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main.cpp
1525 lines (1106 loc) · 45.1 KB
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main.cpp
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/*
* Copyright (C) 2009-2012 Simon A. Berger
*
* This file is part of papara.
*
* papara is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* papara 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with papara. If not, see <http://www.gnu.org/licenses/>.
*/
#include "ivymike/multiple_alignment.h"
#include <stdexcept>
#include <iostream>
#include <iomanip>
#include <vector>
#include <deque>
#include <map>
#include <functional>
#include <cstring>
#include <boost/io/ios_state.hpp>
#include <boost/iostreams/tee.hpp>
#include <boost/iostreams/stream.hpp>
#include <boost/bind.hpp>
#include "parsimony.h"
#include "pvec.h"
#include "align_utils.h"
#include "pars_align_seq.h"
#include "pars_align_gapp_seq.h"
#include "fasta.h"
#include "vec_unit.h"
#include "align_pvec_vec.h"
#include "ivymike/tree_parser.h"
#include "ivymike/time.h"
#include "ivymike/getopt.h"
#include "ivymike/thread.h"
#include "ivymike/demangle.h"
#include "ivymike/stupid_ptr.h"
#include "ivymike/algorithm.h"
#include "ivymike/smart_ptr.h"
using namespace ivy_mike;
using namespace ivy_mike::tree_parser_ms;
using namespace boost::numeric;
// template<typename score_t>
// struct align_arrays_vec {
// aligned_buffer<score_t> s;
//
// };
//
// template<typename score_t, size_t W>
// static void align_pvec_score( aligned_buffer<score_t> &a_prof, aligned_buffer<score_t> &a_aux_prof, const std::vector<uint8_t> &b, score_t mismatch_score, score_t match_cgap, score_t gap_open, score_t gap_extend, align_arrays_vec<score_t> &arr, aligned_buffer<score_t> &out ) {
//
// typedef vector_unit<score_t, W> vu;
// typedef typename vu::vec_t vec_t;
//
// if( arr.s.size() < a_prof.size() ) {
// arr.s.resize( a_prof.size() );
//
// }
//
// const score_t aux_cgap = 0x1;
//
// assert( a_prof.size() % W == 0 );
// size_t asize = a_prof.size() / W;
// assert( asize > b.size() );
//
// const size_t band_width = asize - b.size();
// std::fill( arr.s.begin(), arr.s.end(), 0 );
//
// const score_t LARGE = 32000;
// // std::fill( arr.si.begin(), arr.si.end(), LARGE );
// std::fill( arr.s.begin() + (band_width + 1) * W, arr.s.begin() + (band_width + 2) * W, LARGE );
// //arr.s.at(band_width+1) = LARGE;
//
// // score_t min_score = LARGE;
//
// for( size_t ib = 0; ib < b.size(); ib++ ) {
// const vec_t bc = vu::set1(b[ib]);
//
// vec_t last_sl = vu::set1(LARGE);
// vec_t last_sc = vu::set1(LARGE);
// vec_t last_sdiag = vu::set1(0);
//
// size_t astart = ib;
//
// score_t * __restrict s_iter = &arr.s[0];
//
//
//
//
//
// last_sdiag = vu::load(s_iter);
//
//
// for( size_t ia = astart; ia <= ib + band_width; ++ia, s_iter += W ) {
// vec_t ac = vu::load( a_prof(ia * W) );
// vec_t aaux = vu::load(a_aux_prof(ia * W));
//
// vec_t cgap_mask = vu::cmp_eq( aaux, vu::set1(aux_cgap));
//
//
// // determine match or mis-match according to parsimony bits coming from the tree.
