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/*
This file is a part of KMC software distributed under GNU GPL 3 licence.
The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
Authors: Marek Kokot
Version: 2.3.0
Date : 2015-08-21
*/
#ifndef _PARAMETERS_PARSER_H
#define _PARAMETERS_PARSER_H
#include "defs.h"
#include "parser.h"
#include <memory>
class CParametersParser
{
std::unique_ptr<CParser> complex_parser;
int argc;
char** argv;
int pos;
CConfig& config;
uint32 replace_zero(uint32 val, const char* param_name, uint32 value_to_set_if_zero);
void parse_int_or_float(bool& force_float, bool& force_int, float& float_value, uint32& int_val, const char* param_name);
void parse_global_params();
void read_input_fastq_desc();
void read_output_fastq_desc();
void read_input_desc();
void read_dump_params();
void read_output_desc();
public:
CParametersParser(int argc, char** argv);
void Usage();
template<unsigned SIZE>
CExpressionNode<SIZE>* GetExpressionRoot();
void Parse();
bool validate_input_dbs();
void SetThreads();
};
template<unsigned SIZE>
CExpressionNode<SIZE>* CParametersParser::GetExpressionRoot()
{
if (config.mode == CConfig::Mode::INTERSECTION || config.mode == CConfig::Mode::KMERS_SUBTRACT || config.mode == CConfig::Mode::UNION || config.mode == CConfig::Mode::COUNTERS_SUBTRACT)
{
CExpressionNode<SIZE>* left = new CInputNode<SIZE>(0);
CExpressionNode<SIZE>* right = new CInputNode<SIZE>(1);
CExpressionNode<SIZE>* expression_root = nullptr;
switch (config.mode)
{
case CConfig::Mode::INTERSECTION:
expression_root = new CIntersectionNode<SIZE>;
break;
case CConfig::Mode::KMERS_SUBTRACT:
expression_root = new CKmersSubtractionNode<SIZE>;
break;
case CConfig::Mode::UNION:
expression_root = new CUnionNode<SIZE>;
break;
case CConfig::Mode::COUNTERS_SUBTRACT:
expression_root = new CCountersSubtractionNode<SIZE>;
break;
default:
std::cout << "Error: unknown operation\n";
exit(1);
}
expression_root->AddLeftChild(left);
expression_root->AddRightChild(right);
return expression_root;
}
else if (config.mode == CConfig::Mode::COMPLEX)
{
auto result = complex_parser->ParseOutput<SIZE>();
return result;
}
else if (config.mode == CConfig::Mode::SORT)
{
if (!config.headers.front().IsKMC2())
{
std::cout << "This database contains sorted k-mers already!";
exit(1);
}
return new CInputNode<SIZE>(0);
}
else if (config.mode == CConfig::Mode::REDUCE)
{
return new CInputNode<SIZE>(0);
}
else if (config.mode == CConfig::Mode::COMPACT)
{
return new CInputNode<SIZE>(0);
}
else //should never be here
{
std::cout << "Error: unknown operation\n";
#ifdef ENABLE_DEBUG
std::cout << __FUNCTION__ << " line: " << __LINE__ << "\n";
#endif
exit(1);
}
}
#endif
// ***** EOF
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