diff --git a/modules/seq/alg/pymod/CMakeLists.txt b/modules/seq/alg/pymod/CMakeLists.txt
index 93dd1b348e19c104bc5364eb04dbde4238bd5dfa..3b0a705877194de18c04de5d1b84561cccf22bfc 100644
--- a/modules/seq/alg/pymod/CMakeLists.txt
+++ b/modules/seq/alg/pymod/CMakeLists.txt
@@ -1,6 +1,5 @@
set(OST_SEQ_ALG_PYMOD_SOURCES
wrap_seq_alg.cc
- export_align.cc
)
pymod(NAME seq_alg OUTPUT_DIR ost/seq/alg
diff --git a/modules/seq/alg/pymod/export_align.cc b/modules/seq/alg/pymod/export_align.cc
deleted file mode 100644
index 49a8d1c8bc5dffb55230accdbaf988d8014827bd..0000000000000000000000000000000000000000
--- a/modules/seq/alg/pymod/export_align.cc
+++ /dev/null
@@ -1,59 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 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
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-#include <boost/python/register_ptr_to_python.hpp>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-using namespace boost::python;
-
-#include <ost/info/info.hh>
-
-#include <ost/mol/mol.hh>
-#include <ost/seq/alg/subst_weight_matrix.hh>
-#include <ost/seq/alg/local_align.hh>
-#include <ost/seq/alg/global_align.hh>
-using namespace ost;
-using namespace ost::seq;
-using namespace ost::seq::alg;
-
-void export_Align()
-{
- class_<SubstWeightMatrix, SubstWeightMatrixPtr>("SubstWeightMatrix", init<>())
- .def("GetWeight", &SubstWeightMatrix::GetWeight)
- .def("SetWeight", &SubstWeightMatrix::SetWeight)
- ;
-class_<AlignmentOpts>("AlignmentOpts", init<int,int, SubstWeightMatrixPtr>())
- .def_readwrite("gap_open_penalty", &AlignmentOpts::gap_open_penalty)
- .def_readwrite("gap_extension_penalty",
- &AlignmentOpts::gap_extension_penalty)
- .def_readwrite("subst_weights", &AlignmentOpts::subst_weights)
-;
- def("SubstWeightMatrixToInfo", &SubstWeightMatrixToInfo);
- def("SubstWeightMatrixFromInfo", &SubstWeightMatrixFromInfo);
-
- class_<AlignedPatch>("AlignedPatch", no_init)
- .def_readwrite("alignment", &AlignedPatch::alignment)
- .def_readwrite("offset_a", &AlignedPatch::offset_a)
- .def_readwrite("offset_b", &AlignedPatch::offset_b)
- ;
- class_<AlignedPatchList>("AlignedPatchList", init<>())
- .def(vector_indexing_suite<AlignedPatchList>())
- ;
- def("LocalSequenceAlign", &LocalSequenceAlign);
- def("GlobalSequenceAlign", &GlobalSequenceAlign);
-}
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 561d0379c24210f86a9bee8a321f2ee7431c7723..b9e4b683e0b3b6a599b420488fc08b5f552c1736 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -27,8 +27,6 @@ using namespace boost::python;
using namespace ost::seq;
using namespace ost::seq::alg;
-void export_Align();
-
BOOST_PYTHON_MODULE(_seq_alg)
{
enum_<RefMode::Type>("RefMode")
@@ -48,5 +46,5 @@ BOOST_PYTHON_MODULE(_seq_alg)
;
def("MergePairwiseAlignments", &MergePairwiseAlignments);
def("Conservation", &Conservation, (arg("assign")=true, arg("prop_name")="cons"));
- export_Align();
+
}
diff --git a/modules/seq/alg/src/CMakeLists.txt b/modules/seq/alg/src/CMakeLists.txt
index 5f3cac427b7c4b20094856c135accdd854aac184..7b4f86f53e5bb8c08feeba088deb1c8319691d0d 100644
--- a/modules/seq/alg/src/CMakeLists.txt
+++ b/modules/seq/alg/src/CMakeLists.txt
@@ -3,20 +3,16 @@ sequence_identity.hh
module_config.hh
ins_del.hh
subst_weight_matrix.hh
-local_align.hh
alignment_opts.hh
-global_align.hh
merge_pairwise_alignments.hh
conservation.hh
)
set(OST_SEQ_ALG_SOURCES
merge_pairwise_alignments.cc
-global_align.cc
sequence_identity.cc
ins_del.cc
subst_weight_matrix.cc
-local_align.cc
conservation.cc
)
diff --git a/modules/seq/alg/src/global_align.cc b/modules/seq/alg/src/global_align.cc
deleted file mode 100644
index 6003ab84fe79bfbb754913f906e7b8440abf5b51..0000000000000000000000000000000000000000
--- a/modules/seq/alg/src/global_align.cc
+++ /dev/null