//
// vec_t mismatch_mask = vu::cmp_eq( vu::bit_and( ac, bc ), vu::setzero() );
//
// vec_t sm = vu::add( last_sdiag, vu::bit_and( vu::set1(mismatch_score), mismatch_mask ));
// sm = vu::add( sm, vu::bit_and( vu::set1( match_cgap ), cgap_mask ));
//
// last_sdiag = vu::load(s_iter+W);
//
// // cgap_mask = vu::bit_invert( cgap_mask );
//
// vec_t last_sc_OPEN = vu::add( last_sc, vu::bit_andnot( cgap_mask, vu::set1(gap_open + gap_extend)));
// vec_t sl_score_stay = vu::add( last_sl, vu::bit_andnot( cgap_mask, vu::set1(gap_extend)));
//
//
// vec_t sl = vu::min( sl_score_stay, last_sc_OPEN );
//
// last_sl = sl;
//
//
// vec_t su = vu::add( last_sdiag, vu::set1(mismatch_score));
//
// // std::cout << "x: " << sm << " " << su << " " << sl << " ";
// vec_t sc = vu::min( sm, vu::min( su, sl ) );
//
// last_sc = sc;
//
// vu::store( sc, s_iter );
//
//
// }
// }
//
// vec_t minscore = vu::set1(LARGE);
// for( size_t i = 0; i < band_width + 1; ++i ) {
// minscore = vu::min( minscore, vu::load( arr.s(i * W)));
// }
// out.resize(W);
// vu::store( minscore, out(0));
//
// }
namespace {
typedef boost::iostreams::tee_device<std::ostream, std::ofstream> log_device;
typedef boost::iostreams::stream<log_device> log_stream;
log_stream lout;
template<typename stream_, typename device_>
class bios_open_guard {
stream_ &m_stream;
public:
bios_open_guard( stream_ &stream, device_ &device ) : m_stream(stream) {
m_stream.open( device );
}
~bios_open_guard() {
m_stream.close();
}
};
typedef bios_open_guard<log_stream, log_device> log_stream_guard;
}
class ostream_test {
std::ostream &m_os;
public:
ostream_test( std::ostream &os ) : m_os(os) {}
void operator()(int i) {
m_os << i;
}
};
// static inline parsimony_state dna_to_parsimony_state( uint8_t c ) {
// switch( c ) {
// case 'A':
// case 'a':
// return 0x1;
//
// case 'C':
// case 'c':
// return 0x2;
//
// case 'G':
// case 'g':
// return 0x4;
//
// case 'U':
// case 'u':
// case 'T':
// case 't':
// return 0x8;
//
// default:
// return 0xf;
// };
//
// }
//
//
// static inline int dna_to_cgap( uint8_t c ) {
// switch( c ) {
// case 'A':
// case 'a':
// case 'C':
// case 'c':
// case 'G':
// case 'g':
// case 'T':
// case 't':
// case 'U':
// case 'u':
// return 0x0;
//
// default:
// return AUX_CGAP;
// };
// }
static bool g_dump_aux = false;
// probgap_model *pvec_pgap::pgap_model = 0;
// class pvec_ugly {
// parsimony_state *m_v;
// size_t m_size;
//
// public:
// pvec_ugly() : m_v(0), m_size(0) {}
// ~pvec_ugly() {
// delete[] m_v;
// }
// void init( const std::vector<uint8_t> &seq ) {
// assert( m_v == 0 );
// delete[] m_v;
// m_size = seq.size(0);
// m_v = new parsimony_state[m_size];
//
// std::transform( seq.begin(), seq.end(), m_v, dna_to_parsimony_state );
// }
//
// static void newview( pvec_ugly &p, pvec_ugly &c1, pvec_ugly &c2 ) {
// assert( c1.m_size() == c2.m_size() );
//
// // p.v.resize(0);
// //p.v.resize(c1.v.size());
// #error continue here!
