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// Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
// Biozentrum - University of Basel
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
#include <boost/python.hpp>
#include <promod3/modelling/gap_extender.hh>
#include <promod3/core/export_helper.hh>
using namespace ost;
using namespace boost::python;
using namespace promod3;
using namespace promod3::modelling;
namespace {
GapExtenderPtr wrap_ExtenderInitOne(StructuralGap& gap,
const String& seqres)
{
GapExtenderPtr extender(new GapExtender(gap, seqres));
return extender;
}
GapExtenderPtr wrap_ExtenderInitTwo(StructuralGap& gap,
const ost::seq::SequenceHandle& seqres)
{
GapExtenderPtr extender(new GapExtender(gap, seqres));
return extender;
}
ScoringGapExtenderPtr wrap_ScoringExtenderInitOneB(StructuralGap& gap,
Real extension_penalty,
list& penalties,
const String& seqres,
const int max_length=-2)
{
std::vector<Real> v_penalties;
core::ConvertListToVector(penalties, v_penalties);
ScoringGapExtenderPtr extender(
new ScoringGapExtender(gap, extension_penalty, v_penalties,
seqres, max_length));
return extender;
}
ScoringGapExtenderPtr wrap_ScoringExtenderInitOne(StructuralGap& gap,
Real extension_penalty,
list& penalties,
const String& seqres)
{
return wrap_ScoringExtenderInitOneB(gap, extension_penalty, penalties, seqres);
}
ScoringGapExtenderPtr wrap_ScoringExtenderInitTwoB(
StructuralGap& gap,
Real extension_penalty,
list& penalties,
const ost::seq::SequenceHandle& seqres,
const int max_length=-2)
{
std::vector<Real> v_penalties;
core::ConvertListToVector(penalties, v_penalties);
ScoringGapExtenderPtr extender(
new ScoringGapExtender(gap, extension_penalty, v_penalties,
seqres, max_length));
return extender;
}
ScoringGapExtenderPtr wrap_ScoringExtenderInitTwo(
StructuralGap& gap,
Real extension_penalty,
list& penalties,
const ost::seq::SequenceHandle& seqres)
{
return wrap_ScoringExtenderInitTwoB(gap, extension_penalty, penalties, seqres);
}
}
void export_gap_extender()
{
class_<GapExtender>("GapExtender", no_init)
.def("__init__",make_constructor(wrap_ExtenderInitOne))
.def("__init__",make_constructor(wrap_ExtenderInitTwo))
.def("Extend", &GapExtender::Extend)
;
register_ptr_to_python<GapExtenderPtr>();
class_<FullGapExtender>("FullGapExtender", no_init)
.def(init<StructuralGap&, const String&, const int>(
(arg("gap"), arg("seqres"), arg("max_length")=-1)))
.def(init<StructuralGap&, const ost::seq::SequenceHandle&, const int>(
(arg("gap"), arg("seqres"), arg("max_length")=-1)))
.def("Extend", &FullGapExtender::Extend)
;
register_ptr_to_python<FullGapExtenderPtr>();
class_<ScoringGapExtender>("ScoringGapExtender", no_init)
.def("__init__",make_constructor(wrap_ScoringExtenderInitOne))
.def("__init__",make_constructor(wrap_ScoringExtenderInitTwo))
.def("__init__",make_constructor(wrap_ScoringExtenderInitOneB))
.def("__init__",make_constructor(wrap_ScoringExtenderInitTwoB))
.def("Extend", &ScoringGapExtender::Extend)
;
register_ptr_to_python<ScoringGapExtenderPtr>();
}
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