/
stepwise_addition_gapp.cpp
2014 lines (1333 loc) · 55 KB
/
stepwise_addition_gapp.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 "stepwise_align.h"
#include <functional>
#include <iomanip>
#include <numeric>
#include <deque>
#include <boost/dynamic_bitset.hpp>
#include <boost/thread.hpp>
//#include <boost/thread/future.hpp>
#include <boost/thread/barrier.hpp>
#include <boost/array.hpp>
#ifndef WIN32
// there is some strange linker error on widows. can't be bothered now... visual c++ will probably do better whole program optimization than gcc anyway...
#define PWDIST_INLINE
#endif
#include "pairwise_seq_distance.h"
#include "ivymike/tdmatrix.h"
#include "ivymike/algorithm.h"
// #include "ivymike/cycle.h"
#include "parsimony.h"
#include "pvec.h"
#include "fasta.h"
#include "ivymike/tree_parser.h"
#include "pars_align_seq.h"
#include "ivymike/tree_split_utils.h"
#include "ivymike/time.h"
#include "ivymike/getopt.h"
#include "ivymike/multiple_alignment.h"
#include "ivymike/tree_traversal_utils.h"
#include <boost/tr1/unordered_set.hpp>
#include "ivymike/concurrent.h"
#include "raxml_interface.h"
using std::string;
using std::vector;
using std::map;
using std::pair;
using std::deque;
using std::ios_base;
using std::ifstream;
using std::ofstream;
using ivy_mike::back_insert_ifer;
using ivy_mike::rooted_bifurcation;
using ivy_mike::apply_lnode;
using ivy_mike::iterate_lnode;
using ivy_mike::visit_lnode;
using ivy_mike::tip_collector_dumb;
using ivy_mike::tip_collector;
using ivy_mike::node_level_assignment;
using ivy_mike::visit_edges;
using ivy_mike::edge_collector;
using namespace ivy_mike::tree_parser_ms;
class empty_column_remover {
boost::dynamic_bitset<> m_cm;
size_t m_num_columns;
typedef std::vector<uint8_t> seq_t;
public:
template<typename iter>
empty_column_remover( iter first, iter last ) {
for( iter it = first; it != last; ++it ) {
seq_t &seq = *it;
boost::dynamic_bitset<> cm;
for( seq_t::iterator sit = seq.begin(); sit != seq.end(); ++sit ) {
cm.push_back( *sit != '-' );
}
if( m_cm.empty() ) {
m_cm.swap(cm);
} else {
m_cm |= cm;
}
}
m_num_columns = m_cm.count();
std::cout << "keep: " << m_num_columns << " of " << m_cm.size() << "\n";
}
void filter( const seq_t &in, seq_t &out ) {
assert( in.size() >= m_cm.size() );
assert( out.empty() );
out.reserve(m_num_columns);
size_t next = m_cm.find_first();
while( next != m_cm.npos ) {
out.push_back(in[next]);
next = m_cm.find_next(next);
}
}
};
template<class pvec_t>
class my_adata_gen : public ivy_mike::tree_parser_ms::adata {
// static int ct;
//vector<parsimony_state> m_pvec;
vector<uint8_t> m_raw_seq;
pvec_t m_pvec;
public:
// int m_ct;
my_adata_gen() {
// cout << "my_adata\n";
}
virtual ~my_adata_gen() {
// cout << "~my_adata\n";
}
virtual void visit() {
// cout << "tr: " << m_ct << "\n";
}
void init_pvec(const vector< uint8_t >& seq) {
m_raw_seq = seq;
reset_pvec();
// m_pvec.init( seq );
}
vector<uint8_t>&get_raw_seq() {