//
// for( size_t i = 0; i < c1.v.size(); i++ ) {
// parsimony_state ps = c1.v[i] & c2.v[i];
//
// if( ps == 0 ) {
// ps = c1.v[i] | c2.v[i];
// }
//
// //p.v.push_back( ps );
// p.v[i] = ps;
//
// }
// }
//
// };
template<class pvec_t>
class my_adata_gen : public ivy_mike::tree_parser_ms::adata {
// static int ct;
//std::vector<parsimony_state> m_pvec;
pvec_t m_pvec;
public:
// int m_ct;
my_adata_gen() {
// std::cout << "my_adata\n";
}
virtual ~my_adata_gen() {
// std::cout << "~my_adata\n";
}
virtual void visit() {
// std::cout << "tr: " << m_ct << "\n";
}
void init_pvec(const std::vector< uint8_t >& seq) {
m_pvec.init( seq );
// std::cout << "init_pvec: " << m_pvec.size() << "\n";
// m_pvec.reserve(seq.size());
// for( std::vector< uint8_t >::const_iterator it = seq.begin(); it != seq.end(); ++it ) {
// m_pvec.push_back(dna_to_parsimony_state(*it));
//
// }
}
pvec_t &get_pvec() {
return m_pvec;
}
};
// inline void newview_parsimony( std::vector<parsimony_state> &p, const std::vector<parsimony_state> &c1, const std::vector<parsimony_state> &c2 ) {
//
// }
// inline std::ostream &operator<<( std::ostream &os, const my_adata &rb ) {
//
// os << "my_adata: " << rb.m_ct;
// }
template<class ndata_t>
class my_fact : public ivy_mike::tree_parser_ms::node_data_factory {
virtual ndata_t *alloc_adata() {
return new ndata_t;
}
};
template<class lnode>
void traverse_rec( lnode *n ) {
n->m_data->visit();
if( n->next->back != 0 ) {
traverse_rec(n->next->back);
}
if( n->next->next->back != 0 ) {
traverse_rec(n->next->next->back);
}
}
// template<class lnode>
// void traverse( lnode *n ) {
// n->m_data->visit();
//
// if( n->back != 0 ) {
// traverse_rec(n->back);
// }
//
// if( n->next->back != 0 ) {
// traverse_rec(n->next->back);
// }
//
// if( n->next->next->back != 0 ) {
// traverse_rec(n->next->next->back);
// }
//
//
// }
uint8_t to_hex( double v ) {
int vi = int(fabs(v));
vi = std::min( vi, 15 );
if( vi <= 9 ) {
return '0' + vi;
} else {
return 'a' + (vi - 10);
}
}
template<class pvec_t>
void do_newview( pvec_t &root_pvec, lnode *n1, lnode *n2, bool incremental ) {
typedef my_adata_gen<pvec_t> my_adata;
std::deque<rooted_bifurcation<lnode> > trav_order;
//std::cout << "traversal for branch: " << *(n1->m_data) << " " << *(n2->m_data) << "\n";
rooted_traversal_order( n1, n2, trav_order, incremental );
// std::cout << "traversal: " << trav_order.size() << "\n";
for( std::deque< rooted_bifurcation< ivy_mike::tree_parser_ms::lnode > >::iterator it = trav_order.begin(); it != trav_order.end(); ++it ) {
// std::cout << *it << "\n";
my_adata *p = dynamic_cast<my_adata *>( it->parent->m_data.get());
my_adata *c1 = dynamic_cast<my_adata *>( it->child1->m_data.get());
my_adata *c2 = dynamic_cast<my_adata *>( it->child2->m_data.get());