@@ -1,128 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 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: Marco Biasini
- */
-#include <ost/seq/alg/global_align.hh>
-
-namespace ost { namespace seq { namespace alg {
-
-namespace {
-
-class GlobalAlnMatrix {
-public:
- GlobalAlnMatrix(int num_cols, int num_rows)
- : num_rows_(num_rows), num_cols_(num_cols) {
- data_.resize(num_cols_*num_rows_,0);
- }
- short Get(int x, int y) const {
- assert(x>=0 && x<num_cols_);
- assert(y>=0 && y<num_rows_);
- return data_[num_cols_*y+x];
- }
- void Set(int x, int y, short value) {
- data_[num_cols_*y+x]=value;
- }
-
- int num_rows_;
- int num_cols_;
- std::vector<short> data_;
-};
-
-}
-
-AlignmentHandle GlobalSequenceAlign(const SequenceHandle& seq_a,
- const SequenceHandle& seq_b,
- const AlignmentOpts& opts)
-{
- // using the strings directly is much better for performance reasons
- String ssa=seq_a.GetString();
- String ssb=seq_b.GetString();
- GlobalAlnMatrix mat(ssa.size()+1, ssb.size()+1);
-
- // build-up aln mattrix
- for (size_t i=0; i<ssa.size()+1; ++i) {
- mat.Set(i, 0, i*opts.gap_open_penalty);
- }
- for (size_t i=0; i<ssb.size()+1; ++i) {
- mat.Set(0, i, i*opts.gap_open_penalty);
- }
- for (size_t i=1; i<ssa.size()+1; ++i) {
- for (size_t j=1; j<ssb.size()+1; ++j) {
- short mm=opts.subst_weights->GetWeight(ssa[i-1], ssb[j-1]);
- short m11=mat.Get(i-1, j-1)+mm;
- short m10=mat.Get(i-1, j)-opts.gap_open_penalty;
- short m01=mat.Get(i, j-1)-opts.gap_open_penalty;
- mat.Set(i, j, std::max(m11, std::max(m10, m01)));
- }
- }
-
- // backtracking
- size_t i=ssa.size();
- size_t j=ssb.size();
- String asa;
- String asb;
- asa.reserve(ssa.size());
- asb.reserve(ssb.size());
-
- while (i>0 && j>0) {
- // find out where we came from
- short m11=mat.Get(i-1, j-1);
- short m10=mat.Get(i-1, j);
- short m01=mat.Get(i, j-1);
- short m00=mat.Get(i, j);
- short mm=opts.subst_weights->GetWeight(ssa[i-1], ssb[j-1]);
- if (m11+mm==m00) { // match
- asa.append(1, ssa[i-1]);
- asb.append(1, ssb[j-1]);
- --j;
- --i;
- } else if (m10-opts.gap_open_penalty==m00) { // seq b has a gap
- asa.append(1, ssa[i-1]);
- asb.append(1, '-');
- --i;
- } else if (m01-opts.gap_open_penalty==m00) { // seq a has a gap
- asa.append(1, '-');
- asb.append(1, ssb[j-1]);
- --j;
- }
- }
- while (i>0) {
- asa.append(1, ssa[i-1]);
- asb.append(1, '-');
- --i;
- }
- while (j>0) {
- asa.append(1, '-');
- asb.append(1, ssb[j-1]);
- --j;
- }
- // reverse the two strings
- String rasa, rasb;
- rasa.reserve(asa.size());
- rasb.reserve(asb.size());
- std::copy(asa.rbegin(), asa.rend(), std::back_inserter(rasa));
- std::copy(asb.rbegin(), asb.rend(), std::back_inserter(rasb));
- AlignmentHandle aln=CreateAlignment();
- aln.AddSequence(CreateSequence(seq_a.GetName(), rasa));
- aln.AddSequence(CreateSequence(seq_b.GetName(), rasb));
- return aln;
-}
-
-}}}
diff --git a/modules/seq/alg/src/global_align.hh b/modules/seq/alg/src/global_align.hh
deleted file mode 100644
index 9b477fa9bd2c4c06755b7858b5f1f0d2cea6dcee..0000000000000000000000000000000000000000
--- a/modules/seq/alg/src/global_align.hh
+++ /dev/null
@@ -1,42 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 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
-//------------------------------------------------------------------------------
-#ifndef OST_SEQ_ALG_GLOBAL_ALIGN_HH
-#define OST_SEQ_ALG_GLOBAL_ALIGN_HH
-/*
- Author: Marco Biasini
- */
-#include <ost/seq/alignment_handle.hh>
-#include <ost/seq/alg/module_config.hh>
-#include <ost/seq/alg/alignment_opts.hh>
-
-namespace ost { namespace seq { namespace alg {
-
-/// \brief globally align two sequences
-///
-/// the optimal global alignment of the two sequences, given the substitution
-/// weights and gap opening penalties is computed by using a classical
-/// Needleman-Wunsch algorithm. The algorithm has O(n*m) complexity in both
-/// space and time.