return m_raw_seq;
}
void reset_pvec() {
m_pvec.init( m_raw_seq );
}
pvec_t &get_pvec() {
return m_pvec;
}
};
template<typename pvec_t>
class my_ldata_gen : public ivy_mike::tree_parser_ms::ldata {
pvec_t m_pvec;
volatile int m_generation;
const int m_serial;
int m_level;
public:
my_ldata_gen( int serial ) : m_generation(-1), m_serial(serial), m_level(-1) {
// std::cout << "hello ldata " << sizeof(*this) << "\n";
}
virtual ~my_ldata_gen() {
// std::cout << "bye ldata\n";
}
pvec_t &get_pvec() {
return m_pvec;
}
int get_generation() {
return m_generation;
}
void set_generation( int gen ) {
m_generation = gen;
}
inline int get_serial() {
return m_serial;
}
//inline int get_level()
};
template<class ndata_t, class ldata_t>
class my_fact_gen : public ivy_mike::tree_parser_ms::node_data_factory {
int m_next_serial;
public:
my_fact_gen() : ivy_mike::tree_parser_ms::node_data_factory(), m_next_serial(0) {}
virtual ndata_t *alloc_adata() {
return new ndata_t;
}
virtual ldata_t *alloc_ldata() {
return new ldata_t(m_next_serial++);
}
virtual ~my_fact_gen() {}
};
template<class pvec_t>
void do_newview_from_ldata( pvec_t &root_pvec, lnode *n1, lnode *n2 ) {
// assume that the pvecs in the ldata are already valid
typedef my_adata_gen<pvec_t> my_adata;
typedef my_ldata_gen<pvec_t> my_ldata;
{
my_adata *c1 = dynamic_cast<my_adata *>( n1->m_data.get());
my_adata *c2 = dynamic_cast<my_adata *>( n2->m_data.get());
my_ldata *ldc1 = dynamic_cast<my_ldata *>( n1->m_ldata.get());
my_ldata *ldc2 = dynamic_cast<my_ldata *>( n2->m_ldata.get());
// tip_case tc;
if( c1->isTip && c2->isTip ) {
// cout << "root: TIP TIP\n";
pvec_t::newview(root_pvec, ldc1->get_pvec(), ldc2->get_pvec(), n1->backLen, n2->backLen, TIP_TIP );
} else if( c1->isTip && !c2->isTip ) {
// cout << "root: TIP INNER\n";
pvec_t::newview(root_pvec, ldc1->get_pvec(), ldc2->get_pvec(), n1->backLen, n2->backLen, TIP_INNER );
// root_pvec = c2->get_pvec();
} else if( !c1->isTip && c2->isTip ) {
// cout << "root: INNER TIP\n";
pvec_t::newview(root_pvec, ldc2->get_pvec(), ldc1->get_pvec(), n1->backLen, n2->backLen, TIP_INNER );
// root_pvec = c1->get_pvec();
} else {
// cout << "root: INNER INNER\n";
pvec_t::newview(root_pvec, ldc1->get_pvec(), ldc2->get_pvec(), n1->backLen, n2->backLen, INNER_INNER );
}
}
// cout << hex;
// for( vector< parsimony_state >::const_iterator it = root_pvec.begin(); it != root_pvec.end(); ++it ) {
// cout << *it;
// }
//
// cout << dec << endl;
}
typedef pvec_pgap pvec_t;
typedef my_adata_gen<pvec_t> my_adata;
typedef my_ldata_gen<pvec_t> my_ldata;
typedef my_fact_gen<my_adata, my_ldata> my_fact;
struct my_lnode_to_seq_map_generator {
typedef ::lnode lnode;
std::map<std::string, const std::vector<uint8_t> * const > m_map;
void operator()( lnode *n ) {
my_adata *adata = n->m_data->get_as<my_adata>();
if( adata->isTip ) {
const std::string &name = adata->tipName;
m_map.insert( std::make_pair(name, &(adata->get_raw_seq())));
}
}
};
