adding Replace to AlignmentHandle and AlignedRegion interface

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1912 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/seq/base/pymod/export_sequence.cc

@@ -161,6 +161,8 @@ void export_sequence()
     .def("GetSequences", &AlignmentHandle::GetSequences)
     .def("AttachView", attach_view_a)
     .def("AttachView", attach_view_b)
+    .def("Cut", &AlignmentHandle::Cut)
+    .def("Replace",&AlignmentHandle::Replace)
     .def("__getitem__", &slice_aln)
     .def("__getitem__", &AlignmentHandle::operator[])
     .def("__iter__", iterator<AlignmentHandle>())
@@ -174,6 +176,7 @@ void export_sequence()
   ;
   class_<AlignedRegion>("AlignedRegion", no_init)
     .def("Delete", &AlignedRegion::Delete)
+    .def("Replace", &AlignedRegion::Replace)
     .def("ShiftLeft", &AlignedRegion::ShiftLeft)
     .def("ShiftRight", &AlignedRegion::ShiftRight)
     .def("GetStart", &AlignedRegion::GetStart)
@@ -181,6 +184,7 @@ void export_sequence()
     .def("GetLength", &AlignedRegion::GetLength)
     .def("SetMaster", &AlignedRegion::SetMaster)
     .def("GetMaster", &AlignedRegion::GetMaster)
+    .def("GetAlignmentHandle",&AlignedRegion::GetAlignmentHandle)
     .add_property("master", &AlignedRegion::GetMaster, 
                   &AlignedRegion::SetMaster)
     .def("__getitem__", &AlignedRegion::operator[])                  

modules/seq/base/src/aligned_region.cc

@@ -50,6 +50,11 @@ void AlignedRegion::Delete()
   end_=start_;
 }
 
+void AlignedRegion::Replace(const AlignedRegion& aln_r)
+{
+  aln_.Replace(aln_r,start_, end_);
+  end_=start_+end_;
+}
 
 void AlignedRegion::ShiftLeft(int n)
 {
@@ -118,4 +123,9 @@ int AlignedRegion::GetLength() const
   return end_-start_;
 }
 
+AlignmentHandle AlignedRegion::GetAlignmentHandle() const
+{
+  return aln_;
+}
+
 }}

modules/seq/base/src/aligned_region.hh

@@ -47,9 +47,10 @@ public:
   int GetStart() const;
   int GetMaster() const;
   void SetMaster(int master);
-  /// \brief delete interval
+  /// \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
+  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);
@@ -64,6 +65,9 @@ public:
   /// \sa AlignmentHandle::GetLength()
   int GetLength() const;
   
+  ///\brief retrieve alignment handle for aligned region
+  AlignmentHandle GetAlignmentHandle() const;
+
   /// \brief get aligned column at given index
   /// 
   /// The indices range from 0 to GetLength()-1.

modules/seq/base/src/alignment_handle.cc

@@ -23,9 +23,11 @@
 #include <ost/invalid_handle.hh>
 #include <ost/seq/alignment_handle.hh>
 #include <ost/seq/impl/sequence_list_impl.hh>
+#include <ost/seq/impl/sequence_impl.hh>
 #include <ost/seq/sequence_list.hh>
 #include <ost/seq/aligned_region.hh>
 #include <ost/seq/aligned_column_iterator.hh>
+#include <ost/integrity_error.hh>
 
 namespace ost { namespace seq {
 
@@ -47,24 +49,24 @@ AlignmentHandle::AlignmentHandle(const impl::SequenceListImplPtr& impl):
 int AlignmentHandle::GetPos(int seq_index, int residue_index) const
 {
   this->CheckValidity();
-  return impl_->GetPos(seq_index, residue_index);  
+  return impl_->GetPos(seq_index, residue_index);
 }
 
 int AlignmentHandle::GetResidueIndex(int seq_index, int pos) const
 {
   this->CheckValidity();
-  return impl_->GetResidueIndex(seq_index, pos);  
+  return impl_->GetResidueIndex(seq_index, pos);
 }
 
 
 void AlignmentHandle::AddSequence(const ConstSequenceHandle& sequence)
 {
-  this->CheckValidity();  
+  this->CheckValidity();
   if (impl_->GetCount()>0 && 
       impl_->GetSequence(0)->GetLength()!=sequence.GetLength()) {
-    throw InvalidAlignment();        
+    throw InvalidAlignment();
   }
-  return impl_->AddSequence(sequence.Impl());  
+  return impl_->AddSequence(sequence.Impl());
 }
 
 ConstSequenceHandle AlignmentHandle::GetSequence(int seq_id) const
@@ -77,7 +79,7 @@ ConstSequenceHandle AlignmentHandle::GetSequence(int seq_id) const
 String AlignmentHandle::ToString(int width) const
 {
   this->CheckValidity();
-  return impl_->ToString(width);  
+  return impl_->ToString(width);
 }
 
 int AlignmentHandle::GetLength() const
@@ -163,7 +165,23 @@ void AlignmentHandle::Cut(int start, int end)
     (*i)->Cut(start, end-start);
   }
 }
-  
+
+void AlignmentHandle::Replace(const AlignedRegion& aln_r, int start, int end){
+  this->CheckValidity();
+  //check that alignment handle and aligned region contain same number of sequences
+  if (impl_->GetCount() != aln_r.GetAlignmentHandle().GetCount()) {
+    throw IntegrityError("alignment handle and aligned region are required "\
+                         "to share the same number of sequences");
+  }
+  int aln_rStart=aln_r.GetStart();
+  int aln_rEnd=aln_r.GetEnd();
+  AlignmentHandle aln=aln_r.GetAlignmentHandle();
+  //iterate over sequences and replace part of sequences with the substrings
+  //from aligned region
+  for (int i=0;i<impl_->GetCount() ;++i) {
+    this->GetSequence(i).Impl()->Replace(aln.GetSequence(i).GetString().substr(aln_rStart,aln_rEnd), start, end);
+  }
+}
 
 void AlignmentHandle::ShiftRegion(int start, int end, int amount, 
                                   int master)

modules/seq/base/src/alignment_handle.hh

@@ -138,6 +138,8 @@ public:
   /// \brief cut out half-closed interval start, end
   void Cut(int start, int end);
   
+  ///\brief Replace part of an alignment
+  void Replace(const AlignedRegion& rhs, int start, int end);
   /// \brief shift half-closed interval by amount
   /// 
   /// if master is -1, all sequences of the alignment will be shifted. Otherwise

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

@@ -265,6 +265,12 @@ void SequenceImpl::Cut(int start, int n)
   this->ShiftsFromSequence();
 }
 
+void SequenceImpl::Replace(const String& str,int start, int end)
+{
+  seq_string_.replace(start, end-start, str);
+  this->ShiftsFromSequence();
+}
+
 void SequenceImpl::ShiftRegion(int start, int end, int amount)
 {
   String str1=seq_string_.substr(start, end-start);

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

@@ -77,6 +77,9 @@ public:
   /// \brief Set sequence String
   void SetString(const String& seq);
 
+  /// \brief replace substring starting from start to end
+  void Replace(const String& str,int start, int end);
+
   /// \brief Get sequence as String ignoring gaps
   String GetGaplessString() const;