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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 <iostream>
#include "ivymike/tree_traversal_utils.h"
#include "ivymike/tree_parser.h"
#include "ivymike/multiple_alignment.h"
#include "boost/dynamic_bitset.hpp"
using ivy_mike::tree_parser_ms::ln_pool;
using ivy_mike::tree_parser_ms::parser;
using ivy_mike::tree_parser_ms::lnode;
using ivy_mike::tip_collector_dumb;
using ivy_mike::visit_lnode;
bool is_gap( char c ) {
return c == '-' || c == '?' || toupper(c) == 'N';
}
void pad( std::ostream &os, size_t n, char c ) {
for( size_t i = 0; i < n; ++i ) {
os << c;
}
}
class tip_name_collector {
public:
typedef ivy_mike::tree_parser_ms::lnode lnode;
tip_name_collector( std::vector<std::string> *names ) : names_(names) {}
void operator()(lnode *n) {
if( n->m_data->isTip ) {
names_->push_back(n->m_data->tipName);
}
}
private:
std::vector<std::string> *names_;
};
int main( int argc, char *argv[] ) {
if( argc != 3 ) {
std::cerr << "usage: " << argv[0] << "<tree file> <phylip file>\n";
return 0;
}
ln_pool pool;
parser p(argv[1], pool );
lnode *n = p.parse();
std::vector<std::string> tip_names;
tip_name_collector tnc(&tip_names);
visit_lnode( n, tnc );
// apply_lnode(n, [&](lnode *x) {
// if( x->m_data->isTip ) {
// tip_names.push_back( x->m_data->tipName );
// }
// });
ivy_mike::multiple_alignment ma;
ma.load_phylip(argv[2]);
std::sort( tip_names.begin(), tip_names.end() );
boost::dynamic_bitset<> bs_all(ma.data.front().size() );
//bs_all.flip();
size_t max_name_len = 0;
for( size_t i = 0, e = ma.names.size(); i != e; ++i ) {
const std::string &name = ma.names[i];
max_name_len = std::max( max_name_len, name.size() );
const std::vector<uint8_t> &data = ma.data[i];
if( !std::binary_search( tip_names.begin(), tip_names.end(), name ) ) {
boost::dynamic_bitset<> bs(data.size());
for( size_t j = 0; j < data.size(); ++j ) {
bs[j] = !is_gap(data[j]);
}
bs_all |= bs;
}
}
std::cout << ma.names.size() << " " << bs_all.count() << "\n";
std::vector<size_t> unmasked;
{
size_t i = bs_all.find_first();
while( i != bs_all.npos ) {
unmasked.push_back(i);
i = bs_all.find_next(i);
}
}
for( size_t i = 0, e = ma.names.size(); i != e; ++i ) {
std::cout << ma.names[i];
const std::vector<uint8_t> &data = ma.data[i];
pad( std::cout, max_name_len - ma.names[i].size() + 1, ' ' );
// excract 'unmasked' characters from current sequence
// std::transform(unmasked.begin(), unmasked.end(), std::ostream_iterator<char>(std::cout), [&](size_t u) { return data[u]; });
//
for( std::vector<size_t>::iterator it = unmasked.begin(); it != unmasked.end(); ++it ) {
assert( *it < data.size() );
std::cout << data[*it];
}
std::cout << "\n";
}
}
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