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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
/*
Author: Gerardo Tauriello, Gabriel Studer
*/
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <boost/python.hpp>
#include <ost/seq/profile_handle.hh>
using namespace ost::seq;
using namespace boost::python;
namespace {
boost::python::list wrap_get_names(ProfileDBPtr db) {
std::vector<String> v_names = db->GetNames();
boost::python::list names;
for (std::vector<String>::iterator i = v_names.begin();
i != v_names.end(); ++i) {
names.append(*i);
}
return names;
}
} // anon ns
void export_profile_handle()
{
enum_<HMMTransition>("HMMTransition")
.value("HMM_M2M", HMM_M2M)
.value("HMM_M2I", HMM_M2I)
.value("HMM_M2D", HMM_M2D)
.value("HMM_I2M", HMM_I2M)
.value("HMM_I2I", HMM_I2I)
.value("HMM_D2M", HMM_D2M)
.value("HMM_D2D", HMM_D2D)
;
class_<HMMData, HMMDataPtr>("HMMData", init<>())
.add_property("neff", &HMMData::GetNeff, &HMMData::SetNeff)
.add_property("neff_i", &HMMData::GetNeff_I, &HMMData::SetNeff_I)
.add_property("neff_d", &HMMData::GetNeff_D, &HMMData::SetNeff_D)
.def("GetProb", &HMMData::GetProb, (arg("transition")))
.def("SetProb", &HMMData::SetProb, (arg("transition"), arg("prob")))
;
class_<ProfileColumn>("ProfileColumn", init<>())
.add_property("entropy", &ProfileColumn::GetEntropy)
.def("GetFreq", &ProfileColumn::GetFreq, (arg("aa")))
.def("SetFreq", &ProfileColumn::SetFreq, (arg("aa"), arg("freq")))
.def("GetHMMData", &ProfileColumn::GetHMMData)
.def("SetHMMData", &ProfileColumn::SetHMMData)
.add_property("hmm_data", &ProfileColumn::GetHMMData, &ProfileColumn::SetHMMData)
.def("GetScore", &ProfileColumn::GetScore,
(arg("other"), arg("null_model")))
.def("BLOSUMNullModel", &ProfileColumn::BLOSUMNullModel)
.staticmethod("BLOSUMNullModel")
.def("HHblitsNullModel", &ProfileColumn::HHblitsNullModel)
.staticmethod("HHblitsNullModel")
;
class_<ProfileColumnList>("ProfileColumnList", init<>())
.def(vector_indexing_suite<ProfileColumnList>())
;
class_<ProfileHandle, ProfileHandlePtr>("ProfileHandle", init<>())
.def("__len__",&ProfileHandle::size)
.def("AddColumn", &ProfileHandle::AddColumn, (arg("col"), arg("olc")='X'))
.def("Extract", &ProfileHandle::Extract, (arg("from"), arg("to")))
.def("GetAverageScore", &ProfileHandle::GetAverageScore,
(arg("other"), arg("offset")=0))
.add_property("null_model",
make_function(&ProfileHandle::GetNullModel,
return_value_policy<copy_const_reference>()),
&ProfileHandle::SetNullModel)
.add_property("columns",
make_function(&ProfileHandle::GetColumns,
return_value_policy<copy_const_reference>()))
.add_property("avg_entropy", &ProfileHandle::GetAverageEntropy)
.add_property("sequence", &ProfileHandle::GetSequence,
&ProfileHandle::SetSequence)
.add_property("neff", &ProfileHandle::GetNeff,
&ProfileHandle::SetNeff)
;
class_<ProfileDB, ProfileDBPtr>("ProfileDB", init<>())
.def("Load", &ProfileDB::Load, (arg("filename"))).staticmethod("Load")
.def("Save", &ProfileDB::Save, (arg("filename")))
.def("AddProfile", &ProfileDB::AddProfile, (arg("name"), arg("prof")))
.def("GetProfile", &ProfileDB::GetProfile, (arg("name")))
.def("Size", &ProfileDB::size)
.def("GetNames",&wrap_get_names)
;
}
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