From 44711e0d708ddb210309804253550834dab1fd5f Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Wed, 30 Mar 2011 14:05:59 +0200
Subject: [PATCH] fix BZDNG-187 and BZDNG-148
---
modules/seq/base/pymod/export_sequence.cc | 7 +++++--
modules/seq/base/src/sequence_handle.cc | 9 +++++++++
modules/seq/base/src/sequence_handle.hh | 12 ++++++++++++
modules/seq/base/tests/test_seq.py | 5 ++++-
4 files changed, 30 insertions(+), 3 deletions(-)
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 454245778..87345ad2a 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -208,6 +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)
@@ -287,6 +288,9 @@ void export_sequence()
class_<SeqListIter>("SeqListIter", no_init)
.def("next", &SeqListIter::next)
;
+ to_python_converter<std::pair<mol::EntityView, mol::EntityView>,
+ PairToTupleConverter<mol::EntityView, mol::EntityView> >();
+
class_<AlignmentHandle>("AlignmentHandle", init<>())
.def("GetCount", &AlignmentHandle::GetCount)
.add_property("sequence_count", &AlignmentHandle::GetCount)
@@ -357,8 +361,7 @@ void export_sequence()
.def("__getitem__", &do_slice_b)
;
implicitly_convertible<SequenceList, ConstSequenceList>();
- to_python_converter<std::pair<mol::EntityView, mol::EntityView>,
- PairToTupleConverter<mol::EntityView, mol::EntityView> >();
+
def("CreateSequenceList", &CreateSequenceList);
def("SequenceFromChain", seq_from_chain_a);
def("SequenceFromChain", seq_from_chain_b);
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index 6991a14f7..3065ae9f0 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -58,6 +58,8 @@ char ConstSequenceHandle::operator[](int index) const
}
+
+
void ConstSequenceHandle::CheckValidity() const
{
if (!impl_) {
@@ -380,4 +382,11 @@ const GenericPropContainerImpl* SequenceHandle::GpImpl() const
{
return Impl().get();
}
+
+char SequenceHandle::operator[](size_t index) const
+{
+ this->CheckValidity();
+ return this->GetString()[index];
+}
+
}}
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index 8d370e59e..d6fb0ab3e 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/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()
@@ -118,6 +121,8 @@ 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;
@@ -159,6 +164,7 @@ private:
class DLLEXPORT_OST_SEQ SequenceHandle :
public GenericPropContainer<SequenceHandle> {
public:
+ typedef String::const_iterator iterator;
friend class GenericPropContainer<SequenceHandle>;
friend class SequenceList;
@@ -255,6 +261,12 @@ 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(); }
+
operator ConstSequenceHandle() const;
/// \brief attach entity view to sequence
///
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
index 80f13e364..9ae40d5fc 100644
--- a/modules/seq/base/tests/test_seq.py
+++ b/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'))
--
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