static void build_name_to_seq_map( lnode *tree, std::map<std::string, const std::vector<uint8_t> * const > &map ) {
my_lnode_to_seq_map_generator gen;
visit_lnode(tree, gen );
map.swap(gen.m_map);
}
struct tip_collector_xp {
typedef ::lnode lnode;
std::vector<lnode *> m_nodes;
int m_largest_serial;
public:
void operator()( lnode *n1, lnode *n2 ) {
if( n1->m_data->isTip ) {
m_nodes.push_back(n1->get_smart_ptr().lock().get());
}
if( n2->m_data->isTip ) {
m_nodes.push_back(n2->get_smart_ptr().lock().get());
}
my_ldata *ld1 = dynamic_cast<my_ldata*>(n1->m_ldata.get());
my_ldata *ld2 = dynamic_cast<my_ldata*>(n2->m_ldata.get());
m_largest_serial = std::max( m_largest_serial, std::max( ld1->get_serial(), ld2->get_serial() ));
}
};
class step_add : boost::noncopyable {
//auto_ptr<ivy_mike::tree_parser_ms::ln_pool> m_ln_pool;
// const static int score_match = 3;
// const static int score_match_cgap = -4;
// const static int score_gap_open = -3;
// const static int score_gap_extend = -1;
const static int score_match = 2;
const static int score_match_cgap = -2;
const static int score_gap_open = -4;
const static int score_gap_extend = -1;
const static bool align_global = false;
std::shared_ptr<ln_pool> m_ln_pool;
//string m_seq_file_name;
vector<string> m_qs_names;
vector<vector<uint8_t> > m_qs_seqs;
// vector<vector<uint8_t> > m_qs_seqs_mapped; // the content of m_qs_seqs, but mapped by m_pw_scoring_matrix
vector<vector <uint8_t> > m_qs_nongappy;
ivy_mike::tdmatrix<float> m_pw_dist;
scoring_matrix m_pw_scoring_matrix;
boost::dynamic_bitset<> m_used_seqs;
lnode *m_tree_root;
pars_align_seq<>::arrays m_seq_arrays;
vector<lnode *> m_leafs;
align_arrays_traceback<int> m_align_arrays_traceback;
std::ofstream m_inc_ali;
size_t m_sum_ncup;
int m_pvec_gen;
probgap_model m_pgm;
ivy_mike::stupid_ptr_guard<probgap_model> m_pgm_guard;
// total number of gaps ans characters (including gaps) in the
// current alignment (= gappy sequences stored in tips).
// kept up to date in insertion step.
double m_num_gaps;
double m_num_chars;
static void seq_to_nongappy_pvec( vector<uint8_t> &seq, 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]);
// TEST: we actually allow for 'undefined characters' in the unaligned qs (character N).
// just make sure that there are no real gaps in the qs
assert( seq[i] != '-');
pvec.push_back(ps);
// if( ps != 0xf ) {
// pvec.push_back(ps);
// } else {
// std::cout << "drop: " << seq[i] << "\n";
//
// }
}
}
std::tr1::unordered_set<lnode *> done;
boost::mutex m_ln_mutex;
boost::condition_variable m_ln_cond;
boost::condition_variable m_ln_cond_done;
volatile bool m_ln_exit;
std::vector<lnode *> m_ln_stack;
std::tr1::unordered_set<lnode *> m_ln_inuse;
volatile lnode *m_ln_root;
std::vector<int> m_ln_open_ct;
void lnode_newview_iter( lnode *n_ ) {
tip_collector_xp tc;
visit_edges( n_, tc );
m_ln_open_ct.clear();
m_ln_open_ct.resize(tc.m_largest_serial + 1 );
// std::cout << "finished\n";
