From 13a4eca52d2c68594876f5d3c8802c869db3231d Mon Sep 17 00:00:00 2001
From: juergen <juergen@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 15 Apr 2010 19:31:08 +0000
Subject: [PATCH] adding reverse iterator for AlignedRegion
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2022 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/seq/base/pymod/export_sequence.cc | 76 +++++++++++++------
.../seq/base/src/aligned_column_iterator.hh | 19 +++--
2 files changed, 66 insertions(+), 29 deletions(-)
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index bf2caca97..ce05be244 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -57,8 +57,8 @@ T do_slice(const T& t, slice& sl) {
try {
end=extract<int>(sl.stop());
} catch(error_already_set) {
- PyErr_Clear();
- }
+ PyErr_Clear();
+ }
return t.Slice(start, end-start);
}
@@ -83,18 +83,38 @@ AlignedRegion slice_aln(const AlignmentHandle& aln, slice sl) {
try {
end=extract<int>(sl.stop());
} catch(error_already_set) {
- PyErr_Clear();
- }
+ PyErr_Clear();
+ }
return aln.MakeRegion(start, end-start);
}
+struct RevRegionRangeIter {
+ RevRegionRangeIter(AlignedColumnIterator b,
+ AlignedColumnIterator e):
+ b_(b), e_(e)
+ { }
+
+ AlignedColumn next()
+ {
+ if (b_==e_) {
+ boost::python::objects::stop_iteration_error();
+ }
+ AlignedColumn col=*e_;
+ --e_;
+ return col;
+ }
+private:
+ AlignedColumnIterator b_;
+ AlignedColumnIterator e_;
+};
+
struct RegionRangeIter {
- RegionRangeIter(AlignedColumnIterator b,
+ RegionRangeIter(AlignedColumnIterator b,
AlignedColumnIterator e):
b_(b), e_(e)
{ }
-
+
AlignedColumn next()
{
if (b_==e_) {
@@ -120,6 +140,11 @@ RegionRangeIter iter_range2(AlignedRegion& aln_region)
return RegionRangeIter(aln_region.begin(), aln_region.end());
}
+RevRegionRangeIter iter_range3(AlignedRegion& aln_region)
+{
+ return RevRegionRangeIter(aln_region.begin(), aln_region.end());
+}
+
}
void export_sequence()
@@ -131,12 +156,12 @@ void export_sequence()
.def("GetResidue", &ConstSequenceHandle::GetResidue)
.def("GetOneLetterCode", &ConstSequenceHandle::GetOneLetterCode)
.def("__getitem__", &ConstSequenceHandle::GetOneLetterCode)
- .def("GetSequenceOffset", &ConstSequenceHandle::GetSequenceOffset)
+ .def("GetSequenceOffset", &ConstSequenceHandle::GetSequenceOffset)
.def("Copy", &ConstSequenceHandle::Copy)
.def("GetFirstNonGap", &ConstSequenceHandle::GetFirstNonGap)
- .def("GetLastNonGap", &ConstSequenceHandle::GetLastNonGap)
+ .def("GetLastNonGap", &ConstSequenceHandle::GetLastNonGap)
.add_property("first_non_gap", &SequenceHandle::GetFirstNonGap)
- .add_property("last_non_gap", &SequenceHandle::GetLastNonGap)
+ .add_property("last_non_gap", &SequenceHandle::GetLastNonGap)
.def("GetAttachedView", &ConstSequenceHandle::GetAttachedView)
.def("GetGaplessString", &ConstSequenceHandle::GetGaplessString)
.def("GetString", &ConstSequenceHandle::GetString,
@@ -145,7 +170,7 @@ void export_sequence()
return_value_policy<copy_const_reference>())
.def("HasAttachedView", &ConstSequenceHandle::HasAttachedView)
.def("__len__", &SequenceHandle::GetLength)
- .add_property("length", &SequenceHandle::GetLength)
+ .add_property("length", &SequenceHandle::GetLength)
.add_property("attached_view", &ConstSequenceHandle::GetAttachedView)
.add_property("name",
make_function(&ConstSequenceHandle::GetName,
@@ -155,10 +180,10 @@ void export_sequence()
.add_property("string",
make_function(&ConstSequenceHandle::GetString,
return_value_policy<copy_const_reference>()))
- .def("__str__", &ConstSequenceHandle::GetString,
+ .def("__str__", &ConstSequenceHandle::GetString,
return_value_policy<copy_const_reference>())
- ;
-
+ ;
+
class_<SequenceHandle, bases<ConstSequenceHandle> >("SequenceHandle", init<>())
.def("SetSequenceOffset", &SequenceHandle::SetSequenceOffset)
