diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 581c5494c2ad3386d672dda08223e8d0e45706f4..3f8636fe5ff64b7378ccbfa5d2eda6b2cde27170 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -250,6 +250,7 @@ void export_sequence()
.add_property("sequences", &AlignmentHandle::GetSequences)
.def("SetSequenceName", &AlignmentHandle::SetSequenceName)
.def("SetSequenceOffset", &AlignmentHandle::SetSequenceOffset)
+ .def("GetSequenceOffset", &AlignmentHandle::GetSequenceOffset)
;
class_<AlignedColumn>("AlignedColumn", no_init)
.def("GetIndex", &AlignedColumn::GetIndex)
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 48bb07af5fb0dad628d188aa32ccbeb722e99fc4..ee21b144c3d3674b6dd3dc17bb8fb20e2b1ad252 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -62,7 +62,7 @@ int AlignmentHandle::GetResidueIndex(int seq_index, int pos) const
void AlignmentHandle::AddSequence(const ConstSequenceHandle& sequence)
{
this->CheckValidity();
- if (impl_->GetCount()>0 &&
+ if (impl_->GetCount()>0 &&
impl_->GetSequence(0)->GetLength()!=sequence.GetLength()) {
throw InvalidAlignment();
}
@@ -143,7 +143,7 @@ void AlignmentHandle::AttachView(int seq_index, const mol::EntityView& view)
impl_->GetSequence(seq_index)->AttachView(view);
}
-void AlignmentHandle::AttachView(int seq_index, const mol::EntityView& view,
+void AlignmentHandle::AttachView(int seq_index, const mol::EntityView& view,
const String& chain_name)
{
this->CheckValidity();
@@ -160,7 +160,7 @@ ConstSequenceHandle AlignmentHandle::FindSequence(const String& name) const
void AlignmentHandle::Cut(int start, int end)
{
this->CheckValidity();
- for (impl::SequenceListImpl::Iterator i=impl_->Begin(),
+ for (impl::SequenceListImpl::Iterator i=impl_->Begin(),
e=impl_->End(); i!=e; ++i) {
(*i)->Cut(start, end-start);
}
@@ -183,12 +183,12 @@ void AlignmentHandle::Replace(const AlignedRegion& aln_r, int start, int end){
}
}
-void AlignmentHandle::ShiftRegion(int start, int end, int amount,
+void AlignmentHandle::ShiftRegion(int start, int end, int amount,
int master)
{
this->CheckValidity();
int cnt=0;
- for (impl::SequenceListImpl::Iterator i=impl_->Begin(),
+ for (impl::SequenceListImpl::Iterator i=impl_->Begin(),
e=impl_->End(); i!=e; ++i, ++cnt) {
if (master==-1 || cnt==master) {
(*i)->ShiftRegion(start, end, amount);
@@ -216,7 +216,7 @@ char AlignmentHandle::GetOneLetterCode(int seq_index, int pos) const
AlignedColumnIterator AlignmentHandle::begin() const
{
- // no need to check for validity here
+ // no need to check for validity here
return AlignedColumnIterator(*this, 0, this->GetLength());
}
@@ -244,4 +244,9 @@ void AlignmentHandle::SetSequenceOffset(int seq_index, int offset)
impl_->GetSequence(seq_index)->SetSequenceOffset(offset);
}
+int AlignmentHandle::GetSequenceOffset(int seq_index)
+{
+ this->CheckValidity();
+ return impl_->GetSequence(seq_index)->GetSequenceOffset();
+}
}}
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 7e6ba856767795ae3ef7882f898b7cfffb0559e2..e007b4fb3797cabc72c0da1316c79ffd11f6a96f 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -35,27 +35,27 @@ class AlignedRegion;
class AlignedColumn;
class AlignedColumnIterator;
-/// \brief representation of a multiple sequence alignemnt consisting of two or
+/// \brief representation of a multiple sequence alignemnt consisting of two or
/// more sequences
///
-/// A sequence alignment consists of two or more sequences. The number of
-/// sequences in the alignment can be obtained by #GetCount().
+/// A sequence alignment consists of two or more sequences. The number of
+/// sequences in the alignment can be obtained by #GetCount().
/// All sequences are of length #GetLength().
-///
-/// Typically sequence alignments are used column-based, i.e by looking at an
-/// aligned columns in the sequence alignment. To get a row-based (sequence)
-/// view on the sequence list, use AlignmentHandle::GetSequenceList(). For an
+///
+/// Typically sequence alignments are used column-based, i.e by looking at an
+/// aligned columns in the sequence alignment. To get a row-based (sequence)
+/// view on the sequence list, use AlignmentHandle::GetSequenceList(). For an
/// overview of how to use the sequence module, see \ref module_seq "here"
-///
-/// All operators that operate on an alignment will again produce a valid
-/// alignment. This mean that it is not possible to change the length of one
+///
+/// All operators that operate on an alignment will again produce a valid
+/// alignment. This mean that it is not possible to change the length of one
/// sequence, without adjusting the other sequences, too.
class DLLEXPORT_OST_SEQ AlignmentHandle {
public:
typedef AlignedColumnIterator iterator;
AlignmentHandle();
-
+
/// \brief Get position in sequence with index seq_index that corresponds to
/// the given residue index.