// rooted_bifurcation<ivy_mike::tree_parser_ms::lnode>::tip_case tc = it->tc;
// std::cout << "tip case: " << (*it) << "\n";
pvec_t::newview(p->get_pvec(), c1->get_pvec(), c2->get_pvec(), it->child1->backLen, it->child2->backLen, it->tc);
}
{
my_adata *c1 = dynamic_cast<my_adata *>( n1->m_data.get());
my_adata *c2 = dynamic_cast<my_adata *>( n2->m_data.get());
// tip_case tc;
if( c1->isTip && c2->isTip ) {
// std::cout << "root: TIP TIP\n";
pvec_t::newview(root_pvec, c1->get_pvec(), c2->get_pvec(), n1->backLen, n2->backLen, TIP_TIP );
} else if( c1->isTip && !c2->isTip ) {
// std::cout << "root: TIP INNER\n";
pvec_t::newview(root_pvec, c1->get_pvec(), c2->get_pvec(), n1->backLen, n2->backLen, TIP_INNER );
// root_pvec = c2->get_pvec();
} else if( !c1->isTip && c2->isTip ) {
// std::cout << "root: INNER TIP\n";
pvec_t::newview(root_pvec, c2->get_pvec(), c1->get_pvec(), n1->backLen, n2->backLen, TIP_INNER );
// root_pvec = c1->get_pvec();
} else {
// std::cout << "root: INNER INNER\n";
pvec_t::newview(root_pvec, c1->get_pvec(), c2->get_pvec(), n1->backLen, n2->backLen, INNER_INNER );
}
}
// std::cout << std::hex;
// for( std::vector< parsimony_state >::const_iterator it = root_pvec.begin(); it != root_pvec.end(); ++it ) {
// std::cout << *it;
// }
//
// std::cout << std::dec << std::endl;
}
static void seq_to_nongappy_pvec( std::vector<uint8_t> &seq, std::vector<uint8_t> &pvec ) {
pvec.resize( 0 );
for( unsigned int i = 0; i < seq.size(); i++ ) {
uint8_t ps = dna_parsimony_mapping::d2p(seq[i]);
if( ps == 0x1 || ps == 0x2 || ps == 0x4 || ps == 0x8 ) {
pvec.push_back(ps);
}
}
}
void pairwise_seq_distance( std::vector< std::vector<uint8_t> > &seq );
class papara_nt_i : boost::noncopyable{
public:
virtual ~papara_nt_i() {}
virtual void calc_scores( size_t ) = 0;
virtual void print_best_scores( std::ostream & ) = 0;
virtual void write_result_phylip( std::ostream &, std::ostream &) = 0;
};
struct scoring_result {
size_t edge;
size_t qs;
int res;
scoring_result( size_t edge_, size_t qs_, int res_ ) : edge( edge_), qs(qs_), res(res_) {}
};
template<typename pvec_t>
class papara_nt : public papara_nt_i {
const static int score_gap_open = 3;
const static int score_gap_extend = 1;
const static int score_mismatch = 1;
const static int score_match_cgap = 3;
// const static int score_gap_open = 1;
// const static int score_gap_extend = 1;
// const static int score_mismatch = 3;
// const static int score_match_cgap = 10;
//typedef pvec_pgap pvec_t;
typedef my_adata_gen<pvec_t> my_adata;
const static size_t VW = 8;
struct block_t {
block_t() {
memset( this, 0, sizeof( block_t )); // FIXME: hmm, this is still legal?
}
// WARNING: these are pointers into m_ref_pvecs and m_ref_aux
// make sure they stay valid!