-AlignmentHandle DLLEXPORT_OST_SEQ_ALG
-GlobalSequenceAlign(const SequenceHandle& seq_a, const SequenceHandle& seq_b,
- const AlignmentOpts& opts);
-
-}}}
-
-#endif
\ No newline at end of file
diff --git a/modules/seq/alg/src/local_align.cc b/modules/seq/alg/src/local_align.cc
deleted file mode 100644
index 197a34226b214c09c960be1ab8eb046c1b7ac1cf..0000000000000000000000000000000000000000
--- a/modules/seq/alg/src/local_align.cc
+++ /dev/null
@@ -1,160 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 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
-//------------------------------------------------------------------------------
-#include "local_align.hh"
-
-namespace ost { namespace seq { namespace alg {
-
-namespace {
-
-class AliMatrix {
-public:
- AliMatrix(int num_rows, int num_cols)
- : num_rows_(num_rows), num_cols_(num_cols) {
- data_.resize(num_cols_*num_rows_,0);
- }
- short Get(int x, int y) const {
- assert(x>=0 && x<num_rows_);
- assert(y>=0 && y<num_cols_);
- return data_[num_cols_*x+y];
- }
- void Set(int x, int y, short value) {
- data_[num_cols_*x+y]=value;
- }
-
- int num_rows_;
- int num_cols_;
- std::vector<short> data_;
-};
-
-std::pair<int, int> FindMax(const AliMatrix& mat, int min_col,
- int max_col, int min_row, int max_row) {
- int max_i=0, max_j=0, max_value=-1;
- for (int i=min_col; i<max_col; ++i) {
- for (int j=min_row; j<max_row; ++j) {
- int x=mat.Get(i, j);
- if (x>max_value) {
- max_value=x;
- max_i=i; max_j=j;
- }
- }
- }
- return std::make_pair(max_i, max_j);
-}
-
-// divide and conquer the alignment matrix to get all patches.
-void CollectPatches(AlignedPatchList& patches, const String& seq_a,
- const String& seq_b, const AliMatrix& ali_mat, int min_col,
- int max_col, int min_row, int max_row) {
- if (max_col-min_col<2 || max_row-min_row<2)
- return;
- String seq_c, seq_d;
- seq_c.reserve(std::max(seq_a.length(), seq_b.length()));
- seq_d.reserve(std::max(seq_a.length(), seq_b.length()));
- std::pair<int, int> best=FindMax(ali_mat, min_col, max_col, min_row, max_row);
- std::pair<int, int> max_pair=best;
-
- typedef std::pair<int, int> XY;
- std::vector<XY> stack;
- while(ali_mat.Get(best.first, best.second)>0 && best.first>=min_col &&
- best.second>=min_row) {
- stack.push_back(XY(best.first, best.second));
- int a=ali_mat.Get(best.first-1, best.second-1);
- int b=ali_mat.Get(best.first-1, best.second);
- int c=ali_mat.Get(best.first, best.second-1);
- if (a>=c) {
- if (a>=b) {
- best.first-=1;
- best.second-=1;
- } else {
- best.first-=1;
- }
- } else {
- if (c>b) {
- best.second-=1;
- } else {
- best.first-=1;
- }
- }
- }
- for (int i=static_cast<int>(stack.size())-2; i>=0; --i) {
- XY next=stack[i];
- XY curr=stack[i+1];
- if (next.first==curr.first+1) {
- if (next.second==curr.second+1) {
- seq_c.append(1, seq_a[next.first-1]);
- seq_d.append(1, seq_b[next.second-1]);
- } else {
- seq_c.append(1, seq_a[next.first-1]);
- seq_d.append(1, '-');
- }
- } else {
- if (next.second==curr.second+1) {
- seq_c.append(1, '-');
- seq_d.append(1, seq_b[next.second-1]);
- } else {
- seq_c.append(1, seq_a[next.first-1]);
- seq_d.append(1, '-');
- }
- }
- }
- if (seq_c.size()>2 && seq_c.size()>2) {
- patches.push_back(AlignedPatch());
- patches.back().offset_a=best.first;
- patches.back().offset_b=best.second;
- if (seq_c[0]=='-' || seq_d[0]=='-') {
- seq_c.erase(seq_c.begin());
- seq_d.erase(seq_d.begin());
- }
- patches.back().alignment=CreateAlignment();
- patches.back().alignment.AddSequence(CreateSequence("seq1", seq_c));
- patches.back().alignment.AddSequence(CreateSequence("seq2 ", seq_d));
- CollectPatches(patches, seq_a, seq_b, ali_mat, max_pair.first+1, max_col,
- max_pair.second+1, max_row);
- }
-}
-
-}
-
-AlignedPatchList LocalSequenceAlign(const SequenceHandle& sseq_a,
- const SequenceHandle& sseq_b,
- const AlignmentOpts& opts)
-{
-
- String seq_a=sseq_a.GetString();
- String seq_b=sseq_b.GetString();
- AliMatrix ali_mat(seq_a.length()+1, seq_b.length()+1);
- // build alignment matrix.