///
@@ -68,19 +68,19 @@ public:
int GetResidueIndex(int seq_index, int pos) const;
mol::ResidueView GetResidue(int seq_index, int pos) const;
-
+
char GetOneLetterCode(int seq_index, int pos) const;
-
+
/// \brief Add new sequence to multiple sequence alignment.
- ///
- /// If the sequence length does not match with the length of the other
+ ///
+ /// If the sequence length does not match with the length of the other
/// sequences in the alignment, an InvalidSequence() exception is thrown.
void AddSequence(const ConstSequenceHandle& sequence);
/// \brief Get sequence with given index.
/// \return sequence or invalid handle if the index is out of bounds
- ConstSequenceHandle GetSequence(int seq_id) const;
-
+ ConstSequenceHandle GetSequence(int seq_id) const;
+
/// \brief Convert multiple sequence alignment to string.
String ToString(int width=80) const;
@@ -88,87 +88,88 @@ public:
int GetLength() const;
/// \brief deep-copy multi sequence alignment
- AlignmentHandle Copy() const;
-
+ AlignmentHandle Copy() const;
+
/// \brief find sequence by name.
- ///
- /// If several sequences have the same name, the first matching sequence will
+ ///
+ /// If several sequences have the same name, the first matching sequence will
/// be returned.
ConstSequenceHandle FindSequence(const String& name) const;
-
+
/// \brief attach view to given sequence
/// \sa SequenceHandle::AttachView(const mol::EntityView&)
void AttachView(int seq_index, const mol::EntityView& view);
-
+
/// \brief attach view to given sequence
- /// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)
- void AttachView(int seq_index, const mol::EntityView& view,
+ /// \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);
-
- void SetSequenceOffset(int seq_index, int offset);
+
+ void SetSequenceOffset(int seq_index, int offset);
+ int GetSequenceOffset(int seq_index);
/// \brief Get list of sequences (read-only)
ConstSequenceList GetSequences() const;
-
+
/// \brief create an aligned region.
- ///
+ ///
/// \param start is the index of the first column
/// \param n is the length of the sequence
- /// \param master is the reference system for operations such as shifting.
- /// If set to -1, no master sequence is defined and the operations will
+ /// \param master is the reference system for operations such as shifting.
+ /// If set to -1, no master sequence is defined and the operations will
/// affect all sequences
- ///
- /// This method does not throw any exceptions, even if the aligned region is
+ ///
+ /// This method does not throw any exceptions, even if the aligned region is
/// out of bounds.
AlignedRegion MakeRegion(int start, int n, int master=-1) const;
-
+
/// \brief get number of sequences in alignment
int GetCount() const;
-
+
bool operator==(const AlignmentHandle& rhs) const;
- bool operator!=(const AlignmentHandle& rhs) const;
-
+ bool operator!=(const AlignmentHandle& rhs) const;
+
/// \brief get aligned column at index
- ///
- /// This method does not throw any exception. Upon accessing methods of the
- /// aligned column, exceptions might be thrown when the index is out of
+ ///
+ /// This method does not throw any exception. Upon accessing methods of the
+ /// aligned column, exceptions might be thrown when the index is out of
/// bounds.
AlignedColumn operator[](int index) const;
-
- AlignmentHandle(const impl::SequenceListImplPtr& impl);
-
+
+ AlignmentHandle(const impl::SequenceListImplPtr& impl);
+
/// \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
/// only the sequence with given index is affected.
void ShiftRegion(int start, int end, int amount, int master=-1);
-
+
/// \brief Column iterator start-point
iterator begin() const;
/// \brief Column iterator end-point
iterator end() const;
-
+
private:
void CheckValidity() const;
- impl::SequenceListImplPtr impl_;
+ impl::SequenceListImplPtr impl_;
};
AlignmentHandle DLLEXPORT_OST_SEQ CreateAlignment();
/// \brief convert alignment from sequence list
-///
-/// If the sequences in the SequenceList have different lengths, an
+///
+/// If the sequences in the SequenceList have different lengths, an
/// InvalidAlignment exception is thrown.
-///
+///
/// \return alignment consisting of the sequences in seq_list.
-AlignmentHandle DLLEXPORT_OST_SEQ
+AlignmentHandle DLLEXPORT_OST_SEQ
AlignmentFromSequenceList(const SequenceList& seq_list);
typedef std::vector<AlignmentHandle> AlignmentList;