return;
std::vector<lnode *> stack;
// std::tr1::unordered_set<int> done;
stack.push_back( n_ );
while( !stack.empty() ) {
lnode *n = stack.back();
stack.pop_back();
my_adata *ad = dynamic_cast<my_adata *>( n->m_data.get());
my_ldata *ld = dynamic_cast<my_ldata *>( n->m_ldata.get());
if( done.find( n ) != done.end() ) {
continue;
}
// std::cout << "node: " << ad->m_serial << "\n";
if( ad->isTip ) {
ld->get_pvec() = ad->get_pvec();
done.insert( n );
} else {
lnode *c1 = n->next->back;
lnode *c2 = n->next->next->back;
// int cs2 = c2->m_data->m_serial;
bool hc1 = done.find( c1 ) != done.end();
bool hc2 = done.find( c1 ) != done.end();
if( !(hc1 && hc2) ) {
stack.push_back(n);
if( !hc1 ) {
stack.push_back(c1);
}
if( !hc2 ) {
stack.push_back(c2);
}
} else {
ivy_mike::tip_case tc;
if( c1->m_data->isTip && c2->m_data->isTip ) {
tc = TIP_TIP;
} else if( c1->m_data->isTip && !c2->m_data->isTip ) {
tc = TIP_INNER;
} else if( !c1->m_data->isTip && c2->m_data->isTip ) {
tc = TIP_INNER;
std::swap( c1, c2 );
} else {
tc = INNER_INNER;
}
my_ldata *ldc1 = dynamic_cast<my_ldata *>( c1->m_ldata.get());
my_ldata *ldc2 = dynamic_cast<my_ldata *>( c2->m_ldata.get());
pvec_t &pvc1 = ldc1->get_pvec();
pvec_t &pvc2 = ldc2->get_pvec();
// std::cout << "size: " << pvc1.size() << " " << pvc2.size() << "\n";
pvec_t::newview( ld->get_pvec(), pvc1, pvc2, n->next->backLen, n->next->next->backLen, tc);
done.insert( n );
// std::cout << "nv: " << ad->m_serial << "\n";
}
}
}
// std::cout << "done\n";
}
void lnode_newview( lnode *n ) {
my_adata *ad = dynamic_cast<my_adata *>( n->m_data.get());
my_ldata *ld = dynamic_cast<my_ldata *>( n->m_ldata.get());
//my_adata *c2 = dynamic_cast<my_adata *>( it->child2->m_data.get());
if( ld->get_generation() < m_pvec_gen ) {
if( ad->isTip ) {
ld->get_pvec() = ad->get_pvec();
} else {
lnode *c1 = n->next->back;
lnode *c2 = n->next->next->back;
lnode_newview( c1 );
lnode_newview( c2 );
ivy_mike::tip_case tc;
if( c1->m_data->isTip && c2->m_data->isTip ) {
tc = TIP_TIP;
} else if( c1->m_data->isTip && !c2->m_data->isTip ) {
tc = TIP_INNER;
} else if( !c1->m_data->isTip && c2->m_data->isTip ) {
tc = TIP_INNER;
std::swap( c1, c2 );
} else {
tc = INNER_INNER;
}
my_ldata *ldc1 = dynamic_cast<my_ldata *>( c1->m_ldata.get());
my_ldata *ldc2 = dynamic_cast<my_ldata *>( c2->m_ldata.get());
pvec_t &pvc1 = ldc1->get_pvec();
pvec_t &pvc2 = ldc2->get_pvec();
// std::cout << "size: " << pvc1.size() << " " << pvc2.size() << "\n";
pvec_t::newview( ld->get_pvec(), pvc1, pvc2, n->next->backLen, n->next->next->backLen, tc);
}
ld->set_generation(m_pvec_gen);
//pvec_t::newview(p->get_pvec(), c1->get_pvec(), c2->get_pvec(), it->child1->backLen, it->child2->backLen, it->tc);
// if( n->towards_root ) {
// if (ad->get_pvec() != ld->get_pvec()) {
// throw std::runtime_error( "ad != ld pvec\n" );
// }
//
// // std::cout << ad->get_pvec().size() << " " << ld->get_pvec().size() << " " << << "\n";
// }
}
}