const int *seqptrs[VW];
const unsigned int *auxptrs[VW];
const double *gapp_ptrs[VW];
size_t ref_len;
size_t edges[VW];
int num_valid;
};
// papara_nt( const papara_nt &other );
// papara_nt & operator=( const papara_nt &other );
//multiple_alignment m_ref_ma;
std::vector <std::string > m_ref_names;
std::vector <std::vector<uint8_t> > m_ref_seqs;
std::auto_ptr<ivy_mike::tree_parser_ms::ln_pool> m_ln_pool;
edge_collector<lnode> m_ec;
std::vector <std::string> m_qs_names;
std::vector <std::vector<uint8_t> > m_qs_seqs;
std::vector<std::vector <uint8_t> > m_qs_pvecs;
std::vector<std::vector <int> > m_ref_pvecs;
std::vector<std::vector <unsigned int> > m_ref_aux;
std::vector<std::vector <double> > m_ref_gapp;
ivy_mike::mutex m_qmtx; // mutex for the block queue and the qs best score/edge arrays
std::deque<block_t> m_blockqueue;
std::vector <int> m_qs_bestscore;
std::vector <int> m_qs_bestedge;
class worker {
papara_nt &m_pnt;
size_t m_rank;
public:
worker( papara_nt & pnt, size_t rank ) : m_pnt(pnt), m_rank(rank) {}
void operator()() {
pars_align_seq<>::arrays seq_arrays(true);
pars_align_gapp_seq::arrays seq_arrays_gapp(true);
ivy_mike::timer tstatus;
double last_tstatus = 0.0;
uint64_t ncup = 0;
while( true ) {
block_t block;
{
ivy_mike::lock_guard<ivy_mike::mutex> lock( m_pnt.m_qmtx );
if( m_pnt.m_blockqueue.empty() ) {
break;
}
block = m_pnt.m_blockqueue.front();
m_pnt.m_blockqueue.pop_front();
if( m_rank == 0 && (tstatus.elapsed() - last_tstatus) > 10.0 ) {
std::cerr << tstatus.elapsed() << " " << m_pnt.m_blockqueue.size() << " blocks remaining. " << ncup / (tstatus.elapsed() * 1e9) << " gncup/s\n";
last_tstatus = tstatus.elapsed();
}
}
#if 1
assert( VW == 8 );
const align_pvec_score<short,8> aligner( block.seqptrs, block.auxptrs, block.ref_len, score_mismatch, score_match_cgap, score_gap_open, score_gap_extend );
for( unsigned int i = 0; i < m_pnt.m_qs_names.size(); i++ ) {
size_t stride = 1;
size_t aux_stride = 1;
aligner.align(m_pnt.m_qs_pvecs[i]);
const short *score_vec = aligner.get_scores();
ncup += block.num_valid * block.ref_len * m_pnt.m_qs_pvecs[i].size();
{
ivy_mike::lock_guard<ivy_mike::mutex> lock( m_pnt.m_qmtx );
for( int k = 0; k < block.num_valid; k++ ) {
if( score_vec[k] < m_pnt.m_qs_bestscore[i] || (score_vec[k] == m_pnt.m_qs_bestscore[i] && block.edges[k] < size_t(m_pnt.m_qs_bestedge[i]) )) {
const bool validate = false;
if( validate ) {
const int *seqptr = block.seqptrs[k];
const unsigned int *auxptr = block.auxptrs[k];
pars_align_seq<> pas( seqptr, m_pnt.m_qs_pvecs[i].data(), block.ref_len, m_pnt.m_qs_pvecs[i].size(), stride, auxptr, aux_stride, seq_arrays, 0, score_gap_open, score_gap_extend, score_mismatch, score_match_cgap );
int res = pas.alignFreeshift(INT_MAX);
if( res != score_vec[k] ) {
std::cout << "meeeeeeep! score: " << score_vec[k] << " " << res << "\n";
}
}
m_pnt.m_qs_bestscore[i] = score_vec[k];
assert( block.edges[k] <= size_t(std::numeric_limits<int>::max()) );
m_pnt.m_qs_bestedge[i] = int(block.edges[k]); // TODO: dto, maybe change to size_t
}
}
}
}
}
#else
assert( block.gapp_ptrs[0] != 0 );
assert( VW == 4 );
const align_pvec_gapp_score<4> aligner( block.seqptrs, block.gapp_ptrs, block.ref_len, score_mismatch, score_match_cgap, score_gap_open, score_gap_extend );
for( unsigned int i = 0; i < m_pnt.m_qs_names.size(); i++ ) {