- for (size_t i=0; i<seq_a.length(); ++i) {
- for (size_t j=0; j<seq_b.length(); ++j) {
- int w=opts.subst_weights->GetWeight(seq_a[i], seq_b[j]);
- int match_mism=std::max(0, w+int(ali_mat.Get(i, j)));
- int del=ali_mat.Get(i, j+1)-opts.gap_open_penalty;
- int ins=ali_mat.Get(i+1, j)-opts.gap_open_penalty;
- ali_mat.Set(i+1, j+1, std::max(match_mism, std::max(del, ins)));
- }
- }
- AlignedPatchList patches;
- // backtracking
- CollectPatches(patches, seq_a, seq_b, ali_mat, 0, seq_a.length()+1,
- 0, seq_b.length()+1);
- return patches;
-}
-
-}}}
-
diff --git a/modules/seq/alg/src/local_align.hh b/modules/seq/alg/src/local_align.hh
deleted file mode 100644
index b685851d39994c8106c3368b6127c356898d5428..0000000000000000000000000000000000000000
--- a/modules/seq/alg/src/local_align.hh
+++ /dev/null
@@ -1,70 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 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
-//------------------------------------------------------------------------------
-#ifndef OST_SEQ_LOCAL_ALIGN_HH
-#define OST_SEQ_LOCAL_ALIGN_HH
-
-
-#include <ost/seq/alignment_handle.hh>
-#include <ost/seq/alg/module_config.hh>
-#include <ost/seq/alg/alignment_opts.hh>
-#include <ost/seq/alg/subst_weight_matrix.hh>
-/*
- Author: Marco Biasini
- */
-
-namespace ost { namespace seq { namespace alg {
-
-/// \brief holds the result of a local sequence alignment
-struct DLLEXPORT_OST_SEQ_ALG AlignedPatch {
- /// \brief offset of aligned patch relative to the start of the first sequence
- int offset_a;
- /// \brief offset of aligned patch relative to the start of the first sequence
- int offset_b;
- /// \brief the aligned patch
- AlignmentHandle alignment;
- bool operator==(const AlignedPatch& rhs) const {
- return offset_a==rhs.offset_a && offset_b==rhs.offset_b &&
- rhs.alignment==alignment;
- }
- bool operator!=(const AlignedPatch& rhs) const {
- return !this->operator==(rhs);
- }
-};
-
-typedef std::vector<AlignedPatch> AlignedPatchList;
-
-/// \brief Align pair of sequences locally with Waterman-Smith algorithm
-///
-/// The alignment algorithm will return the set of optimal alignments given the
-/// weights of the substitution matrix and gap opening and extension penalties.
-/// The sequence patches are non-overlapping
-///
-/// \param seq_a is the first sequence to be aligned
-/// \param seq_b is the second sequence to be aligned
-///
-/// \param opts holds a set of alignment options such as gap opening and
-/// extension penalties and the substitution matrix
-///
-/// \return list of locally aligned sequence patches.
-AlignedPatchList DLLEXPORT_OST_SEQ_ALG
-LocalSequenceAlign(const SequenceHandle& seq_a, const SequenceHandle& seq_b,
- const AlignmentOpts& opts);
-}}}
-
-#endif