struct ali_task {
pair< ivy_mike::tree_parser_ms::lnode*, ivy_mike::tree_parser_ms::lnode* > m_edge;
// WARNINIG: the next two members are most likely references to local objects, which are kept in scope between bar1 and bar2, but not longer
const vector<uint8_t> &m_qs_pvec;
int &m_result;
ali_task( pair< ivy_mike::tree_parser_ms::lnode*, ivy_mike::tree_parser_ms::lnode* > edge, const vector<uint8_t> &qs_pvec, int &result )
: m_edge(edge), m_qs_pvec(qs_pvec), m_result(result) {
}
void work() {
}
};
template<size_t W>
static void copy_to_profile( vector<pvec_t> &pvecs, aligned_buffer<short> &prof, aligned_buffer<short> &aux_prof ) {
size_t reflen = pvecs[0].size();
assert( W == pvecs.size() );
assert( reflen * W == prof.size() );
assert( reflen * W == aux_prof.size() );
aligned_buffer<short>::iterator it = prof.begin();
aligned_buffer<short>::iterator ait = aux_prof.begin();
// std::cout << "reflen: " << reflen << " " << size_t(&(*it)) << "\n";
std::vector<short> tmp_aux[W];
for( size_t i = 0; i < W; ++i ) {
pvecs[i].to_aux_vec(tmp_aux[i]);
}
for( size_t i = 0; i < reflen; ++i ) {
for( size_t j = 0; j < W; ++j ) {
// std::cout << "ij: " << i << " " << j << " " << pvecs[j].size() << "\n";
*it = short(pvecs[j].get_v()[i]);
*ait = short( (tmp_aux[j][i] == AUX_CGAP) ? 0xFFFF : 0x0 );
++it;
++ait;
}
}
assert( it == prof.end());
assert( ait == aux_prof.end());
}
static void ali_work_vec_nt( step_add *sa, int rank ) {
// TODO: code review! This went to smoothly, I don' trust it...
const size_t W = 8;
typedef short score_t;
vector<uint8_t> seq_tmp;
vector<uint8_t> aux_tmp;
vector<ali_task *> tasks;
vector<pvec_t> root_pvecs(W);
aligned_buffer<short> a_prof;//(seq_tmp.size() * W);
aligned_buffer<short> a_aux_prof; //(seq_tmp.size() * W);
aligned_buffer<short> out_score(W);
align_vec_arrays<score_t> arr;
ivy_mike::perf_timer pt;
while( true ) {
sa->m_bar1.wait();
// std::cout << sa->m_par_queue[rank].size() << "\n";
while( !sa->m_par_queue[rank].empty() ) {
ivy_mike::perf_timer lpt;
tasks.clear();
while( tasks.size() < W && !sa->m_par_queue[rank].empty() ) {
tasks.push_back(sa->m_par_queue[rank].back());
sa->m_par_queue[rank].pop_back();
}
assert( !tasks.empty() );
size_t ref_len = 0;
// std::cout << "tasks: " << tasks.size() << "\n";
lpt.add_int();
for( size_t i = 0; i < tasks.size(); ++i ) {
do_newview_from_ldata( root_pvecs[i], tasks[i]->m_edge.first, tasks[i]->m_edge.second );
if( i == 0 ) {
ref_len = root_pvecs[i].size();
if( a_prof.size() < ref_len * W ) {
// zero initialize on resize, so that valgrind will not complain about uninitialized reads if tasks.size() < W after resize...
a_prof.resize( ref_len * W, 0 );
a_aux_prof.resize( ref_len * W, 0 );
}
} else {
if( ref_len != root_pvecs[i].size() ) {
throw std::runtime_error( "quirk: ref_len != root_pvecs[i].size()" );
}
}
// FIXME: to_aux_vec sets a_aux_prof to 0xFFFF for cgap columns. The correct value is dependent on the width of the vector unit.
