diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 1c48ec3279da13605f4eeb58ade58b824b9eb7e1..ce9d50ad2e7bca497a6c163a4e708ed3fd41ff9b 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/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[])
diff --git a/modules/seq/base/src/aligned_region.cc b/modules/seq/base/src/aligned_region.cc
index 151e1441a1b207c087aea0b4f9ccdaff610179c8..decb966ef0533f5c9d0a1383d4f8ccb2f1ce36e4 100644
--- a/modules/seq/base/src/aligned_region.cc
+++ b/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_;
+}
+
}}
diff --git a/modules/seq/base/src/aligned_region.hh b/modules/seq/base/src/aligned_region.hh
index 9590be824bf40b606625bc7a2e4a221612bb61fd..cfd6f757d485b72eb25c62c126cdd3039795f23c 100644
--- a/modules/seq/base/src/aligned_region.hh
+++ b/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.
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 7f23a937896d1b7a4e4993d7ffdf2b72a2891252..6d6d5bb63489b1e4463199081f34825850ea34c0 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/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)
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 1dde2b25fa625b578eddd878ac278f9f98489f01..893ec4cf86a0ad6d02bccbe74ee2b4908c7bd4ff 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/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
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 97d2b223e2a543a4f069cfb60b983dde9e793484..69fd3f42f4d3cd3b377f2991e282ff27d86ba116 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/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);
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index 5ca99493ae90c1bd461fb8796bc3c2d1a378c77e..033bf50bf5f331a419b23068b6997d6cdc53c3eb 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/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;