size_t stride = 1;
size_t aux_stride = 1;
aligner.align(m_pnt.m_qs_pvecs[i]);
const float *score_vec = aligner.get_scores();
ncup += block.num_valid * block.ref_len * m_pnt.m_qs_pvecs[i].size();
{
ivy_mike::lock_guard<ivy_mike::mutex> lock( m_pnt.m_qmtx );
for( int k = 0; k < block.num_valid; k++ ) {
if( score_vec[k] < m_pnt.m_qs_bestscore[i] || (score_vec[k] == m_pnt.m_qs_bestscore[i] && block.edges[k] < m_pnt.m_qs_bestedge[i] )) {
const bool validate = false;
if( validate ) {
const int *seqptr = block.seqptrs[k];
const double *gapp_ptr = block.gapp_ptrs[k];
// std::vector<double> gapp_tmp(gapp_ptr, gapp_ptr + block.ref_len);
pars_align_gapp_seq pas( seqptr, m_pnt.m_qs_pvecs[i].data(), block.ref_len, m_pnt.m_qs_pvecs[i].size(), stride, gapp_ptr, aux_stride, seq_arrays_gapp, 0, score_gap_open, score_gap_extend, score_mismatch, score_match_cgap );
int res = pas.alignFreeshift(INT_MAX);
if( res != score_vec[k] ) {
std::cout << "meeeeeeep! score: " << score_vec[k] << " " << res << "\n";
}
}
m_pnt.m_qs_bestscore[i] = score_vec[k];
m_pnt.m_qs_bestedge[i] = block.edges[k];
}
}
}
}
}
#endif
{
ivy_mike::lock_guard<ivy_mike::mutex> lock( m_pnt.m_qmtx );
std::cout << "thread " << m_rank << ": " << ncup / (tstatus.elapsed() * 1e9) << " gncup/s\n";
}
}
};
void build_block_queue() {
// creates the list of ref-block to be consumed by the worker threads. A ref-block onsists of N ancestral state sequences, where N='width of the vector unit'.
// The vectorized alignment implementation will align a QS against a whole ref-block at a time, rather than a single ancestral state sequence as in the
// sequencial algorithm.
assert( m_blockqueue.empty() );
size_t n_groups = (m_ec.m_edges.size() / VW);
if( (m_ec.m_edges.size() % VW) != 0 ) {
n_groups++;
}
// std::vector<int> seqlist[VW];
// const int *seqptrs[VW];
// std::vector<unsigned int> auxlist[VW];
// const unsigned int *auxptrs[VW];
for ( size_t j = 0; j < n_groups; j++ ) {
int num_valid = 0;
block_t block;
for( unsigned int i = 0; i < VW; i++ ) {
size_t edge = j * VW + i;
if( edge < m_ec.m_edges.size()) {
block.edges[i] = edge;
block.num_valid++;
block.seqptrs[i] = m_ref_pvecs[edge].data();
block.auxptrs[i] = m_ref_aux[edge].data();
if( !m_ref_gapp[edge].empty() ) {
block.gapp_ptrs[i] = m_ref_gapp[edge].data();
} else {
block.gapp_ptrs[i] = 0;
}
block.ref_len = m_ref_pvecs[edge].size();
// do_newview( root_pvec, m_ec.m_edges[edge].first, m_ec.m_edges[edge].second, true );
// root_pvec.to_int_vec(seqlist[i]);
// root_pvec.to_aux_vec(auxlist[i]);
//
// seqptrs[i] = seqlist[i].data();
// auxptrs[i] = auxlist[i].data();
num_valid++;
} else {
if( i < 1 ) {
std::cout << "edge: " << edge << " " << m_ec.m_edges.size() << std::endl;
throw std::runtime_error( "bad integer mathematics" );
}
block.edges[i] = block.edges[i-1];
block.seqptrs[i] = block.seqptrs[i-1];
block.auxptrs[i] = block.auxptrs[i-1];
block.gapp_ptrs[i] = block.gapp_ptrs[i-1];
}
}
m_blockqueue.push_back(block);
}
}
void build_ref_vecs() {
// pre-create the ancestral state vectors. This step is necessary for the threaded version, because otherwise, each
// thread would need an independent copy of the tree to do concurrent newviews. Anyway, having a copy of the tree
// in each thread will most likely use more memory than storing the pre-calculated vectors.