/* root_pvecs[i].to_int_vec_strided<aligned_buffer<short>::iterator,W>(a_prof.begin() + i);
* root_pvecs[i].to_aux_vec_strided<aligned_buffer<short>::iterator,W>(a_aux_prof.begin() + i);*/
}
for( size_t i = tasks.size(); i < W; ++i ) {
root_pvecs[i] = root_pvecs[0];
}
lpt.add_int();
copy_to_profile<W>( root_pvecs, a_prof, a_aux_prof );
lpt.add_int();
align_pvec_score_vec<short,W,align_global>(a_prof, a_aux_prof, tasks[0]->m_qs_pvec, score_match, score_match_cgap, score_gap_open, score_gap_extend, out_score, arr );
sa->m_thread_ncup.at(rank) += uint64_t(ref_len) * tasks.size() * tasks[0]->m_qs_pvec.size();
for( size_t i = 0; i < tasks.size(); ++i ) {
tasks[i]->m_result = out_score[i];
}
for( std::vector< ali_task* >::iterator it = tasks.begin(); it != tasks.end(); ++it ) {
delete *it;
}
tasks.clear();
lpt.add_int();
pt += lpt;
}
if( sa->m_queue_exit ) {
boost::lock_guard<boost::mutex> tree_lock( sa->m_gen_mutex );
sa->m_align_pt += pt;
break;
}
sa->m_bar2.wait();
}
}
//
// regarding the aligner threads, bar1 and bar2 separate the program into two sections:
// basic data access policies for the sections:
// between bar1 and bar2:
// the aligner threads are working. the sequential part is sleeping.
// the shared state is read-only, except for:
// m_par_queue[rank] and contained ali_task instances are r/w for the respective thread.
// some additional shared stuff secured by m_gen_mutex is r/w (iff m_gen_mutex is held)
// between bar2 and bar1:
// the aligner threads are sleeping. the sequential part is running.
// the whole shared state is r/w for the sequential part.
//
bool m_queue_exit;
const size_t m_num_ali_threads;
std::vector<std::vector<ali_task *> > m_par_queue;
boost::barrier m_bar1;
boost::barrier m_bar2;
// additional shared stuff, secured by m_gen_mutex
boost::mutex m_gen_mutex;
ivy_mike::perf_timer m_align_pt;
// end of additional shared stuff
boost::thread_group m_thread_group;
std::vector<uint64_t> m_thread_ncup;
ivy_mike::perf_timer m_insert_timer;
boost::thread_group m_ln_thread_group;
ivy_mike::timer m_temp_timer;
void to_nongappy( const std::vector<uint8_t> &in, std::vector<uint8_t> &out ) {
for( std::vector<uint8_t>::const_iterator it = in.begin(); it != in.end(); ++it ) {
if( !dna_parsimony_mapping::is_gap( *it ) ) {
out.push_back( *it );
}
}
}
// FIXME: a private copy constructor would still have to initialize the scoring_matrix (and others without default constructors) member. it's not worth the effort
// wait for c++0x explicit constructor delete...
//step_add( const step_add &other ) {}
//step_add( const step_add & ) {}
//const step_add &operator=( const step_add & other ) { return *this; }
public:
step_add( std::shared_ptr<ln_pool> ln_pool, size_t num_ali_threads )
: m_ln_pool( ln_pool ),
m_pw_scoring_matrix(3,0),
m_seq_arrays(true),
m_sum_ncup(0),
m_pvec_gen(0),
m_pgm_guard( pvec_pgap::pgap_model, &m_pgm ),
m_queue_exit(false),
m_num_ali_threads( num_ali_threads ),
m_par_queue(num_ali_threads),
m_bar1(num_ali_threads + 1),
m_bar2(num_ali_threads + 1)
{
for( size_t i = 0; i < num_ali_threads; i++ ) {
int rank = int(i);
m_thread_group.create_thread( boost::bind( &step_add::ali_work_vec_nt, this, rank ) );
m_thread_ncup.push_back(0);
}
if( !true ) {
m_inc_ali.open( "inc_ali.txt" );
