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#ifndef UTILS_H
#define UTILS_H
#include <string>
#include <memory>
#include <vector>
#define MAX 1024
#define NUMBEROFFILES 128
using namespace std;
int edit_distance(const void *s1, size_t l1, const void *s2, size_t l2, size_t nmemb, int (*comp)(const void*, const void*));
int hamming_distance(const void *s1, size_t l1, const void *s2, size_t l2, size_t nmemb, int (*comp)(const void*, const void*));
int comp(const void *a, const void *b);
char complement(char b);
string reverse_complement(string seq);
char reverse_dir(char dir);
FILE* open_file( char* filename );
string toLowerContext( const string &sequence, const int contextFirst, const int contextLast);
// Wrap std::FILE* in a std::unique_ptr for automatic close on destruction.
struct File {
struct Deleter {
void operator()(std::FILE* ptr) { std::fclose(ptr); }
};
std::unique_ptr<std::FILE, Deleter> file_ptr;
// Access raw file pointer
std::FILE* get_ptr() const { return file_ptr.get(); }
explicit operator std::FILE*() const { return file_ptr.get(); }
// Disable default constructor to force use of File::open_*() methods to open a file.
File() = delete;
// Open a file at path. Stops program and print error message on failure.
static File open_path(const char* path, const char* mode);
static File open_path(const std::string & path, const char* mode) {
return File::open_path(path.c_str(), mode);
}
// Format a path using sprintf then open
template<typename... Args> static File open_path_sprintf(const char* path_format, const char* mode, Args ...args) {
char path[1024];
int written = std::snprintf(path, 1024, path_format, args...);
if(written < 1024) {
return File::open_path(path, mode);
} else {
auto length = static_cast<std::size_t>(std::snprintf(nullptr, 0, path_format, args...));
auto buffer = std::vector<char>(length + 1);
std::snprintf(buffer.data(), buffer.size(), path_format, args...);
return File::open_path(buffer.data(), mode);
}
}
// Just forward to fprintf
template<typename... Args> int fprintf(const char* format, Args ...args) const {
return std::fprintf(this->get_ptr(), format, args...);
}
// Force close the file early
void close() {
this->file_ptr.reset();
}
};
#endif
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