", &AlignmentHandle::GetLength)
-    .def("GetMatchingBackboneViews", &AlignmentHandle::GetMatchingBackboneViews,
-         (arg("index1")=0, arg("index2")=1))
     .def("__len__", &AlignmentHandle::GetLength)
     .def("GetSequences", &AlignmentHandle::GetSequences)
     .def("GetCoverage", &AlignmentHandle::GetSequences)
@@ -357,7 +358,7 @@ void export_sequence()
     .def("__getitem__", &do_slice_b)
   ;
   implicitly_convertible<SequenceList, ConstSequenceList>();
-
+  
   def("CreateSequenceList", &CreateSequenceList);
   def("SequenceFromChain", seq_from_chain_a);
   def("SequenceFromChain", seq_from_chain_b);

modules/seq/base/src/sequence_handle.cc

@@ -58,6 +58,8 @@ char ConstSequenceHandle::operator[](int index) const
 }
 
 
+
+
 void ConstSequenceHandle::CheckValidity() const
 {
   if (!impl_) {
@@ -398,4 +400,11 @@ int SequenceHandle::GetIndex(const String& substr) const
   this->CheckValidity();
   return Impl()->GetIndex(substr);
 }
+
+char SequenceHandle::operator[](size_t index) const
+{
+  this->CheckValidity();
+  return this->GetString()[index];
+}
+
 }}

modules/seq/base/src/sequence_handle.hh

@@ -49,6 +49,9 @@ public:
   friend class AlignmentHandle;
   friend class ConstSequenceList;
   friend class SequenceList;
+  
+  typedef String::const_iterator iterator;
+  
   /// \brief create invalid sequence handle
   /// 
   /// \sa IsValid()
@@ -121,6 +124,8 @@ public:
   
   char operator[](int index) const;
   
+  iterator begin() const { return this->GetString().begin(); }
+  iterator end() const { return this->GetString().end(); }
   
   /// \brief whether the sequence is valid
   bool IsValid() const;
@@ -162,6 +167,7 @@ private:
 class DLLEXPORT_OST_SEQ SequenceHandle : 
   public GenericPropContainer<SequenceHandle> {
 public:
+  typedef String::const_iterator iterator;
   friend class GenericPropContainer<SequenceHandle>;  
   friend class SequenceList;
 
@@ -261,6 +267,10 @@ public:
   
   void SetOneLetterCode(int position, char new_char);
   
+  char operator[](size_t index) const;
+    
+  iterator begin() const { return this->GetString().begin(); }
+  iterator end() const { return this->GetString().end(); }
   
   void Append(char olc);
   operator ConstSequenceHandle() const;

modules/seq/base/tests/test_seq.py

@@ -30,7 +30,10 @@ class TestSeq(unittest.TestCase):
     string_b=''.join([r.one_letter_code for r in b.residues])
     self.assertEqual(string_a, 'ABCDFGH')
     self.assertEqual(string_b, 'ABCDFGH')
- 
+  def testSeqIterBZDNG148(self):
+    s=seq.CreateSequence('A', 'abcdef')
+    for x in s: 
+      pass
   def testViewsFromSequences_02(self):
     seq_a=seq.CreateSequence("A", "ABCD-FGH")
     seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))