}
}
~step_add() {
// cleanup the ali_task worker threads
// when m_queue_exit = true, the worker threads will exit directly after bar1
m_queue_exit = true;
m_bar1.wait();
m_thread_group.join_all();
std::cout << "align perf_timer: \n";
m_align_pt.print();
std::cout << "overall perf_timer: \n";
m_insert_timer.print();
}
template<typename iter, typename idx_t>
void build_index( const iter first, const iter last, idx_t &idx ) {
for( iter it = first; it != last; ++it ) {
idx[*it] = (it - first);
}
}
void load_start_tree( const char *treename, const char *aliname ) {
parser tp( treename, *m_ln_pool );
lnode * n = tp.parse();
m_tree_root = n;
tip_collector_dumb<lnode> tc;
visit_lnode( m_tree_root, tc );
ivy_mike::multiple_alignment ma;
ma.load_phylip( aliname );
std::map<std::string,size_t> ma_nti;
build_index( ma.names.begin(), ma.names.end(), ma_nti );
empty_column_remover ecr( ma.data.begin(), ma.data.end() );
std::vector<uint8_t> tmp;
for( std::vector<lnode *>::iterator it = tc.m_nodes.begin(); it != tc.m_nodes.end(); ++it ) {
std::map<std::string,size_t>::iterator nit = ma_nti.find((*it)->m_data->tipName);
if( nit == ma_nti.end() ) {
throw std::runtime_error( "cannot find tree species in alignment" );
}
size_t idx = nit->second;
tmp.clear();
ecr.filter( ma.data[idx], tmp );
//(*it)->m_data->get_as<my_adata>()->init_pvec(ma.data[idx]);
(*it)->m_data->get_as<my_adata>()->init_pvec(tmp);
}
m_leafs = tc.m_nodes;
}
void load_qs( const char *filename ) {
{
ifstream qsf( filename );
if( !qsf.good() ) {
throw std::runtime_error( "cannot read input fasta" );
}
read_fasta( qsf, m_qs_names, m_qs_seqs);
}
vector<uint8_t> tmp;
for( vector<vector<uint8_t> >::iterator it = m_qs_seqs.begin(); it != m_qs_seqs.end(); ++it ) {
tmp.clear();
to_nongappy( *it, tmp );
// std::copy( tmp.begin(), tmp.end(), std::ostream_iterator<char>(std::cout));
// std::cout << "\n";
// getchar();
it->swap(tmp);
}
m_used_seqs.resize( m_qs_names.size() );
}
pair<size_t,size_t> calc_dist_matrix_from_msa( std::map<std::string,std::vector<uint8_t> > &msa ) {
typedef std::map<std::string,std::vector<uint8_t> > msa_t;
m_pw_dist.init_size(m_qs_names.size(), m_qs_names.size());
vector<vector<uint8_t> > qs_mapped;
qs_mapped.reserve(m_qs_names.size() );
ivy_mike::tdmatrix<int> out_scores(m_qs_names.size(), m_qs_names.size());
if( msa.size() != m_qs_names.size() ) {
throw std::runtime_error( "msa.size() != m_qs_names.size()" );
}
for( size_t i = 0; i < m_qs_names.size(); ++i ) {
out_scores[i][i] = 0;
msa_t::iterator seq_i = msa.find(m_qs_names[i] );
if( seq_i == msa.end() ) {
throw std::runtime_error( "missing sequence in ref msa" );
}
// TODO: maybe cache the seq_i iterators in a vector to get rid of the map.finds in the j-loop...
for( size_t j = 0; j < i; ++j ) {
msa_t::iterator seq_j = msa.find(m_qs_names[j] );
if( seq_j == msa.end() ) {
throw std::runtime_error( "missing sequence in ref msa" );
}
int score = score_for_aligned_pair( seq_i->second, seq_j->second );
// std::cout << "score " << i << " " << j << " " << score << "\n";
out_scores[i][j] = score;
out_scores[j][i] = score;
}
}
return init_pw_dist_from_msa_score_matrix(out_scores);
}
pair<size_t,size_t> init_pw_dist_from_msa_score_matrix( ivy_mike::tdmatrix<int> &out_scores ) {