// TODO: maybe try lazy create/cache of the asv's in the threads
ivy_mike::timer t1;
assert( m_ref_aux.empty() && m_ref_pvecs.empty() );
m_ref_pvecs.reserve( m_ec.m_edges.size() );
m_ref_aux.reserve( m_ec.m_edges.size() );
for( size_t i = 0; i < m_ec.m_edges.size(); i++ ) {
pvec_t root_pvec;
// std::cout << "newview for branch " << i << ": " << *(m_ec.m_edges[i].first->m_data) << " " << *(m_ec.m_edges[i].second->m_data) << "\n";
if( i == 340 ) {
g_dump_aux = true;
}
do_newview( root_pvec, m_ec.m_edges[i].first, m_ec.m_edges[i].second, true );
g_dump_aux = false;
// TODO: try something fancy with rvalue refs...
m_ref_pvecs.push_back( std::vector<int>() );
m_ref_aux.push_back( std::vector<unsigned int>() );
root_pvec.to_int_vec(m_ref_pvecs.back());
root_pvec.to_aux_vec(m_ref_aux.back());
m_ref_gapp.push_back( std::vector<double>() );
if( ivy_mike::same_type<pvec_t,pvec_pgap>::result ) {
// WTF: this is why mixing static and dynamic polymorphism is a BAD idea!
pvec_pgap *rvp = reinterpret_cast<pvec_pgap *>(&root_pvec);
rvp->to_gap_post_vec(m_ref_gapp.back());
// std::transform( m_ref_gapp.back().begin(), m_ref_gapp.back().end(), std::ostream_iterator<int>(std::cout), ivy_mike::scaler_clamp<double>(10,0,9) );
//
// std::cout << "\n";
}
}
std::cout << "pvecs created: " << t1.elapsed() << "\n";
}
void seq_to_position_map(const std::vector< uint8_t >& seq, std::vector< int > &map) {
for( size_t i = 0; i < seq.size(); ++i ) {
uint8_t ps = dna_parsimony_mapping::d2p(seq[i]);
if( ps == 0x1 || ps == 0x2 || ps == 0x4 || ps == 0x8 ) {
map.push_back(int(i));
}
}
}
void gapstream_to_position_map( const std::vector< uint8_t >& gaps, std::vector< int > &map) {
align_utils::trace_to_position_map( gaps, &map );
// int seq_ptr = 0;
//
// for ( std::vector<uint8_t>::const_reverse_iterator git = gaps.rbegin(); git != gaps.rend(); ++git ) {
//
// if ( *git == 1) {
// ++seq_ptr;
// } else if ( *git == 0 ) {
//
// map.push_back(seq_ptr);
//
// ++seq_ptr;
// } else {
// map.push_back(seq_ptr);
//
// }
// }
}
void write_qs_pvecs( const char * name ) {
std::ofstream os( name );
os << m_qs_pvecs.size();
for( std::vector< std::vector< uint8_t > >::iterator it = m_qs_pvecs.begin(); it != m_qs_pvecs.end(); ++it ) {
os << " " << it->size() << " ";
os.write( (char *)it->data(), it->size() );
}
}
void write_ref_pvecs( const char * name ) {
std::ofstream os( name );
os << m_ref_pvecs.size();
for( size_t i = 0; i < m_ref_pvecs.size(); ++i ) {
os << " " << m_ref_pvecs[i].size() << " ";
os.write( (char *)m_ref_pvecs[i].data(), m_ref_pvecs[i].size() * sizeof(int));
os.write( (char *)m_ref_aux[i].data(), m_ref_aux[i].size() * sizeof(unsigned int));
}
}
public:
papara_nt( const char* opt_tree_name, const char *opt_alignment_name, const char *opt_qs_name, bool write_testbench )
: m_ln_pool(new ln_pool( std::auto_ptr<node_data_factory>(new my_fact<my_adata>) ))
{
//std::cerr << "papara_nt instantiated as: " << typeid(*this).name() << "\n";
lout << "papara_nt instantiated as: " << ivy_mike::demangle(typeid(*this).name()) << "\n";