.def("AttachView", attach_one)
@@ -174,7 +199,7 @@ void export_sequence()
return_value_policy<copy_const_reference>()),
&SequenceHandle::SetName)
.add_property("sequence_offset", &SequenceHandle::GetSequenceOffset,
- &SequenceHandle::SetSequenceOffset)
+ &SequenceHandle::SetSequenceOffset)
;
def("CreateSequence", &CreateSequence);
/*class_<SequenceHandleList>("SequenceHandleList", init<>())
@@ -182,6 +207,9 @@ void export_sequence()
;*/
class_<RegionRangeIter>("RegionRangeIter", no_init)
.def("next", &RegionRangeIter::next)
+ ;
+ class_<RevRegionRangeIter>("RevRegionRangeIter", no_init)
+ .def("next", &RevRegionRangeIter::next)
;
class_<AlignmentHandle>("AlignmentHandle", init<>())
.def("GetCount", &AlignmentHandle::GetCount)
@@ -199,6 +227,7 @@ void export_sequence()
.def("AttachView", attach_view_a)
.def("AttachView", attach_view_b)
.def("Cut", &AlignmentHandle::Cut)
+ .def("MakeRegion", &AlignmentHandle::MakeRegion)
.def("Replace",&AlignmentHandle::Replace)
.def("__getitem__", &slice_aln)
.def("__getitem__", &AlignmentHandle::operator[])
@@ -224,13 +253,14 @@ void export_sequence()
.def("SetMaster", &AlignedRegion::SetMaster)
.def("GetMaster", &AlignedRegion::GetMaster)
.def("GetAlignmentHandle",&AlignedRegion::GetAlignmentHandle)
- .add_property("master", &AlignedRegion::GetMaster,
+ .add_property("master", &AlignedRegion::GetMaster,
&AlignedRegion::SetMaster)
- .def("__getitem__", &AlignedRegion::operator[])
+ .def("__getitem__", &AlignedRegion::operator[])
.def("__len__", &AlignedRegion::GetLength)
.def("__iter__", iter_range2)
+ //~ .def("__iter__", iter_range3)
.add_property("start", &AlignedRegion::GetStart)
- .add_property("end", &AlignedRegion::GetEnd)
+ .add_property("end", &AlignedRegion::GetEnd)
;
class_<ConstSequenceList>("ConstSequenceList", init<>())
CONST_SEQ_LIST_DEF(ConstSequenceList)
@@ -238,20 +268,20 @@ void export_sequence()
;
class_<SequenceList>("SequenceList", init<>())
CONST_SEQ_LIST_DEF(SequenceList)
- .def("__getitem__", &do_slice_b)
- ;
+ .def("__getitem__", &do_slice_b)
+ ;
class_<AlignmentList>("AlignmentList", init<>())
.def(vector_indexing_suite<AlignmentList>())
- .def("__getitem__", &do_slice_b)
- ;
+ .def("__getitem__", &do_slice_b)
+ ;
implicitly_convertible<SequenceList, ConstSequenceList>();
def("CreateSequenceList", &CreateSequenceList);
def("SequenceFromChain", seq_from_chain_a);
- def("SequenceFromChain", seq_from_chain_b);
+ def("SequenceFromChain", seq_from_chain_b);
def("SequenceToInfo", &SequenceToInfo);
def("SequenceListToInfo", &SequenceListToInfo);
def("SequenceFromInfo", &SequenceFromInfo);
def("CreateAlignment", &CreateAlignment);
def("AlignmentFromSequenceList", &AlignmentFromSequenceList);
- def("SequenceListFromInfo", &SequenceListFromInfo);
+ def("SequenceListFromInfo", &SequenceListFromInfo);
}
diff --git a/modules/seq/base/src/aligned_column_iterator.hh b/modules/seq/base/src/aligned_column_iterator.hh
index 5fa8b932c..5967d65f4 100644
--- a/modules/seq/base/src/aligned_column_iterator.hh
+++ b/modules/seq/base/src/aligned_column_iterator.hh
@@ -41,36 +41,43 @@ public:
{
this->UpdateVal();
}
-
+
AlignedColumnIterator& operator++()
{
++curr_;
this->UpdateVal();
return *this;
}
-
+
+ AlignedColumnIterator& operator--()
+ {
+ --curr_;
+ this->UpdateVal();
+ return *this;
+ }
+
AlignedColumnIterator operator++(int)
{
AlignedColumnIterator ans(*this);
++(*this);
return ans;
}
-
+
AlignedColumn* operator->()
{
return &val_;
}
-
+
AlignedColumn& operator*()
{
return val_;
}
-
+
bool operator==(const AlignedColumnIterator& rhs) const
{
return aln_==rhs.aln_ && rhs.curr_==curr_;
}
-
+
bool operator!=(const AlignedColumnIterator& rhs) const
{
return !(*this==rhs);
--
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