From 7bd977aea884b1163b9685c0b2fb9bb699b9aa0c Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 1 Apr 2010 14:27:09 +0000
Subject: [PATCH] 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 | 5 ++++-
modules/seq/base/src/aligned_region.hh | 4 +++-
modules/seq/base/src/alignment_handle.cc | 7 +++++++
modules/seq/base/src/alignment_handle.hh | 5 ++++-
4 files changed, 18 insertions(+), 3 deletions(-)
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index ce9d50ad2..fe3502c1b 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/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)
diff --git a/modules/seq/base/src/aligned_region.hh b/modules/seq/base/src/aligned_region.hh
index cfd6f757d..ca8166ee1 100644
--- a/modules/seq/base/src/aligned_region.hh
+++ b/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);
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 6d6d5bb63..0c9d312d2 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/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);
+}
+
}}
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 893ec4cf8..d097d90bd 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/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;
--
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