73 lines
2.8 KiB
C
73 lines
2.8 KiB
C
|
#ifndef __SEQ_CONFIG_H
|
||
|
|
#define __SEQ_CONFIG_H
|
||
|
|
|
||
|
|
#define CFREV 1
|
||
|
|
|
||
|
|
#include <iostream>
|
||
|
|
#include <fstream>
|
||
|
|
#include <string>
|
||
|
|
#include <vector>
|
||
|
|
#include "opt_info.h"
|
||
|
|
|
||
|
|
using std::vector;
|
||
|
|
using std::ifstream;
|
||
|
|
|
||
|
|
class Config {
|
||
|
|
public:
|
||
|
|
Config(const int argc, const char *argv[]); // Constructor; reads
|
||
|
|
// configuration file and command
|
||
|
|
// line arguments
|
||
|
|
string cfg_name; // Name of configuration file
|
||
|
|
string db_name; // Name of database
|
||
|
|
int seq_len; // Sequence Length
|
||
|
|
int max_elements; // Maximum number of different
|
||
|
|
// data elements we may encounter
|
||
|
|
int max_streams; // Maximum number of different
|
||
|
|
// streams we may encounter
|
||
|
|
int pair_offset; // Number by which to offset
|
||
|
|
// num_pairs_read
|
||
|
|
string add_output_format; // Format for verbose-mode output
|
||
|
|
// when adding to database
|
||
|
|
string compare_output_format; // Format for verbose-mode output
|
||
|
|
// when comparing with an
|
||
|
|
// existing database
|
||
|
|
int lf_size; // Size of locality frames: 1
|
||
|
|
// effectively means don't
|
||
|
|
// compute locality frames
|
||
|
|
int add_to_db; // Flag indicating that we should
|
||
|
|
// add to the database rather
|
||
|
|
// than make comparisons
|
||
|
|
int output_graph; // Output graphing information in
|
||
|
|
// Dot format
|
||
|
|
int compute_hdist; // Compute Hamming distance
|
||
|
|
int write_db_stats; // Write statistics about the
|
||
|
|
// database
|
||
|
|
int verbose; // Output information about each
|
||
|
|
// anomaly or each new sequence
|
||
|
|
// added to the database
|
||
|
|
int very_verbose; // Output information about each
|
||
|
|
// sequence encountered
|
||
|
|
char fmt_str[10][50]; // String used for outputting
|
||
|
|
// information in verbose mode
|
||
|
|
char write_val[7]; // Do we write the value? used
|
||
|
|
// with fmt_str
|
||
|
|
int num_fvars; // Number of format variables
|
||
|
|
|
||
|
|
void Config::InitOptArray(vector<OptInfo> &opt_array);
|
||
|
|
void Config::SetDefaults();
|
||
|
|
void Config::ReadCommandLine(const int argc, const char *argv[],
|
||
|
|
vector<OptInfo> &opt_array);
|
||
|
|
void Config::AssignValToVar(vector<OptInfo> &opt_array, const
|
||
|
|
string &var_val, const string
|
||
|
|
&var_name, const int name_type);
|
||
|
|
void Config::ReadConfigFile(vector<OptInfo> &opt_array);
|
||
|
|
void Config::ReadOldConfigFile(ifstream &cfg_file,
|
||
|
|
vector<OptInfo> &opt_array);
|
||
|
|
void Config::InitOutputFormat();
|
||
|
|
void Config::CheckValues();
|
||
|
|
void Config::OuputConfigInfo(const vector<OptInfo> &opt_array) const;
|
||
|
|
void Config::WriteHelpInfo() const;
|
||
|
|
};
|
||
|
|
|
||
|
|
#endif
|