lout << "scores: " << score_gap_open << " " << score_gap_extend << " " << score_mismatch << " " << score_match_cgap << "\n";
std::cerr << ivy_mike::isa<papara_nt<pvec_cgap> >(*this) << " " << ivy_mike::isa<papara_nt<pvec_pgap> >(*this) << "\n";
// load input data: ref-tree, ref-alignment and query sequences
//
// parse the reference tree
//
ln_pool &pool = *m_ln_pool;
tree_parser_ms::parser tp( opt_tree_name, pool );
tree_parser_ms::lnode * n = tp.parse();
n = towards_tree( n );
//
// create map from tip names to tip nodes
//
typedef tip_collector<lnode> tc_t;
tc_t tc;
visit_lnode( n, tc );
std::map<std::string, std::shared_ptr<lnode> > name_to_lnode;
for( std::vector< std::shared_ptr<lnode> >::iterator it = tc.m_nodes.begin(); it != tc.m_nodes.end(); ++it ) {
// std::cout << (*it)->m_data->tipName << "\n";
name_to_lnode[(*it)->m_data->tipName] = *it;
}
{
//
// read reference alignment: store the ref-seqs in the tips of the ref-tree
//
multiple_alignment ref_ma;
ref_ma.load_phylip( opt_alignment_name );
for( unsigned int i = 0; i < ref_ma.names.size(); i++ ) {
std::map< std::string, std::shared_ptr<lnode> >::iterator it = name_to_lnode.find(ref_ma.names[i]);
// process sequences fomr the ref_ma depending on, if they are contained in the tree.
// if they are, they are 'swapped' into m_ref_seqs
// if they are not, into m_qs_seqs. (gaps in the QS are removed later)
if( it != name_to_lnode.end() ) {
std::shared_ptr< lnode > ln = it->second;
// adata *ad = ln->m_data.get();
assert( ivy_mike::isa<my_adata>(ln->m_data.get()) ); //typeid(*ln->m_data.get()) == typeid(my_adata ) );
my_adata *adata = static_cast<my_adata *> (ln->m_data.get());
m_ref_names.push_back(std::string() );
m_ref_seqs.push_back(std::vector<uint8_t>() );
m_ref_names.back().swap( ref_ma.names[i] );
m_ref_seqs.back().swap( ref_ma.data[i] );
// WARNING: make sure not to keep references to elements of m_ref_seqs at this point!
adata->init_pvec( m_ref_seqs.back() );
} else {
//std::cout << "transfer ref -> qs: " << ref_ma.names[i] << "\n";
m_qs_names.push_back(std::string() );
m_qs_seqs.push_back(std::vector<uint8_t>() );
m_qs_names.back().swap( ref_ma.names[i] );
m_qs_seqs.back().swap( ref_ma.data[i] );
}
}
}
probgap_model pm( m_ref_seqs );
std::cout << "p: " << pm.setup_pmatrix(0.1) << "\n";
stupid_ptr_guard<probgap_model> spg( pvec_pgap::pgap_model, &pm );
//
// collect list of edges
//
visit_edges( n, m_ec );
lout << "edges: " << m_ec.m_edges.size() << "\n";
// std::vector< pvec_t > m_parsvecs;
// m_parsvecs.resize( m_ec.m_edges.size() );
//
// read query sequences
//
if( opt_qs_name != 0 ) {
std::ifstream qsf( opt_qs_name );
if( qsf.bad() ) {
throw std::runtime_error( "cannot open qs file");
}
// mix them with the qs from the ref alignment
read_fasta( qsf, m_qs_names, m_qs_seqs);
}
if( m_qs_names.empty() ) {
throw std::runtime_error( "no qs" );
}
//
// setup qs best-score/best-edge lists
//
m_qs_pvecs.resize( m_qs_names.size() );
m_qs_bestscore.resize(m_qs_names.size());
std::fill( m_qs_bestscore.begin(), m_qs_bestscore.end(), 32000);
m_qs_bestedge.resize(m_qs_names.size());