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/* BaitFisher (version 1.2.8) a program for designing DNA target enrichment baits
* Copyright 2013-2016 by Christoph Mayer
*
* This source file is part of the BaitFisher-package.
*
* This program 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.
*
* This program 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 BaitFisher. If not, see <http://www.gnu.org/licenses/>.
*
*
* For any enquiries send an Email to Christoph Mayer
* c.mayer.zfmk@uni-bonn.de
*
* When publishing work that is based on the results please cite:
* Mayer et al. 2016: BaitFisher: A software package for multi-species target DNA enrichment probe design
*
*/
#ifndef CTAXONNAMESDICTIONARY_H
#define CTAXONNAMESDICTIONARY_H
#include "faststring2.h"
#include "CDistance_matrix.h"
#include "CSequences2.h"
#include "CFile/CFile2_1.h"
#include "CSeqNameList.h"
#include <set>
#include <list>
#include <map>
#include <vector>
class CTaxonNamesDictionary
{
CSeqNameList *snl;
CSeqNameList all;
// Each index stored in the taxon_names_to_index map is equal to the index of the same taxon name in the taxon_names_vec.
// This allows us to translate indices and names back and forth.
std::vector<faststring> taxon_names_vec;
std::map<faststring, unsigned> taxon_names_to_index;
public:
CTaxonNamesDictionary(faststring directoryname, std::list<faststring> &list_of_fasta_file_names, unsigned short sequence_name_taxon_field_number, char field_delimiter):all(true)
{
// Collect all taxon names to build a taxon name dictionary
// The collection of all sequence names is stored in the all object.
faststring full_transcript_file_name;
std::list<faststring>::iterator file_names_it, file_names_it_end, file_names_it_begin;
file_names_it_begin = file_names_it = list_of_fasta_file_names.begin();
file_names_it_end = list_of_fasta_file_names.end();
// For each fasta file
while (file_names_it != file_names_it_end)
{
full_transcript_file_name = directoryname + "/" + *file_names_it;
// std::cout << "Reading sequence names in " << full_transcript_file_name << std::endl;
snl = new CSeqNameList(full_transcript_file_name.c_str(), true);
if (file_names_it == file_names_it_begin)
{
all.set_to(*snl, "all-names-union");
}
else
{
all.add_List_non_redundant(*snl);
}
++file_names_it;
}
// all.print(cout,0);
// TAXON NAMES DICTIONARY: consists of a vector, and map
// A set is used to store all names temporarily.
std::set<faststring> taxon_names_set;
bool error_get_set_of_name_field;
// Take the names of the sequences, divide it according to the delimiter '|' and
// extract field number sequence_name_taxon_field_number. Store all names in the set.
error_get_set_of_name_field = all.get_set_of_name_field(sequence_name_taxon_field_number+1, field_delimiter, taxon_names_set);
if (error_get_set_of_name_field)
{
std::cerr << "WARNING: At least one error occurred when trying to read taxon names from the fasta sequence headers."
<< " Usually this error occurs, when headers are not in the proper format, when the parameter file contains a wrong"
<< " wrong sequence name field delimiter or if the taxon name field number is wrong." << std::endl;
std::cerr << "This error will influence: TODO." << std::endl;
}
// Now we have a set that contains all taxon names found in all fasta files.
std::set<faststring>::iterator it, it_end;
it = taxon_names_set.begin();
it_end = taxon_names_set.end();
unsigned i;
i=0;
while (it != it_end)
{
// Since the taxon_names_vec was empty originally, the names have an index equal to i.
taxon_names_vec.push_back(*it); // push all names into the vector. unique-index -> name
taxon_names_to_index[*it] = i; // for each name store its index in the map. name -> unique-index
++it;
++i;
}
// Now we can translate unique indices and taxon names back and forth.
}
void print(std::ostream &outfile)
{
outfile << "## Index <-> taxon name:" << std::endl;
unsigned i, N = taxon_names_vec.size();
for (i=0; i<N; ++i)
{
outfile << i << " " << taxon_names_vec[i] << std::endl;
}
}
// Main dictionary retrieval function.
unsigned dictionary_get_index_of_taxonname(faststring taxonname)
{
/* map<faststring, unsigned>::iterator it, it_end; */
/* it = taxon_names_to_index.begin(); */
/* it_end = taxon_names_to_index.end(); */
/* cout << "taxon_names_to_index map" << endl; */
/* while (it != it_end) */
/* { */
/* cout << it->first << "=>" << it->second << endl; */
/* ++it; */
/* } */
std::map<faststring, unsigned>::iterator it_find = taxon_names_to_index.find(taxonname);
if (it_find != taxon_names_to_index.end() )
return it_find->second;
else
return -1u;
}
const std::vector<faststring> & get_taxon_names_vec()
{
return taxon_names_vec;
}
void print_taxon_names_to_index(std::ostream &os)
{
std::map<faststring, unsigned>::iterator it, it_end;
it = taxon_names_to_index.begin();
it_end = taxon_names_to_index.end();
os << "Content of taxon names to global index dictionary: " << std::endl;
while (it != it_end)
{
os.width(30);
os << it->first << " " << it->second << std::endl;
++it;
}
}
};
#endif
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